WO2015138231A1 - Nucleic acid polyhedra from self-assembled vertex-containing fixed-angle nucleic acid structures - Google Patents

Abstract

Provided herein are compositions comprising nucleic acid structures comprising three or more arms arranged at fixed angles from each other, composites thereof such as DNA cages, and methods for their synthesis and use.

Description

NUCLEIC ACID POLYHEDRA FROM SELF-ASSEMBLED VERTEX-CONTAINING FIXED-ANGLE NUCLEIC ACID STRUCTURES

RELATED APPLICATION

This application claims the benefit under 35 U.S.C. § 119(e) of U.S. provisional application number 61/950,098, filed March 8, 2014, which is incorporated by reference herein in its entirety.

FEDERALLY SPONSORED RESEARCH

This invention was made with U.S. Government support under grant number

N000141110914, N000141010827 and N00014130593, awarded by the Office of Naval Research; grant number W911NF1210238, awarded by the Army Research Office; grant numbers 1DP2OD007292, 1R01EB018659 and 5R21HD072481, awarded by the National Institutes of Health; and grant numbers CCF1054898, CCF1317291, CCF1162459 and CMM11333215, awarded by the National Science Foundation. The U.S. Government has certain rights in the invention.

FIELD OF INVENTION

Provided herein are a novel compositions and methods for generating nucleic acid structures such as DNA cages.

BACKGROUND OF INVENTION DNA nanotechnology has produced a wide range of shape-controlled nanostructures (1- 10). Hollow polyhedra (1, 5, 11-26) are particularly interesting, as they resemble natural structures such as viral capsids and promise applications for scaffolding and encapsulating functional materials. Previous work has constructed diverse polyhedra, such as tetrahedra (13, 16, 20, 24), cubes (1, 19, 23), bipyramids (15), truncated octahedra (11), octahedra (12), dodecahedra (16, 18), icosahedra (17, 21), nano-prisms (14, 22, 25, 26), and buckyballs (16), with sub-80 nm sizes and sub-5 megadalton (MD) molecular weights (e.g. structures 1-8 in FIG. 1A). Assembly strategies include step-wise synthesis (1, 11, 21, 22), folding of a long scaffold (12, 19, 20, 24, 25), cooperative assembly of individual strands (13-15, 18, 26), and hierarchical assembly of branched DNA tiles (16, 17, 23).

Another route to scaling up polyhedra is the hierarchical assembly of larger monomers. Previous work using small three-arm-junction (16, 21) (80 kD) and five-arm junction tiles (17) (130 kD) has produced several sub-5 MD polyhedra (e.g. structures 5-7 in FIG. 1A). Additionally, a 15 MD icosahedron (5) (FIG. 1A, structure 9) was assembled from three double-triangle shaped origami monomers. However, this icosahedron was generated in low yield (5) and this method has not been generalized to construct more complex polyhedra.

SUMMARY OF INVENTION

The invention provides a novel, general strategy for, optionally, one- step self- assembly of wireframe DNA polyhedra that are larger than previous structures and that are produced at higher yield than previous structures. A stiff three-arm-junction tile motif, which can be made using for example DNA origami, with precisely controlled angles and arm lengths is used for hierarchical assembly of polyhedra. Using these methods, it was possible to construct a tetrahedron (20 megadaltons or MD), a triangular prism (30 MD), a cube (40 MD), a pentagonal prism (50 MD), and a hexagonal prism (60 MD) with edge widths of 100 nanometers. The structures were visualized by transmission electron microscopy and by three-dimensional DNA-PAINT super-resolution fluorescent microscopy of single molecules in solution.

Thus, in one aspect, provided herein is a nucleic acid structure comprising a first (x), a second (y), and a third (z) nucleic acid arm, each connected at one end to the other arms to form a vertex, and a first, a second, and a third nucleic strut, wherein the first nucleic acid strut connects the first (x) nucleic arm to the second (y) nucleic arm, the second nucleic acid strut connects the second (y) nucleic arm to the third (z) nucleic arm, and the third nucleic acid strut connects the third (z) arm to the first (x) nucleic acid strut.

In another aspect, provided herein is a nucleic acid structure comprising three nucleic acid arms radiating from a vertex at fixed angles.

In another aspect, provided herein is a nucleic acid structure comprising N nucleic acid arms radiating from a vertex, wherein N is the number of nucleic acid arms and is 3 or more, and M nucleic acid struts, each strut connecting two nucleic acid arms to each other, wherein M is the number of nucleic acid struts and is 3 or more. In some embodiments, N is equal to M. In some embodiments, N is less than M.

Embodiments relating to one or more of the foregoing aspects are now provided.

In some embodiments, the nucleic acid structure comprises 4 nucleic acids and at least 4 nucleic acid struts, or 5 nucleic acid arms and at 5 nucleic acid struts.

In some embodiments, the nucleic acid arms are equally spaced apart from each other (or the arms are separated from each other by the same angle). In some embodiments, the nucleic acid arms are not equally separated from each other (or the arms are separated from each other by different angles).

In some embodiments, the nucleic acid structure comprises three nucleic acid arms separated from each other by 60° - 60° - 60°. When four such structures are connected to each other at their free ends, they form a tetrahedron.

In some embodiments, the nucleic acid structure comprises three nucleic acid arms separated from each other by 60° - 90° - 90°. When six such structures are connected to each other at their free ends, they form a triangular prism.

In some embodiments, the nucleic acid structure comprises three nucleic acid arms separated from each other by 90° - 90° - 90°. When eight such structures are connected to each other at their free ends, they form a cube.

In some embodiments, the nucleic acid structure comprises three nucleic acid arms separated from each other by 108° - 90° - 90°. When ten such structures are connected to each other at their free ends, they form a pentagonal prism. In some instances, pentagonal prisms may be formed by connecting nucleic acid structures defined as 120° - 90° - 90°.

In some embodiments, the nucleic acid structure comprises three nucleic acid arms separated from each other by 120° - 90° - 90°. When twelve such structures are connected to each other at their free ends, they form a hexagonal prism. In some instances, pentagonal prisms may be formed by connecting nucleic acid structures defined as 140° - 90° - 90°.

In some embodiments, the nucleic acid structure further comprises a vertex nucleic acid.

In some embodiments, the nucleic acid structure further comprises a connector nucleic acid.

In some embodiments, the nucleic acid arms, nucleic acid struts, and/or vertex nucleic acid are comprised of parallel double helices.

In some embodiments, nucleic acid arms are of identical length.

In some embodiments, the nucleic acid struts are of identical length. In some embodiments, the nucleic acid struts are of different lengths.

In some embodiments, at least one nucleic acid arm comprises a blunt end.

In some embodiments, at least one nucleic acid arm comprises a connector nucleic acid at its free (non- vertex) end that is up to 16 nucleotides in length. In some embodiments, at least one nucleic acid arm comprises a connector nucleic acid at its free (non- vertex) end, thereby comprising a 1 or 2 nucleotide overhang.

In some embodiments, the nucleic acid structure is up to 5 megadaltons (MD) in size. In some embodiments, the nucleic acid arms are 50 nm in length.

In another aspect, provided herein is a composite nucleic acid structure comprising L nucleic acid structures selected from any of the foregoing nucleic acid structures, wherein L is an even number of nucleic acid structures, and wherein the L nucleic acid structures are connected to each other at free (non-vertex) ends of the nucleic acid arms.

In some embodiments, the two more nucleic acid structures are two, four, six, eight, ten, twelve or more nucleic acid structures.

In some embodiments, the composite nucleic acid structure is a tetrahedron, a triangular prism, a cube, a pentagonal prism, or a hexagonal prism.

In some embodiments, the composite nucleic acid structure is 20 megadaltons (MD),

30 MD, 40 MD, 50 MD, or 60 MD in size.

In some embodiments, the composite nucleic acid structure has edge widths, comprised of two nucleic acid arms from adjacent nucleic acid structures, of 100 nm.

In another aspect, provided herein are methods of synthesis of any of the foregoing nucleic acid structures and the composite nucleic acid structures. In some embodiments, the methods comprise combining a nucleic acid scaffold strand with nucleic acid staple strands in a reaction vessel, wherein the nucleic acid staple strands are selected to form any of the foregoing nucleic acid structures when hybridized to the nucleic acid scaffold strand. In some embodiments, the methods further comprise combining the nucleic acid scaffold strand, the nucleic acid staple strands, and nucleic acid connector strands, wherein when the nucleic acid scaffold strand, the nucleic acid staple strands, and nucleic acid connector strands are hybridized to each other, they form a composite nucleic acid structure, such as any of the foregoing composite nucleic acid structures.

These and other aspects and embodiments provided herein are described in greater detail herein.

BRIEF DESCRIPTION OF DRAWINGS FIGs. 1A-1B. DNA-origami polyhedra. (FIG. 1A) Polyhedra self-assembled from DNA tripods with tunable inter-arm angles, and comparison of their sizes and molecular weights with selected previous polyhedra (structures 1-9; see FIG. 5 for details). (FIG. IB) Design diagram of a tripod. Cylinders represent DNA double helices. See FIG. 6 for details of the arm connection at the vertex. (FIG. 1C) Cylinder model illustrating the connection between two tripod monomers. (FIG. ID and FIG. IE) Connection schemes for assembling (FIG. IE) the tetrahedron and (FIG. ID) other polyhedra (represented here by the cube design).

FIGs. 2A-2F. Self-assembly of DNA tripods and polyhedra. (FIG. 2A) Gel electrophoresis and (FIG. 2B) TEM images of the 60°-60°-60° (lane 1 in the gel) and 90°- 90°-90° (lane 2) tripods. Gel lane 3: lkb ladder. Gel electrophoresis: 1.5 % native agarose gel, ice water bath. (FIGS. 2C and 2D) Two schemes of connector designs and

corresponding gel electrophoresis results. For each scheme, the strand model depicts the connection between two pairs of DNA duplexes. The number above a gel lane denotes the number of connected helices between two adjacent arms. Lane L: 1 kb ladder. Lane S:

scaffold. Arrowheads indicate the bands corresponding to assembled cubes. (FIG. 2C)

Scheme i: long (30 nt) connector (colored red) including a 2 nt sticky end. The complete 30 nt connector is only shown on the left, with a 28 nt segment anchored on the left helices and a 2 nt exposed sticky end available for hybridization with the 90°-90°-90° right neighbor (dashed circle depicts hybridization site). (FIG. 2D) Scheme ii: short (11 nt) connector including a 2 nt sticky end. (FIG. 2E) Assembly yields of the cubes, calculated as intensity ratio between a cube band and the corresponding scaffold band. (FIG. 2F) Agarose gel electrophoresis of the polyhedra. Lane 1 : 90°-90°-90° monomer. Lanes 2-6: polyhedra. Lane 7: assembly reaction containing tripods without struts. Lane 8: assembly reaction containing 90°-90°-90° tripods without vertex helices. Lane 9: 1 kb ladder. Gel bands corresponding to desired products are marked with arrowheads. Gel electrophoresis: 0.8% native agarose gel, ice water bath.

FIGs. 3A-3E. TEM images of polyhedra. The zoomed-in (columns 1 and 2) and zoomed-out (column 3) images are shown for the tetrahedron (FIG. 3A), the triangular prism (FIG. 3B), the cube (FIG. 3C), the pentagonal prism (FIG. 3D), and the hexagonal prism (FIG. 3E). Images of the tetrahedron, the triangular prism, and the cube were acquired from purified samples. Images of the pentagonal prism and hexagonal prism were collected from crude samples (denoted with "*"). Scale bars are 100 nm in the zoomed-in TEM images and 500 nm in the zoomed-out images. Note that aggregates are clearly visible for unpurified samples (e.g. in the rightmost panel of D).

FIGs. 4A1-4G. 3D DNA-PAINT super-resolution fluorescence imaging of polyhedra.

(FIG. 4A1) Staple strands at the vertices of each polyhedron were extended with single- stranded docking sequences for 3D DNA-PAINT super-resolution imaging. (FIGs. 4A1-4E1) Schematics of polyhedra with DNA-PAINT sites highlighted. (FIGs. 4A2-4E2) 3D DNA- PAINT super-resolution reconstruction of typical polyhedra shown in the same perspective as depicted in Al-El. (FIGs. 4A3-4E3) 2D x-y-projection. (FIGs. 4A4-4E4) 2D x-z-projection. (FIG2. 4A5-4E5) Height measurements of the polyhedra obtained from the cross- sectional histograms in the x-z-projections. (FIG. 4F) A larger 2D super-resolution x-y-projection view of tetrahedra and drift markers (bright individual dots). The diffraction-limited image is super imposed on the super-resolution image in the upper half. (FIG. 4G) Tilted 3D view of a larger field of view image of the tetrahedron. Drift markers appear as bright individual dots. Scale bars: 200 nm. Color indicates height in the z direction.

FIG. 5. 20-60 megadalton DNA polyhedra. 20-60 megadalton DNA wireframe polyhedra assembled from tunable DNA-origami tripods. Top, schematics showing the assembly process of tripod monomers and the polyhedra; middle, TEM images of polyhedra; bottom, super-resolution fluorescence images of polyhedra. These polyhedra are significantly larger than previous DNA polyhedra in FIG. 1A, including (1) a cube (1), a truncated octahedron (11), a tetrahedron (13), an octahedron (12), (2) a tetrahedron, a dodecahedron, and a buckyball assembled from three-arm DNA tiles (16), (3) a DNA-origami tetrahedron (24), and (4) an icosahedron assembled from three DNA-origami monomers (5).

FIG. 6. Connections at the vertex the three-arm monomer. Three layers of connections at the vertex: (1) the first-layer (innermost) connections are formed by the scaffold strand only. There are no extra bases between the duplexes. (2) the second-layer (middle) connections and (3) the third-layer (outmost) connections are DNA duplexes (i.e., the vertex helices) formed by staple strands and their complementary strands. Each polyhedron used different number of vertex helices with different lengths (see Table 2), which were estimated on the distances between the ends of the 16-helix arms at the vertexes. For detailed design and sequence information, refer to FIG. 8 to FIG. 13. The "*"s denote the helices where DNA handles were placed for DNA-PAINT.

FIGs. 7A-7C. Connection pattern. (FIG. 7A) A three-arm tripod monomer. (FIG. 7B)

The cross-section of an arm of the three-arm monomer. The arrows in A and B indicate the same direction. The dotted line indicates the line of reflection symmetry. (FIG. 7C) The connection patterns that were implemented in FIG. 2B to FIG. 2E. See FIG. 8 to FIG. 13 for design and sequence details.

FIG. 8. Strand diagrams of the tetrahedron. The sequences used are provided in Table

4. The horizontal axis provides the position or length of the helix from the first base thereof. The vertical axis provides the helix number. As illustrated, there are three groupings of helices, each representing an arm. The 3 protrusions on the right side correspond to the 3 struts. The right end of the helices represents the free ends, while the left ends represent the ends at the vertex. Similarly renderings are provided in FIGs. 9-13.

FIG. 9. Strand diagrams of the triangular prism. The sequences used are provided in Table 5.

FIG. 10. Strand diagrams of the cube (short connectors). The sequences used are provided in Table 6.

FIG. 11. Strand diagrams of the cube (long connectors). The sequences used are provided in Table 7.

FIG. 12. Strand diagrams of the pentagonal prism. The sequences used are provided in Table 8.

FIG. 13. Strand diagrams of the hexagonal prism. The sequences used are provided in Table 9.

FIGs. 14A-14B. Schematics of nucleic acid structures having N arms, and N or more nucleic acid struts.

DETAILED DESCRIPTION OF INVENTION

The invention is based, in part, on the discovery and development of a general strategy for hierarchical self-assembly of polyhedra from megadalton monomers using a DNA "tripod", a 5 MD three-arm-junction origami tile that is 60 times more massive than previous three-arm tiles (16). The tripod motif features inter-arm angles controlled by supporting struts and strengthened by vertex helices. The invention further provides self- assembly of tripods into wireframe polyhedra using a dynamic connector design. Using this robust methodology, we constructed a tetrahedron (-20 MD), a triangular prism (-30 MD), a cube (-40 MD), a pentagonal prism (-50 MD), and a hexagonal prism (-60 MD) (FIG. 1A and FIG. 5).

These structures have a variety of applications including but not limited to biological applications. For example, when generated having edges widths on the order of about 100 nm, these polyhedra have a size comparable to bacterial microcompartments such as carboxysomes. Additional applications include without limitation use in or as photonic devices, nanoelectronics and drug delivery systems.

To characterize the 3D single-molecule morphology of these polyhedra, we used a DNA-based super-resolution fluorescence imaging method (resolution below the diffraction limit) called DNA-PAINT (28, 29) (a variation of point accumulation for imaging in nanoscale topography (30)). Unlike traditional transmission electron microscopy (TEM) which images the samples in a vacuum under dried and stained conditions and thus may not render the structure in its native form, 3D DNA-PAINT introduces minimal distortion to the structures by rendering them in a more "native" hydrated imaging environment.

General Tripod Design and Methodology

Disclosed herein are nucleic acid structures (alternatively referred to herein as structures) comprising at a minimum three nucleic acid arms (or arms). Such three arm structures are referred to herein as tripods. As will be understood, given the structure of a tripod, the three arms meet each other at a vertex and radiate outwards towards a free end on each arm. This disclosure contemplates and provides nucleic acid structures comprising more than three nucleic acid arms, including structures comprising four, five, six, seven, or more arms. Examples of such structures are provided in FIG. 14. In FIG. 14A, the longer thicker lines correspond to nucleic acid arms and the shorter thinner lines correspond to nucleic acid struts. In FIG. 14B and C, only nucleic acid arms are illustrated but it is to be understood that such nucleic acid structures comprise nucleic acid struts also.

The nucleic acid arms within a structure (or within a composite structure) are typically of identical length. They are not however so limited and may differ in length depending on the embodiment.

Of particular significance and as provided herein, the nucleic acid arms exist at fixed angles with each other. This is achieved through the use of nucleic acids that are positioned between arms of a structure; these nucleic acids are referred to as nucleic acid struts (or struts). Each nucleic acid strut is connected to two nucleic acid arms in a single structure, thereby maintaining the angular distance between the two arms. The nucleic acid struts may be positioned anywhere along the length of the arms. The position of the strut along the length of the arm (from the vertex) and the length of the strut together can influence the angular distance between the arms. The angular distance between the arms can also be controlled in part by the vertex nucleic acids and other connections existing at the vertex including the nucleic acid connectors interactions. Examples of strut lengths and strut positions along an arm from the vertex are provided in Table 1 for a number of nucleic acid structures. As will be clear from the Table and from the remaining disclosure, struts in a structure (or within a composite structure) may be of identical length or of differing length.

It is to be understood nucleic acid structures may be produced having any particular defined angular distance between their arms, and any number of arms, based on the methodology provided herein. In this respect, the structures are considered to be "tunable" because an end user is able to modify the synthesis method in order to obtain structures of choice.

The arms of the structure may be referred to herein for clarity as the x, y and z arms, for example in the context of a tripod structure. In this structure, typically one (but optionally more than one) strut connects arms x and y, typically one (but optionally more than one) strut connects arms y and z, and typically one (but optionally more than one) strut connects arms z and x. These struts may be referred to, again for clarity, as the xy strut, the yz strut, and the zx strut. In the case of a tripod, each arm is connected to every other arm in the structure. In the case of a structure having more than three arms, all adjacent arms will typically be connected to each other by struts, and optionally non-adjacent arms may also be connected to each other by struts as well. It may be desirable to include struts between non-adjacent arms in order to provide greater structural integrity. As an example, in FIG. 14A, the second structure shown comprises four arms, and four struts between adjacent arms. This structure may also comprise additional struts between non-adjacent arms such as between the "north" and "south" arms and/or the "west" and "east" arms, imagining that the arms are directions on a compass for the sake of explanation.

Thus, the minimum number of arms is 3, and the minimum number of struts is 3. The disclosure contemplates structures having 3 or more arms and 3 or more struts. The number of struts is typically equal to or greater than the number of arms.

Accordingly, provided herein is a nucleic acid structure comprising a first (x), a second (y), and a third (z) nucleic acid arm, each connected at one end to the other arms to form a vertex, and a first, a second, and a third nucleic strut, wherein the first nucleic acid strut connects the first (x) nucleic arm to the second (y) nucleic arm, the second nucleic acid strut connects the second (y) nucleic arm to the third (z) nucleic arm, and the third nucleic acid strut connects the third (z) arm to the first (x) nucleic acid strut.

Provided herein is a nucleic acid structure comprising three nucleic acid arms radiating from a vertex at fixed angles. Such structures may have more than three arms, including 4, 5, 6, 7 or more arms.

Further provided herein is a nucleic acid structure comprising N nucleic acid arms radiating from a vertex, wherein N is the number of nucleic acid arms and is 3 or more, and

M nucleic acid struts, each strut connecting two nucleic acid arms to each other, wherein M is the number of nucleic acid struts and is 3 or more. N may be equal to M or it may be less than M. Examples include a nucleic acid structure that comprises 4 nucleic acids and at least 4 nucleic acid struts, or a nucleic acid structure that comprises 5 nucleic acid arms and at 5 nucleic acid struts.

In some embodiments, nucleic acid arms (including adjacent arms) within a structure are equally spaced apart from each other. In other words, the arms are separated from each other by the same angle, or the angular distance between the arms is the same. An example of this is a three arm structure in which adjacent arms are separated from each other by a 60°C angle. This tripod is referred to as 60°C - 60°C - 60°C. Tripods of this type, when connected to each other, will form a tetrahedron. Thus, it will be understood that the angular distance between the arms also dictates how to such structures will connect with each other and the ultimate 3D shape (or composite nucleic acid structure) to be formed. Another example is a three arm structure in which adjacent arms are separated from each other by a 90°C angle. This tripod is referred to as 90°C - 90°C - 90°C. Tripods of this type, when connected to each other, will form a cube.

In some embodiments, nucleic acid arms (including adjacent arms) within a structure are not equally spaced apart from each other. In other words, the arms are separated from each other by a different angle, or the angular distance between the arms is different. An example of this is a three arm structure in which some adjacent arms are separated from each other by a 60°C angle and other adjacent arms are separated from each other by a 90°C angle. Such a tripod may be referred to as 90°C - 90°C - 60°C. Tripods of this type, when connected to each other, will form a triangular prism. Another example is a three arm structure in which some adjacent arms are separated from each other by a 108°C angle and other adjacent arms are separated from each other by a 90°C angle. This tripod is referred to as 90°C - 90°C - 108°C. Tripods of this type, when connected to each other, will form a pentagonal prism. Another example is a three arm structure in which some adjacent arms are separated from each other by a 120°C angle and other adjacent arms are separated from each other by a 90°C angle. This tripod is referred to as 90°C - 90°C - 120°C. Tripods of this type, when connected to each other, will form a hexagonal prism.

As will be understood based on this disclosure, the nucleic acid structures arrange their arms (three or more of their arms) so as to form a vertex. The arm ends that exist at the vertex may be connected to each other through nucleic acid helices or through nucleic acid connectors (or connector strands), or through a combination of helices and connector strands.

Examples of this are illustrated in FIG. 6. The lengths of vertex helices in the first and second layers are provided in Table 2. Typically 0-6 vertex helices are present in a structure.

Thus, the structures may further comprise vertex nucleic acids such as vertex helices. Some composite structures may not comprise vertex helices. An example is the tetrahedron which can be formed from the attachment of two tripod structures without vertex helices.

The structures may further comprise connector nucleic acids. These connector nucleic acids may be located at the vertex and/or at the free ends of arms. In the latter instance, such connector nucleic acids facilitate the attachment of two nucleic acid structures to each other, thereby forming a composite nucleic acid structure.

Each nucleic acid arm in a structure therefore typically has one end located at the vertex and one free end (i.e., an end not located at the vertex). The free end may be a blunt end, meaning that it lack any single stranded nucleic acid sequence. Alternatively it may be a sticky end, meaning that it comprises a single-stranded nucleic acid sequence. That sequence, referred to as an overhang, may be 1 or 2 nucleotides in length. It may be longer, although 1-2 nucleotides are suitable and in some instances may result in more efficient synthesis of composite nucleic acids (and thus greater yields of such composites). The overhang may be provided by connector nucleic acids. Such connector nucleic acids may be present in the initial hybridization reaction or they may be added post-synthesis of the nucleic acid structures, with or without purification of the synthesized structures. The connector nucleic acids (also referred to herein as connector strands) may be of any length although it has been found that shorter lengths result in higher composite nucleic acid structure yields. FIG. 2 C provides a schematic of a longer connector strand (on the order of 30 nucleotides with a 2 nucleotide overhang). FIG. 2D provides a schematic of a shorter connector strand (on the order of 11 nucleotides with a 2 nucleotide overhang). The structures of FIG. 2C and 2D were used to form composite nucleic acid structures that are cubes. The yields of such cubes are shown in FIG. 2E. The top line corresponds to the shorter connector and the bottom line corresponds to the longer connector. Thus, the shorter connector led to higher yield of its composite cube. Although not intending to be bound by any theory, the lower yields using the longer connector strands may be because mismatched composites (or mismatched composite intermediates) comprising longer connector strands may be more stable while mismatched composites (or mismatched composite intermediates) comprising shorter connectors may be less stable and therefore more likely to dissociate and re-associate to form properly matched composite and composite intermediates. As used herein, a composite intermediate comprises a subset of the nucleic acid structures needed to form a composite structure. For example, if the desired composite is a cube (which requires 4 structures), then an intermediate may consist of 2 or 3 structures. The disclosure contemplates that the connector may be of any length, including lengths of 50 or fewer nucleotides, 40 or fewer nucleotides, 30 or fewer nucleotides, 25 or fewer nucleotides, 20 or fewer nucleotides, 15 or fewer nucleotides, 10 or fewer nucleotides, or 5 or fewer nucleotides. The connector may be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides.

The nucleic acid structures may be of any size although typically they are in the range of up to about 5 megadaltons (MD). Thus, they may be 3, 4, 5, or 6 MD in some

embodiments. The length of the nucleic acid arms is dictated by the desired rigidity and by their method of synthesis. For example, the structures described herein have arms made of 16 parallel double helices. Since they were made using DNA origami techniques starting with the Ml 3 scaffold strand, the length of the arms is typically about 50 nm. It is to be understood that if a scaffolds of a different length was used, or if the arms were designed to have a different number of double helices (for example if more or less rigidity and strength was desired), then the length of the arm could vary from that described herein. Assuming the nucleic acid structures have arms of 50 nm, and assuming all arms are of equal length, then it will be understood that composite nucleic acid structures will have edges widths on the order of 100 nm. Thus the composites that may be generated according to this disclosure may be defined as having edge widths that are at least 100 nm, including 120, 140, 160, 180, 200, or more nm. In some instances, the composites may have edge widths of 80 nm or more.

The nucleic acid arms, nucleic acid struts and vertex nucleic acids may be comprised of double helices such as parallel double helices. Illustrated herein are arms comprised of 16 parallel double helices each, struts comprised of 2 parallel double helices each, and vertex nucleic acids comprised of a single double helix each. When more than one double helix is present, there typically be cross-over strands that hybridize to parallel helices and thereby promote the proximity of the helices and ultimately rigidity thereof.

It is to further understood that the nucleic acid structures disclosed herein may be synthesized using any number of nucleic acid nanostructure synthesis methods including without limitation DNA origami and DNA single stranded tiles (SST). These techniques are known in the art, and are described in greater detail in U.S. Patent Nos. 7,745,594 and 7,842,793; U.S. Patent Publication No. 2010/00696621; and Goodman et al. Nature

Nanotechnology.

The nucleic acid structures may be used to generate larger structures referred to herein as composite nucleic acid structures (or composites or composite structures). Composite structures are formed through the connection of nucleic acid structures to each other. Typically the nucleic acid structures are identical in terms of length and angle definition. Thus a plurality of identical nucleic acid structures are combined in a single reaction vessel, and allowed to attached to each other to form larger 3D structures via connections of their free arm ends. Such connections may be facilitated by the presence (or inclusion) of connector strands, although the synthesis method is not so limited.

Therefore, disclosed and provided herein is a composite nucleic acid structure comprising L nucleic acid structures, wherein L is the number of nucleic acid structures, and wherein the L nucleic acid structures are connected to each other at free (non- vertex) ends of the nucleic acid arms. The number of structures needed to make a composite will depend on the composite structure desired and the structures used as components. In some instances, the composite structure may comprise two, four, six, eight, ten, twelve or more nucleic acid structures each of which has three arms. As illustrated throughout, this methodology may be used to generate composite nucleic acid structures that are tetrahedrons, triangular prisms, cubes, pentagonal prisms, or hexagonal prisms. It is to be understood that any arbitrary composite structure may be made using the methodology provided herein. These composites may be of virtually any size, including but not limited to . Illustrated herein are composite nucleic acid structures that are 20 megadaltons (MD), 30 MD, 40 MD, 50 MD, and 60 MD in size.

The composites may be generated immediately following the generation of the nucleic acid structures and thus in the same vessel as the structures. Connector strands, if used, may be present at the beginning of the hybridization reaction or may be added once the structures are formed and prior to formation of the composites. Such single reaction vessel synthesis is referred to as "one-pot" annealing.

Below are more detailed and exemplary descriptions of the particular nucleic acid structures, and particular composite nucleic acid structures, and their methods of synthesis. These descriptions are meant to be exemplary and not limiting as to the breadth of this disclosure. For example, it is to be understood that although much of the following description and exemplification involves 3-arm "tripod" nucleic acid structures, the teachings may be generalized to structures of any number of arms as described herein.

Exemplary Tripod Design and Methodology

Assembly strategy of polyhedra and design features of tripods.

In one-pot annealing, the scaffold and staple strands first assemble into a tripod origami monomer, and then the tripods (without intermediate purification) assemble into the polyhedron (FIG. 1A). It is also contemplated that the tripod monomers may be purified prior to the final assembly into composite nucleic acid structures. Diverse polyhedra can be constructed by using tripods with different designed inter-arm angles. The tripod has three typically equal-length (e.g., -50 nm) stiff arms connected at the vertex (see FIG. 6 for connection details) with controlled inter-arm angles (FIG. IB). To ensure stiffness, each arm contains a sufficient number (e.g., 16) of parallel double-helices packed on a honeycomb lattice (5) with twofold rotational symmetry. A supporting "strut" consisting of two double- helices controls the angle between the two arms. The tripod is named according to its three inter-arm angles (e.g. the tetrahedron and the cube are respectively assembled from 60°-60°- 60° and 90°-90°-90° tripods). To avoid potential unwanted aggregation resulting from blunt- end stacking of DNA helices (5), up to six short DNA double-helices (denoted "vertex helices") are included at the vertex to partially conceal its blunt duplex ends (FIG. IB; the number of helices and their lengths vary for different polyhedra, see FIG. 6 and Table 2 for details). Additionally, the vertex helices are expected to help maintain inter- arm angles by increasing rigidity of the vertices. Two connection strategies are used to assemble tripods into polyhedra. To facilitate exposition, the three arms are denoted as X-arm, Y-arm, and Z-arm (FIG. 1C). Connecting X-arm to X-arm and Y-arm to Z-arm produces polyhedra (such as a cube; FIG. ID) other than the tetrahedron, which is assembled by connecting X to X, Y to Y, and Z to Z (FIG. IE).

Tripod conformation control with struts.

First, we verified that the inter-arm angle was controlled by the length of the supporting strut. Gel electrophoresis of 60°-60°-60° and 90°-90°-90° tripods revealed a dominant band for each tripod (FIG. 2A), confirming their correct formation. Consistent with its more compact designed conformation, the 60°-60°-60° tripod migrated slightly faster than the 90°-90°-90° one. The two tripod bands were each purified, imaged by TEM, and showed designed tripod- like morphologies (FIG. 2B). The measured inter- arm angles were slightly smaller than designed (53+5° [SD, n = 60] for 60°-60°-60° tripods; 87+4° [SD, n = 60] for 90°-90°-90° tripods), possibly reflecting a small degree of strut bending.

Connector designs.

The strands connecting the tripods are called "connectors." Connector designs affected the polyhedra assembly yields. Two designs were tested for the cube. In scheme i, each 30-base connector spanned two adjacent tripods, with a 28-base segment anchored on one tripod and another 2-base (sticky end) on the other (FIG. 6; see FIG. 7 for details). Gel electrophoresis (quantified in FIG. 2E) revealed that the assembly yield was affected by the number of connected helices (n): a product band was only observed for 4 < n < 12; for n < 4, the dominant band were monomers, likely reflecting overly weak inter-monomer

connections; for n > 12, aggregations dominated.

In scheme i, the connectors were stably anchored (forming 28 base pairs) on tripods before inter-monomer connection occurred. In scheme ii, the connector was shortened from 30 to 11 bases so that it should only be anchored to two adjacent tripods by 9-base and 2-base segments in the assembled cube (FIG. 2D), and only dynamically binds to a monomeric tripod. Compared with the stably attached connector design, the dynamic connector design is expected to reduce inter-monomer mismatches that may occur during the assembly, as such mismatches would be less likely frozen in a kinetic trap. Indeed, scheme ii showed substantially increased assembly yield (FIG. 2E). It was thus used for subsequent polyhedra designs, except for the tetrahedron, where scheme i produced sufficient yield for this relatively simple structure. The assembly yields were estimated from the gel (FIG. 2F). The 90°-90°-90° monomer sample (FIG. 2F, lane 1) showed a strong monomer band and a putative dimer band (not studied by TEM, -27% intensity compared to the monomer). We define the assembly yield of a polyhedron as the ratio between its product band intensity and the combined intensity of the 90°-90°-90° monomer and dimer bands (lane 1), and obtained yields of 45%, 24%, 20%, 4.2%, and 0.11% for the tetrahedron, the triangular prism, the cube, the pentagonal prism, and the hexagonal prism, respectively (FIG. 2F).

Polyhedra assembly.

The lengths and the attachment points of the struts varied for each polyhedron (Table 1). The tetrahedron, the triangular prism, the cube, the pentagonal prism, and the hexagonal prism should be assembled from monomers with designed 60°-60°-60°, 90°-90°-60°, 90°- 90°-90°, 90°-90°-108°, and 90°-90°-120° angles, respectively (FIG. IB). The first three monomers indeed produced tetrahedra, triangular prisms, and cubes [verified by gel electrophoresis (FIG. 2F) and TEM imaging (FIG. 3, A to C)], suggesting accurate control for angles within 90°. However, the pentagonal prism was assembled from monomers with designed angles of 90°-90°-120° (instead of 90°-90°-108°), and the hexagonal prism from 90°-90°-140° (instead of 90°-90°-120°). Thus the assembly of these two polyhedra requires monomers with designed Y-Z angles greater than the design criteria. This requirement likely reflects slight bending of the relevant struts, which could be compensated by using longer struts.

Effects of struts and vertex helices on polyhedra assembly.

We next verified that both the struts and the vertex helices were required for the tripods to assemble into the designed polyhedron. Three samples were prepared for cube assembly using tripods that contain (i) both the struts and the vertex helices (FIG. 2F, lane 4), (ii) the vertex helices but not the struts (lane 7), and (iii) the struts but not the vertex helices (lane 8; the samples were subjected to gel electrophoresis after annealing). The first sample showed a sharp strong band corresponding to the cube (verified by TEM, FIG. 3B). The second failed to produce any clear product band. The third produced substantial aggregates, and a clear but weak band with mobility comparable to the triangular prism. This band may correspond to a hexamer, but its molecular morphology was not investigated. Based on the above experiments, we included both the struts and the vertex helices in the tripods for subsequent polyhedra assembly.

TEM characterization.

Product bands were purified and imaged under TEM. For the tetrahedron, the triangular prism, and the cube, most structures appeared as intact polyhedra; a small fraction of broken structures (< 20%) were likely ruptured during the purification and imaging (FIG. 3, A to C). In contrast, few intact structures were observed for the purified pentagonal and hexagonal prisms (data not shown). Thus, unpurified samples for these two were directly imaged and the expected molecular morphologies were observed (FIG. 3, D and E, for exemplary images, further images available but not shown). The struts are clearly visible in many images.

3D DNA-PAINT super-resolution microscopy.

Localization-based 3D super-resolution fluorescence microscopy (31-33) offers a minimally invasive way to obtain true single molecule 3D images of DNA nanostructures in their "native" hydrated environment. In stochastic reconstruction microscopy (34), most molecules are switched to a fluorescent dark (OFF) state, and only a few emit fluorescence (ON state). Each molecule is localized with nanometer precision by fitting its emission to a 2D Gaussian function. In DNA-PAINT, the "switching" between ON- and OFF-states is facilitated by repetitive, transient binding of fluorescently labeled oligonucleotides ("imager" strands) to complementary "docking" strands (24, 28, 29, 35).

We extended DNA-PAINT to 3D imaging (29) by using optical astigmatism (31, 36), in which a cylindrical lens used in the imaging path "converts" the spherical point spread function (PSF) of a molecule to an elliptical PSF when imaged out of focus. The degree and orientation of the elliptical PSF depends on the displacement and direction of the point source from the current focal imaging plane, and is used to determine its z position (31, 36). We applied 3D DNA-PAINT to obtain sub-diffraction-resolution single-molecule images of the polyhedra. To ensure all the vertices of a polyhedron will be imaged, each vertex is modified with multiple (about eighteen) 9-nt docking strands (Staple-TTATCTAC ATA-3 ' ; SEQ ID NO: 1) (FIG. 4A1) in a symmetric arrangement (FIG. 6). For surface immobilization, a subset of strands along the polyhedron edges were modified with 21-nt extensions (Staple- TTCGGTTGTACTGTGACCGATTC-3' ; SEQ ID NO: 2), which were hybridized to biotinylated complementary strands attached to a streptavidin covered glass slide (Biotin- GAATCGGTC ACAGTAC AACCG-3 ' ; SEQ ID NO: 3).

Using 3D DNA-PAINT microscopy, all five polyhedra showed designed 3D patterns of vertices (FIG. 4, columns 1-4) with expected heights (FIG. 4, A5-E5), suggesting that the solution shape of the structures is maintained during surface immobilization and imaging. We quantified the tetrahedra formation and imaging yields (FIG. 4, F and G). 253 out of 285 structures (89%) contained 4 spots in the expected tetrahedral geometry. Height measurement yielded 82+15 nm, consistent with the designed value (82 nm). Single DNA-PAINT binding events were localized with an accuracy of 5.4 nm in x-y and 9.8 nm in z [see below for how localization accuracy was determined] . This z localization accuracy almost completely accounts for the 15 nm spread in the height measurement distribution. The calculated localization precisions translate to an obtainable resolution of -13 nm in x and y, and -24 nm in z.

Previous work demonstrated diverse DNA polyhedra self- assembled from small 3- arm-junction tiles (-80 kD) (16), which consist of three double-helix arms connected by flexible single- stranded hinges. However, straightforward implementation of megadalton 3- arm origami tiles using similar flexible inter- arm hinges (i.e. tripods with no struts or vertex helices) failed to produce well-formed polyhedra (Fig. 2B, lane 7). An origami tripod contains 50 times more distinct strands than previous 3-arm-junction tiles (formed from 3 distinct strands) and is 60 times more massive in molecular weight. Apart from the challenges associated with the more error-prone construction of the more complex monomers from individual strands, successful hierarchical assembly of such large monomers into polyhedra also needs to overcome much slower reaction kinetics, caused by the larger size and lower concentration of the tripod monomers. The stiff DNA tripods, with rationally designed inter- arm angles controlled by supporting struts and vertex helices, lead to successful construction of diverse polyhedra, suggesting that conformation control of branched megadalton monomers can facilitate their successful assembly into higher order structures.

The design principles of DNA tripods may be extended to stiff megadalton w-arm (n≥ 4) branched motifs with controlled inter-arm angles. Self-assembly with such w-arm motifs could be used to construct more sophisticated polyhedra, and potentially extended 2D and 3D lattices with sub- 100 nm tunable cavities.

Such structures could potentially be used to template guest molecules for diverse applications, e.g. spatially arranging multiple enzymes into efficient reaction cascades (37) or nanoparticles to achieve useful photonic properties (38, 39). Furthermore, the DNA polyhedra constructed here, with a size comparable to bacterial microcompartments, may potentially be used as skeletons for making compartments with precisely controlled dimensions and shapes by wrapping lipid membranes around their outer surfaces (40). Such membrane-enclosed microcompartments could potentially serve as bioreactors for synthesis of useful products or as delivery vehicles for therapeutic cargo (25).

For 3D characterization of DNA nanostructures, super-resolution fluorescence microscopy (e.g. 3D DNA-PAINT) provides complementary capabilities to present electron microscopy (e.g. cryo-EM (12, 16, 17, 23)). While cryo-EM offers higher spatial resolution imaging of unlabeled structures, DNA-PAINT is less technically involved to implement, obtains true single molecule images of individual structures (rather than relying on class averaging), and preserves the multi-color capability of fluorescence microscopy (29).

Additionally, DNA-PAINT in principle allows for observation of dynamic structural changes of nanostructures in their "native" hydrated environment, currently suitable for slow changes on the minutes timescale (e.g. locomotion of synthetic DNA walkers) and potentially for faster motions with further development. Table 1. Strut designs of the polyhedra. All units are nanometers. Designed length of the strut connecting (i) Y-arm and Z-arm, (ii) X-arm and Z-arm, or (iii) X-arm and Y-arm. Designed distance from the vertex to the strut attachment point on (iv) X-, (v) Y-, or (vi) Z- arm.

Table 2.

Nucleic Acid Nanostructure Methodology Generally

The nucleic acid structures provided herein may be formed using any nucleic acid folding or hybridization approach. One such approach is DNA origami (Rothemund, 2006, Nature, 440:297-302, incorporated herein by reference in its entirety). In a DNA origami approach, a structure is produced by the folding of a longer "scaffold" nucleic acid strand through its hybridization to a plurality of shorter "staple" oligonucleotides, each of which hybridize to two or more non-contiguous regions within the scaffold strand. In some embodiments, a scaffold strand is at least 100 nucleotides in length. In some embodiments, a scaffold strand is at least 500, at least 1000, at least 2000, at least 3000, at least 4000, at least 5000, at least 6000, at least 7000, or at least 8000 nucleotides in length. The scaffold strand may be naturally or non-naturally occurring. The scaffold typically used in the M13mpl8 viral genomic DNA, which is approximately 7 kb. Other single stranded scaffolds may be used including for example lambda genomic DNA. Staple strands are typically less than 100 nucleotides in length; however, they may be longer or shorter depending on the application and depending upon the length of the scaffold strand. In some embodiments, a staple strand may be about 15 to about 100 nucleotides in length. In some embodiments the staple strand is about 25 to about 50 nucleotides in length.

In some embodiments, a nucleic acid structure may be assembled in the absence of a scaffold strand (e.g. , a scaffold- free structure). For example, a number of oligonucleotides (e.g. ,< 200 nucleotides or less than 100 nucleotides in length) may be assembled to form a nucleic acid nano structure. This approach is described in WO 2013/022694 and WO

2014/018675, each of which is incorporated herein by reference in its entirety.

Other methods for assembling nucleic acid structures are known in the art, any one of which may be used herein. (See for example Kuzuya and Komiyama, 2010, Nanoscale, 2:310-322. It is also to be understood that a combination or hybrid of these methods may also be used to generate the nucleic acid structures disclosed herein. These methods may be modified based on the teaching provided herein in order to obtain the fixed-angle nucleic acid structures of this disclosure. Nucleic acids

The nucleic acid structures may comprise naturally occurring and/or non-naturally occurring nucleic acids. If naturally occurring, the nucleic acids may be isolated from natural sources or they may be synthesized apart from their naturally occurring sources. Non- naturally occurring nucleic acids are synthetic.

The terms "nucleic acid", "oligonucleotide", and "strand" are used interchangeably to mean multiple nucleotides attached to each other in a contiguous manner. A nucleotide is a molecule comprising a sugar (e.g. a deoxyribose) linked to a phosphate group and to an exchangeable organic base, which is either a pyrimidine (e.g. , cytosine (C), thymidine (T) or uracil (U)) or a purine (e.g. , adenine (A) or guanine (G)). In some embodiments, the nucleic acid may be L-DNA. In some embodiments, the nucleic acid is not RNA or an

oligoribonucleotide. In these embodiments, the nucleic acid structure may be referred to as a DNA structure. A DNA structure however may still comprise base, sugar and backbone modifications. Modifications

A nucleic acid structure may be made of DNA, modified DNA, and combinations thereof. The oligodeoxyribonucleotides (also referred to herein as oligonucleotides, and which may be staple strands, connector strands, and the like) that are used to generate the nucleic acid structure or that are present in the nucleic acid structure may have a

homogeneous or heterogeneous {i.e., chimeric) backbone. The backbone may be a naturally occurring backbone such as a phosphodiester backbone or it may comprise backbone modification(s). In some instances, backbone modification results in a longer half-life for the oligonucleotides due to reduced nuclease-mediated degradation. This is turn results in a longer half-life. Examples of suitable backbone modifications include but are not limited to phosphorothioate modifications, phosphorodithioate modifications, p-ethoxy modifications, methylphosphonate modifications, methylphosphorothioate modifications, alkyl- and aryl- phosphates (in which the charged phosphonate oxygen is replaced by an alkyl or aryl group), alkylphosphotriesters (in which the charged oxygen moiety is alkylated), peptide nucleic acid (PNA) backbone modifications, locked nucleic acid (LNA) backbone modifications, and the like. These modifications may be used in combination with each other and/or in combination with phosphodiester backbone linkages.

Alternatively or additionally, the oligonucleotides may comprise other modifications, including modifications at the base or the sugar moieties. Examples include nucleic acids having sugars which are covalently attached to low molecular weight organic groups other than a hydroxyl group at the 3' position and other than a phosphate group at the 5' position {e.g., a 2'-0-alkylated ribose), nucleic acids having sugars such as arabinose instead of ribose. Nucleic acids also embrace substituted purines and pyrimidines such as C-5 propyne modified bases (Wagner et ah, Nature Biotechnology 14:840-844, 1996). Other purines and pyrimidines include but are not limited to 5-methylcytosine, 2-aminopurine, 2-amino-6- chloropurine, 2,6-diaminopurine, hypoxanthine. Other such modifications are well known to those of skill in the art.

Modified backbones such as phosphorothioates may be synthesized using automated techniques employing either phosphoramidate or H-phosphonate chemistries. Aryl-and alkyl-phosphonates can be made, e.g., as described in U.S. Pat. No. 4,469,863, and alkylphosphotriesters (in which the charged oxygen moiety is alkylated as described in U.S. Pat. No. 5,023,243 and European Patent No. 092574) can be prepared by automated solid phase synthesis using commercially available reagents. Methods for making other DNA backbone modifications and substitutions have been described (Uhlmann, E. and Peyman, A., Chem. Rev. 90:544, 1990; Goodchild, J., Bioconjugate Chem. 1: 165, 1990).

Nucleic acids can be synthesized de novo using any of a number of procedures known in the art including, for example, the b-cyanoethyl phosphoramidite method (Beaucage and Caruthers Tet. Let. 22: 1859, 1981), and the nucleoside H-phosphonate method (Garegg et ah, Tet. Let. 27:4051-4054, 1986; Froehler et al., Nucl. Acid. Res. 14:5399-5407, 1986; Garegg et al, Tet. Let. 27:4055-4058, 1986, Gaffney et al, Tet. Let. 29:2619-2622, 1988). These chemistries can be performed by a variety of automated nucleic acid synthesizers available in the market. These nucleic acids are referred to as synthetic nucleic acids. Modified and unmodified nucleic acids may also be purchased from commercial sources such as IDT and Bioneer.

An isolated nucleic acid generally refers to a nucleic acid that is separated from components with which it normally associates in nature. As an example, an isolated nucleic acid may be one that is separated from a cell, from a nucleus, from mitochondria, or from chromatin.

The nucleic acid structures and the composite nucleic acid structures may be isolated and/or purified. Isolation, as used herein, refers to the physical separation of the desired entity {e.g., nucleic acid structures, etc.) from the environment in which it normally or naturally exists or the environment in which it was generated. The isolation may be partial or complete.

Isolation of the nucleic acid structure may be carried out by running a hybridization reaction mixture on a gel and isolating nucleic acid structures that migrate at a particular molecular weight and are thereby distinguished from the nucleic acid substrates and the spurious products of the hybridization reaction. As another example, isolation of nucleic acid structures may be carried out using a buoyant density gradient, sedimentation gradient centrifugation, or through filtration means.

Agents

The composite nucleic acid structures may contain an agent that is intended for use in vivo and/or in vitro, in a biological or non-biological application. For example, an agent may be any atom, molecule, or compound that can be used to provide benefit to a subject

(including without limitation prophylactic or therapeutic benefit) or that can be used for diagnosis and/or detection (for example, imaging) in vivo, or that may be used for effect in an in vitro setting (for example, a tissue or organ culture, a clean-up process, and the like). The agents may be without limitation therapeutic agents and diagnostic agents. Examples of agents for use with any one of the embodiments described herein are described below.

In some aspects, the composite nucleic acid structures are used to deliver agent either systemically or to localized regions, such as for example tissues or cells. Any agent may be delivered using the methods of the invention provided that it can be loaded into the composite strucure.

The agent may be without limitation a chemical compound including a small molecule, a protein, a polypeptide, a peptide, a nucleic acid, a virus-like particle, a steroid, a proteoglycan, a lipid, a carbohydrate, and analogs, derivatives, mixtures, fusions,

combinations or conjugates thereof. The agent may be a prodrug that is metabolized and thus converted in vivo to its active (and/or stable) form. The invention further contemplates the loading of more than one type of agent in a composite structure and/or the combined use of composite structures comprising different agents.

One class of agent is peptide-based agents such as (single or multi-chain) proteins and peptides. Examples of peptide-based agents include without limitation antibodies, single chain antibodies, antibody fragments, enzymes, co-factors, receptors, ligands, transcription factors and other regulatory factors, some antigens (as discussed below), cytokines, chemokines, hormones, and the like.

Another class of agents includes chemical compounds that are non-naturally occurring.

A variety of agents that are currently used for therapeutic or diagnostic purposes include without limitation imaging agents, immunomodulatory agents such as

immuno stimulatory agents and immunoinhibitory agents (e.g., cyclosporine), antigens, adjuvants, cytokines, chemokines, anti-cancer agents, anti-infective agents, nucleic acids, antibodies or fragments thereof, fusion proteins such as cytokine-antibody fusion proteins, Fc-fusion proteins, analgesics, opioids, enzyme inhibitors, neurotoxins, hypnotics, antihistamines, lubricants, tranquilizers, anti-convulsants, muscle relaxants, anti-Parkinson agents, anti-spasmodics, muscle contractants including channel blockers, miotics and anticholinergics, anti-glaucoma compounds, modulators of cell-extracellular matrix interactions including cell growth inhibitors and anti-adhesion molecules, vasodilating agents, inhibitors of DNA, RNA or protein synthesis, anti-hypertensives, anti-pyretics, steroidal and nonsteroidal anti-inflammatory agents, anti- angiogenic factors, anti- secretory factors, anticoagulants and/or antithrombotic agents, local anesthetics, ophthalmics, prostaglandins, targeting agents, neurotransmitters, proteins, cell response modifiers, and vaccines. In some embodiments, an agent is a diagnostic agent such as an imaging agent. As used herein, an imaging agent is an agent that emits signal directly or indirectly thereby allowing its detection in vivo. Imaging agents such as contrast agents and radioactive agents can be detected using medical imaging techniques such as nuclear medicine scans and magnetic resonance imaging (MRI). Imaging agents for magnetic resonance imaging (MRI) include Gd(DOTA), iron oxide or gold nanoparticles; imaging agents for nuclear medicine include 201 Tl, gamma-emitting radionuclide 99 mTc; imaging agents for positron-emission tomography (PET) include positron-emitting isotopes, (18)F-fluorodeoxyglucose ((18)FDG), (18)F-fluoride, copper-64, gadoamide, and radioisotopes of Pb(II) such as 203Pb, and l lln; imaging agents for in vivo fluorescence imaging such as fluorescent dyes or dye-conjugated nanoparticles.

The present disclosure further provides the following numbered embodiments:

1. A nucleic acid structure comprising

a first (x), a second (y), and a third (z) nucleic acid arm, each connected at one end to the other arms to form a vertex, and

a first, a second, and a third nucleic strut, wherein the first nucleic acid strut connects the first (x) nucleic arm to the second (y) nucleic arm, the second nucleic acid strut connects the second (y) nucleic arm to the third (z) nucleic arm, and the third nucleic acid strut connects the third (z) arm to the first (x) nucleic acid strut.

2. A nucleic acid structure comprising

three nucleic acid arms radiating from a vertex at fixed angles.

3. A nucleic acid structure comprising

N nucleic acid arms radiating from a vertex, wherein N is the number of nucleic acid arms and is 3 or more, and

M nucleic acid struts, each strut connecting two nucleic acid arms to each other, wherein M is the number of nucleic acid struts and is 3 or more.

4. The nucleic acid structure of embodiment 3, wherein N is equal to M.

5. The nucleic acid structure of embodiment 3, wherein N is less than M.

6. The nucleic acid structure of any one of embodiments 1-5, wherein the nucleic acid structure comprises 4 nucleic acids and at least 4 nucleic acid struts, or 5 nucleic acid arms and at 5 nucleic acid struts.

7. The nucleic acid structure of any one of embodiments 1-6, wherein the nucleic acid arms are equally spaced apart from each other (or the arms are separated from each other by the same angle). 8. The nucleic acid structure of any one of embodiments 1-7, wherein the nucleic acid arms are not equally separated from each other (or the arms are separated from each other by different angles).

9. The nucleic acid structure of any one of embodiments 1-8, further comprising a vertex nucleic acid.

10. The nucleic acid structure of any one of embodiments 1-9, further comprising a connector nucleic acid.

11. The nucleic acid structure of any one of embodiments 1-10, wherein the nucleic acid arms, nucleic acid struts, and/or vertex nucleic acid are comprised of parallel double helices.

12. The nucleic acid structure of any one of embodiments 1-11, wherein nucleic acid arms are of identical length.

13. The nucleic acid structure of any one of embodiments 1-12, wherein the nucleic acid struts are of identical length.

14. The nucleic acid structure of any one of embodiments 1-13, wherein the nucleic acid struts are of different lengths.

15. The nucleic acid structure of any one of embodiments 1-14, wherein at least one nucleic acid arm comprises a blunt end.

16. The nucleic acid structure of any one of embodiments 1-15, wherein at least one nucleic acid arm comprises a connector nucleic acid at its free (non-vertex) end that is up to 16 nucleotides in length.

17. The nucleic acid structure of any one of embodiments 1-16, wherein at least one nucleic acid arm comprises a connector nucleic acid at its free (non-vertex) end, thereby comprising a 1 or 2 nucleotide overhang.

18. The nucleic acid structure of any one of embodiments 1-17, wherein the nucleic acid structure is up to 5 megadaltons (MD) in size.

19. The nucleic acid structure of any one of embodiments 1-18, wherein the nucleic acid arms are 50 nm in length.

20. The nucleic acid structure of any one of embodiments 1-19, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 60° - 60° - 60° (tetrahedron). 21. The nucleic acid structure of any one of embodiments 1-20, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 60° - 90° - 90° (triangular prism).

22. The nucleic acid structure of any one of embodiments 1-21, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 90° - 90° - 90° (cube).

23. The nucleic acid structure of any one of embodiments 1-22, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 108° - 90° - 90° (pentagonal prism).

24. The nucleic acid structure of any one of embodiments 1-23, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 120° - 90° - 90° (hexagonal prism).

25. A composite nucleic acid structure comprising L nucleic acid structures selected from the nucleic acid structures of any one of embodiments 1-24, wherein L is an even number of nucleic acid structures, and wherein the L nucleic acid structures are connected to each other at free (non-vertex) ends of the nucleic acid arms.

26. The composite nucleic acid structure of embodiment 25, wherein the two more nucleic acid structures are two, four, six, eight, ten, twelve or more nucleic acid structures.

27. The composite nucleic acid structure of embodiment 25 or 26, wherein the composite nucleic acid structure is a tetrahedron, a triangular prism, a cube, a pentagonal prism, or a hexagonal prism.

28. The composite nucleic acid structure of any one of embodiments 25-27, wherein the composite nucleic acid structure is 20 megadaltons (MD), 30 MD, 40 MD, 50 MD, or 60 MD in size.

29. The composite nucleic acid structure of any one of embodiments 25-28, wherein the composite nucleic acid structure has edge widths, comprised of two nucleic acid arms from adjacent nucleic acid structures, of 100 nm.

EXAMPLES

Materials and sample preparation.

DNA strands were synthesized by Integrated DNA Technology, Inc. or Bioneer Corporation. To assemble the structures, unpurified 100 μΜ DNA strands were mixed with p8064 scaffold in a molar stoichiometric ratio of 10: 1 in 0.5 x TE buffer (5 mM Tris, pH 7.9, 1 mM EDTA) supplemented with 12 mM MgCl₂. The final concentration of p8064 scaffold was adjusted to 10 nM. Cy3b-modified DNA oligonucleotides were purchased

from Biosynthesis (Lewisville, TX) (5 ' -TATGTAGATC-Cy3b ; SEQ ID NO: 4). Streptavidin was purchased from Invitrogen (S-888, Carlsbad, CA). Bovine serum albumin (BSA), and BSA-Biotin was obtained from Sigma Aldrich (A8549, St. Louis, MO). Glass slides and coverslips were purchased from VWR (Radnor, PA). Two buffers were used for sample preparation and imaging for super-resolution DNA-PAINT imaging: Buffer A (10 mM Tris- HC1, 100 mM NaCl, 0.05% Tween-20, pH 7.5), buffer B (5 mM Tris-HCl, 10 mM MgCl₂, 1 mM EDTA, 0.05% Tween-20, pH 8).

Annealing ramps.

The strand mixture was then annealed in a PCR thermo cycler using a fast linear cooling step from 80 °C to 65 °C over 1 hour, then a 42 hour linear cooling ramp from 64°C to 24°C.

Agarose gel electrophoresis.

Annealed samples were subjected to gel electrophoresis in 0.5% TBE buffer that includes 10 mM of MgCl₂, at 90V for 3 hours in an ice- water bath. Gels were stained with Syber^® Safe before imaging.

TEM imaging.

For imaging, 2.5 μΐ_^ of annealed sample were adsorbed for 2 minutes onto glow- discharged, carbon-coated TEM grids. The grids were then stained for 10 seconds using a 2% aqueous uranyl formate solution containing 25 mM NaOH. Imaging was performed using a JEOL JEM- 1400 TEM operated at 80 kV.

Super-resolution imaging.

Fluorescence imaging was carried out on an inverted Nikon Eclipse Ti microscope

(Nikon Instruments, Melville, NY) with the Perfect Focus System, applying an objective-type TIRF configuration using a Nikon TIRF illuminator with an oil-immersion objective (CFI

Apo TIRF 100, NA 1.49, Oil). For Cy3b excitation a 561 nm laser (200 mW nominal,

Coherent Sapphire) was used. The laser beam was passed through cleanup filters

(ZET561/10, Chroma Technology, Bellows Falls, VT) and coupled into the microscope objective using a multi-band beam splitter (ZT488rdc/ZT561rdc/ZT640rdc, Chroma Technology). Fluorescence light was spectrally filtered with an emission filter (ET600/50m, Chroma Technology) and imaged on an EMCCD camera (iXon X3 DU-897, Andor

Technologies, North Ireland). Imaging was performed without additional magnification in the detection path, yielding 160 nm pixel size.

Sample preparation and imaging.

For sample preparation, a piece of coverslip (No. 1.5, 18x18 mm , 0.17 mm thick) and a glass slide (3x1 inch , 1 mm thick) were sandwiched together by two strips of double-sided tape to form a flow chamber with inner volume of 20 μΐ_^. First, 20 μΐ_^ of biotin-labeled bovine albumin (1 mg/mL, dissolved in buffer A) was flown into the chamber and incubated for 2 min. The chamber was then washed using 40 μΐ_^ of buffer A. 20 μΐ_^ of streptavidin (0.5 mg/mL, dissolved in buffer A) was then flown through the chamber and allowed to bind for 2 min. After washing with 40 μΐ_^ of buffer A and subsequently with 40 μΐ_^ of buffer B, 20 μΐ_^ of biotin-labeled microtubule-like DNA structures (~ 300 pM monomer concentration) and DNA origami drift markers (~ 100 pM) in buffer B were finally flown into the chamber and incubated for 5 min. The chamber was washed using 40 μΐ_^ of buffer B. The final imaging buffer solution contained 3 nM Cy3b-labeled imager strands in buffer B. The chamber was sealed with epoxy before subsequent imaging. The CCD readout bandwidth was set to 3 MHz at 14 bit and 5.1 pre-amp gain. No EM gain was used. Imaging was performed using inclined illumination with an excitation intensity of -200 W/cm at 561 nm. 3D images were acquired with a cylindrical lens in the detection path (Nikon). All images were reconstructed from 5000 frame long time-lapsed movies acquired with 200 ms integration time, resulting in ~17 min imaging time. Image processing and drift correction.

Super-resolution DNA-PAINT images were reconstructed using spot-finding and 2DGaussian fitting algorithms programmed in Lab VIEW (Jungmann, R., et al. Nature Methods, advance online publication, 2014). A simplified version of this software is available for download at the "dna-paint" website. The N-STORM analysis package for NIS Elements (Nikon) was used for data processing. 3D calibration was carried out according to the manufacturer's instructions. DNA origami drift markers (Lin, C, et al. Nature Chemistry 4,

832-839, 2012) were used as fiducial markers. The high binding site density increases the probability to observe one bound imager strand per structure in each image frame.

Furthermore, the fluorescence intensity of the origami drift markers is similar to single imager strand binding events and the markers never "bleach". These properties render DNA origami structures as ideal drift markers. Drift correction was performed by tracking the position of each origami drift marker structure throughout the duration of each movie. The trajectories of all detected drift markers were then averaged and used to correct the drift in the final super-resolution reconstruction.

Determination of localization accuracy.

Fitting a ID-Gaussian function to the distribution of z localizations from DNA origami drift markers and calculating the standard deviation was used to determine the localization accuracy in z. As origami drift markers are 2D structures, all binding events occur in a 2D plane on the surface, and thus at the same z location. Localization accuracy in x and y was determined by calculating the average separation of single-molecule localizations in neighboring frames, which can be attributed to an imager strand binding to a single docking strand. As multiple docking strands are used in each vertex of the polyhedral (-18 strands per vertex), one cannot fit the distribution of binding events per vertex, as this would result in an overestimation of the localization accuracy. The measured value per vertex would represent a convolution of the actual localization accuracy with the spatial extent of the binding sites in this vertex. Spatial vs. temporal imaging resolution.

In stochastic super-resolution microscopy such as DNA-PAINT, one can generally make the statement that there is a tradeoff between spatial and temporal resolution. Higher spatial resolution can be obtained by collecting a larger amount of photons per binding or photo switching event. This can be achieved by increasing fluorescence ON times and matching the camera integration time to these ON times. In DNA-PAINT imaging, this can be accomplished by increasing the binding stability of the imager/docking complex (i.e. going from a 9 to a 10-nt interaction region) and increasing the camera integration time to match the longer binding time, which in turn results in a longer image acquisition time.

Higher temporal resolution can be obtained by reducing the binding stability of the imager/docking complex (i.e. going from a 9 to a 8-nt interaction region) and decreasing the camera integration time to match the shorter binding time. Table 3. Sequences for super-resolution DNA-PAINT ima:

Table 4. Sequences of the tetrahedron.

5'— end Sequence Note SEQ ID NO:

1 [84] TGAGGCCAACGCTCATGGACGTACTATGGTTTTTACAGCCTCCGGA Core staple 5

0[54] ACGTATTACGCCACCAAACATCCCTTAGCCAGCGAAAG Core staple 6

3[102] TCGATTGCAACAGGAAAACCGAGTGTTTTTTTGGT Core staple 7

3 [144] CACTCGGCCTTGCTGGTAGCAATATAATTACATTTATGTATT Core staple 8

2[44] AACATAAATCAAAAGAAGCAGCAAGTTTTTCTCCA Core staple 9

2[51] ATTGTGCCGGCACTGCGGCACGCGGTCATAGCTGTTTCCATA Core staple 10

2[72] AGTGACGGATTCGCCTGTCGCTGGTAATCAG Core staple 11

2[93] ATGTGAATACACCTTTTTGATCAATATAATCTTTC Core staple 12

2[107] GACCATCGCCATTAAAAATGAAAATGGTCAGTACA Core staple 13

2[114] TGGGCGCAGAAGATGAATTTGGATTCCTGATTATCAGAATTA Core staple 14

2[135] ACCTTCAATTTAGATTTATGGAAGGGAGCGGAATTATCTTAT Core staple 15

5[39] CTTGTGGACTCGTAACCTTTCCTCGTTAGAAAGGG Core staple 16

5 [60] CCGAAGAGTCGCTTAATTGACGAGC Core staple 17

5[123] CGAGTAAGAATTTACATAGAACAATATTACCATCACGCCCGT Core staple 18

4[83] CCCTTCAGTTAATGGTCTTTGCGAATACCTACATTTTGACGCTTGA Core staple 19

7 [32] TATGCCAGCTATACGAGCCGGAAGCTGTGTGGGGGGTTTAAT Core staple 20

7[74] GCACGTTGCGTGAGTGAGCTAACTGGGTACCAGCCTCCCAAA Core staple 21

7[81] CTGGAGAAACAATAACGGTCCGTGGAGCTCGAATTCGTTGCC Core staple 22

7[91] ATCAAACATTAGACTTTACCATTAATTGACAG Core staple 23

7[109] ATCATCTAAAGCATCACCCTAAAAAATATTTTCAA Core staple 24

6[51] GTCTGTAAAGCCTGGGGAATCATGTGCC Core staple 25

6[114] TTTCCTTTGCCCGAACGATCATATTATACTTAAAT Core staple 26

8 [44] TGTCAGGGTGGCGGTCCACGCTGGATCC Core staple 27

8 [65] AGCCAGTGAGGCCCTGAGAGAGTTTAGC Core staple 28

9 [60] TGTCCAACGCATAACGGAACGTGCCGGC Core staple 29

9[130] ATATCAGGTTATCAACAAGAGCCAGCAGCAAATAC Core staple 30

11[88] CTTGCTATTACGCGAACTGATAGCCTTGCTGAACCTTG Core staple 31

11[130] CATTGAAAGCACGAACCACCAGCACACGCTGGTTG Core staple 32

10[37] GGTTTAGACAGGAACGGAACGTGCACCACACCCGCCGCCACT Core staple 33

10[58] CATGAATCCTGAGAAGTGTTGCTTGCGCCGCTACAGGGTTCC Core staple 34

10[65] CAGTGCATCATTGGAACAGATAGGGTTGAGTCCGCCTGACGG Core staple 35

10[100] TCCAAAAGAGTCTGTCCGCCAGCCTCTGAAATGGATTATACG Core staple 36

10[114] TCCGGGTAAACGCTATTAATTAATCTGATTGTATACAGCAAT Core staple 37

10[121] TTGAAATTAACCGTTGTAATATCCTGGCAGATTCACCATCTG Core staple 38

13 [74] CTTTTACCAGTATAAAGTCTTCGCATCC Core staple 39

13[95] GCTTCATATGCGTTATATCACAGTACATCGGATCAAAT Core staple 40

12[37] TGAAGGTTTCTTTGCTCGTCATTCTCAACAGTAGGGCTTCTGCCACGCC Core staple 41

12[79] TTCGTAGAACGTCAGCGCGTCTCGATTG Core staple 42

12[100] CCTGCTTTAGTGATGAAGGCAAACCAAAATCCACA Core staple 43

12[121] CGTGTTAAACGAACAATTTCATTTAACCTTGCTTCTGTCTGA Core staple 44

15[46] AAGGGGAAACCTGTCGTTGGGCGCGCACTCTACCTGCACACT Core staple 45

15[67] TAACTCACTGCCCGCTTTTTTCACGCAGTGTTGCCCCCAGCA Core staple 46

15[88] ACAATTCGACAACTCGTTGATGGCAATTCAGGATCCCCCAAA Core staple 47

15[109] AATGAGGATTTAGAAGTCCTCAATTAACAGTCAAGTTAGCGG Core staple 48

15[130] TAACCGTCAATAGATAATTGGCAATAACGTCGGCGAATCTGA Core staple 49

17[147] GTCTGGTCAGCAGCAACCGCAAAAAAAAGCCGCACAGGCGGC Core staple 50

16[188] ATCGACATAAAAAAATCCCGTAGAATGCCAACGGCAGCACCG Core staple 51 '— end Sequence Note SEQ ID NO:6[209] AGCAGTTGGGCGGTTGTGTACTCGGTGGTGCCATCCCACGCA Core staple 526[229] ATTTCTGCTCATTTGCCGCCACCAGCTTACGGCTGGAGGT Core staple 539[53] GAACTGACCAACTTTGAATCAAGATAAT Core staple 549[84] CATTTCGAGCTAAATCGGTGAGCTTAATTTGACCAAGAG Core staple 559[116] ATAAGCAGCGCCGCTTTAGAAACAGCGGATCGGAAGATTATT Core staple 568[44] CATCTCCTTTTGATAAGCGCGTTTGTAA Core staple 578[65] GAATTTTGCGGATGGCTAGCC Core staple 581[39] TTGGTTTTAAATATGCATATAACACAGATGAACGG Core staple 591[102] GTAGCCTCAGAGCATAACAAATGGAACG Core staple 601[144] AAATCATACAGGCAAGGGCGAGCTCGGCGAAACGTAGTCAGT Core staple 610[44] TCGTCAGAAGCAAAGCGCCCCCTCGTAATAGGCAA Core staple 620[65] CTTTCAAAAAGATTAAGCGTCATATGGATAGGAAT Core staple 630[72] CGATAATTAAGTTGGGTCGGCTACTTAGATA Core staple 640[93] ATCGGGTTTTGCGAAAGTTGTATCGGCCTCAAAAC Core staple 650[107] CCGTAATGCCGGAGAGGGCATGTCGTATAAGAAAA Core staple 660[114] AGATGTAAAATCTTCGCCGCACTCTCTGCCAGTTTGAGTGAG Core staple 670[135] AGGAAGCTTTGAAGGGCGCACCGCTGGGCGCATCGTAAGATT Core staple 683 [60] GCACAAATATAGGTCATTATAATGCTGTAGCCTGC Core staple 693 [123] CTATCAAAAGGAAGCCTTTAGCAAAATTAAGAGCT Core staple 702[97] CGGTTGATAATCCTGCGGAATAGATATTCAACCGTTCTAGCT Core staple 715[32] AAGTTTACCAAGAAAGATTCATCATTAATAAATTGGGCGTTG Core staple 725[60] ATGCAAATCATGACAAGCTAAAGACGAGTAGATTTAGTTGCT Core staple 734[51] CACTTTAGGAATACCACCGTTGGGTTTCAACGCA Core staple 744[72] TACT AATGCAGATACATGGCTCAT ATT ACCTGGGG Core staple 754[90] GCCAGCGCCAAAAGCGTCCAATGCTGCAAGGCGTTATTG Core staple 764[114] TAAGTAACAACCCGTCGCCGTGCACAGCCAGGAGA Core staple 776[44] CTGAGAGGGGAAATGCTTTAAACAATTATAGAGCTTCATTAA Core staple 786[65] ACCTTTAGACAATATTCATTGAATGATT Core staple 796[86] ATGTAAGAAAAGCCCCATCCTGTA Core staple 806[107] ACGGAAGATTAATCATATGTACCCGATAAATGAGACAGCCCT Core staple 817[74] TGATATACCAGTCAGGAATTCAACGAGGCATAGTAAGATAAA Core staple 827[129] TCCGGATCGGTTTAAATTTAATCGTAAAACTAGTAG Core staple 839[39] TTCAAGAGGAGTTGATTCCCAATTTCAA Core staple 849[53] TCTACGTAACGGTTTAAAAGAAAAATCTACGGTTG Core staple 859[88] CCAACCATCAATATGGATATGTACCAAAAACATTATGATCAA Core staple 869[102] GTCGCATCGGTCAATAACCTGTTTCAATAAAATACTTTTGCGGGAGGTG Core staple 879[130] GCCTAAAGATTTTTTGAGAGATCTTGAACGGGTAA Core staple 888[72] GCTTCCATTATTGCAGGCGCTTTCTTTAATCCATT Core staple 898[93] AGGGTAATGCAGTCCAGCATCAGCTATGCGAGGGG Core staple 908[121] CTCTTTTCATTTGGGGCCAAAGAATTATTTCAACGCAAGTGT Core staple 910[37] CGGATCATAAGGGAACCGAACTTTATCCGCCGGGCGCGTTGAGATAAAG Core staple 920[59] CTCATTCATGAGGAAGTTTTGAGGAAACCGGAAAGA Core staple 930[79] TCAAACGGGTAAAATACGTAGCAAAACG Core staple 940[100] TTACAGGGAGTTAAAGGAAAGACAACGACGTAAGG Core staple 950[121] CGCTGCGGGATCCAGCGCCATGTTCTCTCACGGAAAAACTT Core staple 963[46] AGATATCATAACCCTCGTTTTGCCCTCATTCGACC Core staple 973[91] ATCAACATTAAATGGGGACGACGACATTAAGAACTAACTTTC Core staple 983[109] CGATTCGCGTCTGGCCTAAAACAGCCAGCTGCCCA Core staple 993[130] CTCTAGGAACGCCATCACAAATATGCGGGCCCGACGGCCACC Core staple 1005[147] ACTACGAAGGCACCAACCTAATATTCGGTCGCTGAGGCTTGC Core staple 1014[188] ATCGCCCACGCATAACCGATAAACGAAAGAGGCAAAAGAATA Core staple 1024[209] GCGCCGACAATGACAACAACCCACTAAAACACTCATCTTTGA Core staple 1034[229] ACAGCTTGATACCGATAGTTCCCCCAGCGATTATACCAAG Core staple 1047[53] TATAATAAGAGAATATAATGTTCAAGCA Core staple 1057[84] GGTTTACCAAGGCCGGAAACTG Core staple 1067[116] TTCTAACTATAACCTCCGCTTTCGAGGTGAACGCCACCAACT Core staple 1076[44] TTACCGAGGAAACGCAAATGAAATGCTAATGTCCT Core staple 1086[65] GACGGAATACCCAAAAGCAAT Core staple 1096[75] GCATGATAGAAAAAGAACGCTTCATCTAGATTTG Core staple 1109[39] AAAGCAAACGTAGAAAAACGCAAAGACAAAAAGGC Core staple 1119[102] GCAACCATTACCATTAGCAGCGCCGCAAATCAATGGTTACGCGAA Core staple 1129[144] GCGTTGAGCCATTTGGGGGGAAGGACAACTAAAGGATGTCTG Core staple 1138[44] ATATAATATCAGAGAGAAATAACACCCAATCAATT Core staple 1148[65] GCACAAGAATTGAGTTAAATAGCATTTTTTGTGCT Core staple 1158[72] AATTTTTAGCGTAACGAAAGACAATTCATAT Core staple 1168[83] GGAACCCAACGTCACCAATGAAACCATCCCAG Core staple 1178[93] AGCTTTTGTCTAGCATTACGAGGTTTAGTACTTTC Core staple 1188[107] ATCGAACCGCCACCCTCTATTCACACCGTTCCAGT Core staple 1198[114] AATTAGTAAACAGTACACTCAGAACGGAATAGGTGTATATTA Core staple 1208[135] TAGGGGATTTCGTAACAACCGCCAAGGGTTGATATAAGAAGA Core staple 121 '— end Sequence Note SEQ ID NO:1 [60] CCAAGAAACATAATAACTCCTTATTACGCAGAGTT Core staple 1221[123] CCACATCTTTAGCGACAGCCAGCAAAATCACGACA Core staple 1230[97] TCATTAAAGCCAAAAAATGAAAGCGCCTCCCTCAGAGCCGCC Core staple 1243[32] ACAAACGCTAGAACGCGAGGCGTTAAGCAAAGTCTTTCTCCG Core staple 1253 [60] TAAAGATAAGCAGAACGCTTTTTCTTTGTCACAATCAATTAA Core staple 1263[130] ATAACGATTGGCCTTGAAGAG Core staple 1272[51] TTAACCTCCCGACTTGCATCATTAAACGGGTGCCT Core staple 1282[72] ATTTTTGAAGCCTTAAAGTTTTTACGCACTCACAA Core staple 1292[90] CCTATAAGATTAGTTTTAACGCAGCCCTCATAGATCAAG Core staple 1302[114] TAAGGCTGAGACTCCTCTATAGCCCCGCCACTCAGCTTGGCTTAG Core staple 1314[51] GAATTCCAAGCCGCGCCCAATAGCTTAG Core staple 1324[107] ACATGAATTTAAACAAATAAATCCACCCTCAACCGGAAGATA Core staple 1335[46] TCACAAGAAATATTTATTAAAAACAGGGAAGTGAGCGCGCTATCTAAGG Core staple 1345[74] TACTTTTCATCGTAGGAGGGAGGTTTGCACCCAGCTACCAAA Core staple 1357[39] AACAAGTACCGACACCACGGAATATATG Core staple 1367[102] TTCTGCTGATAAAGACAAAAGGGCCAGTAGCGCACCGTAATCAGTTCAT Core staple 1377[130] TATCGTTTGCCCACCCTCAGAGCCAGGTCAGCATGGCTGAGT Core staple 1386[121] ATAAACCGATTGAGGGAAATTAGAGAATCAAGTTTGCCTTAT Core staple 1399[126] GTATTGCGAATAATATTGTATCGGTTTACCTCAGACTGAGTTCGTC Core staple 1408[37] CGAGGCATTTTCGAGCCAGTAAATAAATTGTGTCGAAACTTA Core staple 1418[58] GATATATTTTAGTTAATGAGAAAACGCCTGTAAGA Core staple 1428[69] TATCATCATTAAACCAACAATGAAACGAGCCTTTACAGAGAGTAAC Core staple 1438[79] CGGTCTGACCTAAATTTCAATCGCTCTAAAGCACCACC Core staple 1448[90] ACAAAGTATCGAGACCACAGATCGAATGGAAAGCGTTCGGAA Core staple 1458[100] TTATAGACTACCTTTTTATGTAAACAGACGTCAAA Core staple 1460[104] CACCGTACTCAGAAGCAAGCCTCTATTCTGAAACATGAAAGT Core staple 1471 [46] CGATCCTGAATCTTACCGCCATATAATAATAAAAC Core staple 1481[109] AGATGCCCCCTGCCTATCAGTCTCACGCCTGGTCT Core staple 1491[130] GAAAGTGCCCGTATAAACAGTAAGTCGTCACTGAATTTGGTT Core staple 1503[147] GAAATACCGACCGTGTGATAATATCAAAATCATAGGTCTGAG Core staple 1512[188] GAGAAGAGTCAATAGTGAATTATAAGGCGTTAAATAAGAATA Core staple 1522[209] GATAGCTTAGATTAAGACGCTAACACCGGAATCATAATTACT Core staple 1532[229] AGAATCCTTGAAAACATAGCAGAAAAAGCCTGTTTAGTAT Core staple 154[137] AAAATTAGAGTTTTAAAAGTTTGAACCAGAAGGTTAGAAGTG Core staple 155[151] AGGGCCTGCAACAGTGCGAAGATAGAACCCTGTCA Core staple 156[146] CTAATAGGGAATTGAATTGCGACCTGAGACAA Core staple 1572[142] AATGAATTACCTTTTTTCAAGAAACAAA Core staple 1585[137] ACGTAACCAACGTGGGAACAAACGGTGTAGATTCTGGTGGGA Core staple 1595[151] TTAAACAAGAGAATCGAACAAAGGGAGTAATGGAT Core staple 1604[146] CATTTTTTTAATATCTGTTGGCAGAGGTAAAC Core staple 1610[142] TAGTACCAGTCCCGGAATCACCGGGGAG Core staple 1623[151] AGGCAGGAGGTTGAGGCGCCACCAAGCCCCCTTTA Core staple 1632[135] AACGGATTAGGATTAGCCGTCGAGCCCTCAGGCCT Core staple 1642[146] GTGCCTTTTTGATGCATGTACTGCTAAAGAAA Core staple 1658[142] TTAAATTTTTTCACGTTGAGAATACAAC Core staple 166[166] GAGTAGAAGAACTAATAACATCACTTGCGC Connector staple 167[163] TCTGGCCAACAGATGATGAGC Connector staple 168[163] TATTAACACCTTATCTAAAATAAT Connector staple 169[163] TTTAGGAGCATATCATTTTCT Connector staple 170[166] ACGTAAAACAGAAATATCAAAATTATTTAA Connector staple 1711[151] AGAAGAGATAAAACAGAGGTGAGGCGGTCAG Connector staple 1720[142] AATCTTCTTTGATTAGTCAAACTAGACCAGTAATAAAAGGGACTC Connector staple 1730[160] CAAACATAATGGAAACAGTAC Connector staple 1742[163] ATAAATCAATATATGTGACCTACCATAAAGAAGGA Connector staple 1754[160] GGAACAAAGAAACCGTAACATCTAACAA Connector staple 1768[166] TAGCATTAACATCAATTCTACTAATAGTGG Connector staple 1770[163] TTTTAAATGCCCACGGGAAAT Connector staple 1782[163] GTCTGGAGCAAAATTCGCATTATA Connector staple 1794[163] TTTTTGTTAAGACCGTAATAG Connector staple 1806[166] TCGCCATTCAGGCACCAGGCAAAGCGCCCG Connector staple 1819[151] CCGAATGCCTCTATCAGGTCATTGCCTGAGA Connector staple 1828[142] AATGAAAAGGTGGCATCCAATAAAAATTTTTAGAACCCTCATAAA Connector staple 1838[160] GATAACCTTTGTGAGAGATAG Connector staple 1840[163] ACTTTCTCCGTGGTGAAGCCGGAATGCGCAATTTG Connector staple 1852[160] GATAGGTCACGTTGGCGGATTATCAGCT Connector staple 1866[166] GAATTATCACCGTAATTATTCATTAAAGCC Connector staple 1878[163] TCGGCATTTTCAACAGTTTGA Connector staple 1880[163] CCAGCATTGAAGTGTACTGGTACA Connector staple 1892[163] AAGTTTTAACTGCTCAGTAGT Connector staple 1904[166] TAGCAAGCCCAATACCCTCATTTTCAGGCA Connector staple 191 5'— end Sequence Note SEQ ID NO:

47[151] TTTCGGTCATGAACCACCACCAGAGCCGCCG Connector staple 192

46[142] GGATAAATATTGACGGACACCGACTCAGACTGTAGCGCGTTTTAT Connector staple 193

46[160] GCGGAGTGAAAATCTCCAAAA Connector staple 194

48[163] AAAAGGCTCCAAAAGGAAGCCACCAGGAACCATAC Connector staple 195

50[160] AGGCGGATAAGTGCGGGGTTTGGGGTCA Connector staple 196

1 [12] ACAGGAGGCCGATTAATCAGAGCGCGGTCACGCTGCGCCAA Vertex staple 197

1 [32] ATTGTGTTCATGGGTAAGAATCGCCATATTTAACAACG Vertex staple 198

3 [9] TATCAAAGTGTAGGGAGCTAA Vertex staple 199

2[30] CGTCCGGGTTGTGGTGCTCATACCAAATTGTTATCCGCTCACA Vertex staple 200

5[9] TTGATGGTGGTTCGAAAAACCGTC Vertex staple 201

7[9] CGCGCGGGGAGAAGAATGCGG Vertex staple 202

9[12] CGGGCCGTTTTCACGGTGCGGCCGGCGGTTCAGCAGGCGAAAATCCTGT Vertex staple 203

11[16] CGGCATCAGATGCAAAGGGCCGAAATCGGCAAATTTGCCCTGCG Vertex staple 204

13[14] CCTGCGGCTGGTAAGCAAATCGTTAA Vertex staple 205

15[16] ATTCCACACAACGCATTAATGAATCGGCCAA Vertex staple 206

19[12] TGGAAGTTTCATTCCAACTAAAGATTAGAGAGTACCTAAG Vertex staple 207

21[9] CAACAGGTCAGGTACGGTGTC Vertex staple 208

20[31] CGAAGCTGGCTAGTGAATGTAGTAAAACGAACTAACGGAACAAC Vertex staple 209

23 [9] TCAAAAATCAGGGGAAGCAAACTC Vertex staple 210

25[9] ATAGCGAGAGGCGCCCTGACG Vertex staple 211

27[12] AGAAACACCAGAACGAAAGGCTTTTTTGCAAAACGAGAATGACCATAAA Vertex staple 212

29[16] CCAGGCGCATAGCCAGACCTCTTTACCCTGACTGTTCAGAAAAG Vertex staple 213

31[14] GGAACGAGGCGCAGACGGTGTACAGA Vertex staple 214

31 [32] TCATATGAGCCGGGTCACTGTTGC Vertex staple 215

33[16] ATTATTACAGGTGACGACGATAAAAACCAAA Vertex staple 216

37[12] GCAACATATAAAAGAATACATACAACAAAGTTACCAGTACC Vertex staple 217

39[9] AGCAGATAGCCGATAAAGGTG Vertex staple 218

38[30] GAACGACAATTCCCATCATCGGCTTCAGATATAGAAGGCTTAT Vertex staple 219

41[9] CACCCTGAACAATTAAGAAAAGTA Vertex staple 220

43[9] CTAATTTGCCAGACGAGCATG Vertex staple 221

45[12] TAGAAACCAATCAATACTAATTTTTACAAAGACGGGAGAATTAACTGAA Vertex staple 222

47[16] CTGTCCAGACGAGCCCTTTAGTCAGAGGGTAATCGCATTAATAA Vertex staple 223

49[14] CCAACATGTAATTTGGTAAAGTAATT Vertex staple 224

49[32] AGACCTGCTCCATGTTACTTAGCC Vertex staple 225

51[16] CCGGTATTCTAAACGAGCGTCTTTCCAGAGC Vertex staple 226

Table 5. Sequences of the triangular prism.

5'— end Sequence Note SEQ ID

NO:

1 [53] CGCCAACCGCAAGAAAAGTTACCTGTCC Core staple 227

1 [84] AGTGAGGAAAACGCTCATGCGCGTACTAGTGTTTTTGGT Core staple 228

0[44] CGTCCACCACACCCGCCAACAAGAGCAG Core staple 229

3[102] AATCCATTGCAACAGGACCACCGACGGACTTGCGGTCCCTTAGAA Core staple 230

3 [144] CACTATCGGCCTTGCTGGTAGCAAATTAATTACATTGCATTA Core staple 231

2[44] ACTAAAATCCCTTATAATGAGAGACGCCAGGCTGC Core staple 232

2[65] TCCGAATAGCCCGAGATTTGCCCTCACC Core staple 233

2[72] GTGCCAACGGATTCGCCGTCAGCGTATAATC Core staple 234

2[93] GAATTTGAATGTACCTTTCTCATCAATATAAATTT Core staple 235

2[107] CAGAACATCGCCATTAAAAATGAATCTGGTCAATA Core staple 236

2[114] CGTTCGCGCATCAGATGTGTTTGGATTCCTGATTATCAGTAT Core staple 237

2[135] TGAATTTCAACGTAGATTAATGGAAAGGAGCGGAATTACGTT Core staple 238

5 [60] AAAAGTTTGGGCGCTTATTTGACGAGCACGTGGTA Core staple 239

5[123] ACCGCGTAAGTATTTACCCAGAACAATATTACCATCACCATC Core staple 240

4[41] CAAGCGGAATCGGCATTAAAGCGCGTAAGCTTTCC Core staple 241

4[97] ACCTTGCTGAACAACAGCTGAAGTTTAATGCGCGAACTGATA Core staple 242

4[135] CGCCAGTTGAAGATTAGAATTTTAAAAGTTTCCAC Core staple 243

7 [32] GCGAACCTGTTCCACACAACATACTAGCTGTCGGTCATTGAG Core staple 244

7[60] TTTACGATCCGCGGTGCTCAG Core staple 245

7[74] AGTACATTAAGGGTGCCTAATGAGGAGGATCCGCGTCCAAAC Core staple 246

7[109] ATAAAATCTAAAGCATCGCCCTAAACAATATGCTC Core staple 247 '— end Sequence Note SEQ ID

NO:

[51] CCGAAGCATAAAGTGTATCGAATTCCAG Core staple 248[90] ACTTTAGCTAACTCGAGACGGGGGAGAAACAATCTTGTTCTTCCCGG Core staple 249 GT

[114] CATATCCTTTGCCCGAATCATCATATTATACGTAA Core staple 250 [65] CAGTTCTTTTTCACCGCCTGGCCCATCA Core staple 251 [60] CACCGCTCAACACCGTCGGTGATGGGTCTGGCGGTGCCTTGT Core staple 252[130] GAATTTCAGGAAATCAATGAGAGCCAGCAGCAAAT Core staple 2531 [39] CGGACATCCCTTTTAGACAGGAACATAA Core staple 2541 [53] CCAAGCGCAGGTTTCTGCGTAATCATGGTCAGAGC Core staple 2551[88] TGCTGGCTATTAGTCGGGGGAAATACCTACATTTTGACTTTT Core staple 2561[130] TTCCCTGAAAGAACGAACCACCAGGCCA Core staple 2570[58] CAGCAGAATCCTGAGAATGGTTGCATGCGCCGCTACAGTTGA Core staple 2580[72] GCTCTGATTGCCGTTCCGGCAAACGTAGAACTGAT Core staple 2590[100] TGCGTAAAAGAGTCTGTCCGCCAGCGTCTGAAATGGATAATA Core staple 2600[114] CTCTCGCTGGGTCGCTATTAATTATCCTGATAATATACATCA Core staple 2610[121] GCAGCAAATTAACCGTTGTAATATATTGGCAGATTCACCTTC Core staple 2622[37] AATGCTCGTCATTGCCAACGGCAGCAGTAGG Core staple 2632[48] GCTTAATACCGGGGTGTCACTTATTGGGGTTGCAG Core staple 2642[79] ATAGCGATAGCTTACAAGCGTGCCGCAT Core staple 2652[90] TCCTTGAGTGAGCCTTACATCGCCTCAAATATCAAGTATTAG Core staple 2662[100] TCCGTTTTTTCGTCTCGATAACGGTACAAAAGGCA Core staple 2672[121] ATCCAGCCTCCGTAACAATTTCATATAACCTTGCTTCTTTCT Core staple 2684[69] ACCGAGCAAGCCTGTTGCGTTGCGCTCAGTGG Core staple 2695[46] CGGCTTTCCAGTCGGGAGTTTGCGGCGCGCCATGC Core staple 2705[98] ACAACTCGATGATGGCAATCTCACAGTTTGACAAACAATTCG Core staple 2715[109] TAATTGAGGATTTAGAAACCCTCAAGTAACAACCAAGTAACG Core staple 2725[130] ATTAGCCGTCAATAGATAGTTGGCTTTAACGGAGGCGACAGA Core staple 2737[130] GTGCCATCCCACGCAACAAGGGTAAAGTTAAACG Core staple 2746[167] CACAGGCGGCCTTTAGTGATGCAGCTTACGGCTGGAGGTGTC Core staple 2756[188] AAAATCCCGTAAAAAAAGCCGCAGCATCAGCGGGGTCATTGC Core staple 2766[205] GTGTACATCGACATAAAAGGCGCTTTCGCACTCA Core staple 2779[53] GAGCACCAACCTAAAGAAGAGTAATCGA Core staple 2789[84] TCGCAAAAAATCGGTTGTATTAATTGCTCCATTAGTACG Core staple 2798[44] TTTTTTTGATAAGAGGTTTTTAATTCTT Core staple 2801[102] TACCAGAGCATAAAGCTTGGTCAAGTTTCCAACAGCATTCTGCTC Core staple 2811[144] ATTACAGGCAAGGCAAAGCTGAAAGAAACGTACAGCTTGCCA Core staple 2820[44] GCTAAGCAAAGCGGATTCTCAAATTAGTAAACACT Core staple 2830[65] AAAAAAGATTAAGAGGAATAAATATAGC Core staple 2840[72] AGACAAGTTGGGTAACGGGTAAAAATACATT Core staple 2850[93] CCATTTCCCAAAGGGGGAACGGCCTCAGGAATTAA Core staple 2860[107] AGAGCCGGAGAGGGTAGGTCAATCAAGCAAATAAT Core staple 2870[114] AGGAAACGACCGCTATTCTCCAGCCCAGTTTGAGGGGACGAG Core staple 2880[135] AAATTTCAGAGGCGATCCGCTTCTCGCATCGTAACCGTCTCC Core staple 2893 [60] CAATATCGCGCATTTTTATGCTGTAGCTCAAGAAC Core staple 2903 [123] TTTAAGGGTGCCTTTATCAAAATTAAGCAATATATTTTTAAA Core staple 2912[41] ACAGTTCTAGTCAGTCAAAGCTTGCTCCTAAATAT Core staple 2922[97] TGATAATCAGAAGGAATCGTCAGTCAACCGTTCTAGCTGATA Core staple 2932[135] AATACGTTAACAATAGGGGAACAAACGGCGGAGAT Core staple 2945[32] TTTCCAGACGAGATTCATCAGTTGTAAAACGGGCTTGAGAGC Core staple 2955[60] TTATCAACGTAAGAACCACGA Core staple 2965[74] GTCTACGAGGGCAGATACATAACGCATTATACCTTATGGCCA Core staple 297 '— end Sequence Note SEQ ID

NO:4[51] ATCGGAATACCACATTCGGGAAGAAACT Core staple 2984[90] GCTTTAAAAGGAATCAATACTGCAAGGCGATTATTTGAATTACCAGT Core staple 299 CA

4[114] TCGCAACCCGTCGGATTGCATCTGCAGCTTTCGCA Core staple 3006[65] AAAGACTGGATTCATTGAATCCCCGCAT Core staple 3016[107] CAGATTGTATATATGTACCCCGGTAATTAATCAGTCAAGTAA Core staple 3027[60] TTACGCCGGGAAAGAATACACGATTGCCACTGGATATTCTTC Core staple 3037[129] GCACGGTGCGGATTGTAACGTAAAACTAGCATCTAT Core staple 3049[39] TCAGGACAGAATTCCCAATTCTGCCATG Core staple 3059[53] GACAACAAAGTAATTTCAAAATCTACGTTAAAGAT Core staple 3069[88] GGTTCAATATGATATCCGCCCAAAAACATTATGACCCTATCA Core staple 3079[130] AGCGATTCAATGAGAGATCTACAACGGT Core staple 3088[58] AGGTAGATTTAGTTTGAGAATATAGCGGATGGCTTAGACGAA Core staple 3098[72] TAACGTCACCCTCAGCAGCGAAAGTTAAACGCCAG Core staple 3108[100] GAATAACCTGTTTAGCTAAAGCCTTTTTGCGGGAGAAGAGAA Core staple 3118[114] GACCAACGGCACAGCGGATCAAACGATCGCAACGC Core staple 3128[121] GACCATTTGGGGCGCGAGAATTAGTTCAACGCAAGGATAGGT Core staple 3130[37] CGGACTTTGAAAACGAAAGAGGCACGCGGTT Core staple 3140[48] GCGGTATGATGGTTCTGCTCAGGGGTAAGCTTTAA Core staple 3150[79] GCAGTTGGGCGGTTATCATCATTGACCC Core staple 3160[90] ATTTGCCCGATTTTATGTGCTGCAAGCCCCAAAAAGTAGCCA Core staple 3170[100] ATTCGGAACGAGGGTAGTTTTTCACGTTGTACCGG Core staple 3180[121] GAATACAGAGGCGCCATGTTTACCCACGGAAAAAGAGACCG Core staple 3192[69] GGACGTTAACTAATCATAGTAAGAGCAAATGT Core staple 3203[46] TTAATAACCCTCGTTTAGCCAGAGTTCAGTGTTCA Core staple 3213[98] ATGTGAGCGACGACAGTATGAACTGGCTCCCATCAACATTAA Core staple 3223[109] TAACGTCTGGCCTTCCTCAGGAAGCTGGCGAGTCACGATGAG Core staple 3233[130] GTGAACGCCATCAAAAATATTTAAGCCTCTTGGCCAGTTGAG Core staple 3245[132] TAAAACACTCATCTTAGGCCGCTTTTGCGG Core staple 3254[224] TAGTTGCGCCGACAATAAATTGTGTCGAAA Core staple 3267[53] CACCGACCGTGTGATCAGACGACACAAG Core staple 3277[84] AATAGAAGCACCATTACCAGGAATACCCATTTTGTAAAT Core staple 3286[44] CTTAGTTACCAGAAGGAATAAGAGATAA Core staple 3296[65] GAAGAAACGCAATAATAAGAA Core staple 3309[102] AATCAAAATCACCAGTAAATTCATGTTAATTTGTAAATCGAGGTG Core staple 3319[144] ATCTATCACCGTCACCGTCAACCGGTGAGAATAGAAACGTTA Core staple 3328[44] AAAGAGGGTAATTGAGCCAGCCTTCAGCCATTTTT Core staple 3338[65] AAGTCAGAGAGATAACCTAACGTCTCCA Core staple 3348[72] TTGTGCAGACAGCCCTCCTGACCTCACAATC Core staple 3358[93] AAAGCGTAACCAAACTAACGTATCACCGTACTTGC Core staple 3368[107] TCTAGAGCCGCCACCCTAGACGATCGCAGTCACAG Core staple 3378[114] TTTTCGTCTTCACTGAGGTTTAGTTGATATAAGTATAGTCTG Core staple 3388[135] GTCAATGAATATAGGAAAACCGCCGATAAGTGCCGTCGGAGG Core staple 3391 [60] ATACCCAATAAACCGAGCTGGCATGATTAAGAAGA Core staple 3401[123] ACCCCTTATTCAGCACCCCATTTGGGAATTACCAAAGAAACT Core staple 3410[41] AGAATAAAAAGTCACAATGAACGAACAAATTACGC Core staple 3420[97] ACAAACAAATAATTTTTTGTTCAGAGCCACCACCGGAACCGC Core staple 3430[135] GGATCCAGTAACGGGGTAGACTCCTCAAGAGCCAG Core staple 3443[32] GCCTATCCTGTTATCCGGTATTCTTACCGCGCAATCAAAGCC Core staple 3453 [60] TTTCCTGTTTACATGTTGAAA Core staple 3463 [74] AATTTAAATCCCGACTTGCGGGAGCGAGAACGTATTAATAAA Core staple 347 '— end Sequence Note SEQ ID

NO:2[51] GCACGAGGCGTTTTAGCTATTTTCTCCT Core staple 3482[90] CCTGCTTTGAAGCCAAGAAACTGTAGCATTCCACAAGAACGGAAGCA Core staple 349 AG

2[114] TGCCATGAAAGTATTAAAGAGGGTACCGCCATAAT Core staple 3504[65] GCGATCCCAAAAAAATGAAAATAGGCTA Core staple 3514[107] GTCTGGAAAGTGGCCTTGATATTCCTCCCTCTTTCATACACC Core staple 3525[60] TATGCGACCTAAATAAGAATACTTATGGTTTCAGCTAAAGTT Core staple 3535[129] TCAGCCCATGTTTACCGTGGTTGAGGCAGGTCCAGA Core staple 3547[39] GACGTAATAAATAAAAGAAACGCAACTC Core staple 3557[53] ACAATCAACACTGTCTTATCGTAGGAATCATAAGA Core staple 3567[88] TTATCACCGGAACCACAACTTAGCAAGGCCGGAAACGTATCA Core staple 3577[130] GTAATAGCCCGCCACCCTCAGAGCGACA Core staple 3586[58] TACCACGGAATAAGTTTAAAA Core staple 3596[72] TTAAGGTTGGGTTATATAACTATATCATCTTATAG Core staple 3606[100] TTAATGGTTTACCAGCGGAGCCAGGAAACCATCGATAGAGCG Core staple 3616[114] TTTAATCGCAATCGGTTTATCAGCTCAGGAGTTTC Core staple 3626[121] GAACAAAAGGGCGACATACTTGAGGTAATCAGTAGCGATTCG Core staple 3638[37] GGATTTTCGAGCAAATAAGGCGTTGCTCCAT Core staple 3648[48] GTTACTTTAATCGGATAGATAAAATAAATACAGAG Core staple 3658[79] CAGCTTGATACCGATCCCATTCCAGAAC Core staple 3668[90] AATTTCTACCAAGTCAACGCCGAATCCTCATTAAAAATGCCC Core staple 3678[100] TTTGCTGATGCAAATCCTCAAATAAGTTTTGGCCA Core staple 3688[121] TGTAGACAAAGAAGGAACAACTAACCAAAAGGAGCCTTCCC Core staple 3690[69] CCGTTTTGAACCTCAAGATTAGTTGCTAATTA Core staple 3701 [46] ACGCCCAGCTACAATTTAGTTACAAGTCCTGTCCA Core staple 3711 [98] CTATTATCCCGGAATAGGTCGCACTCATGTCTATTTCGGAAC Core staple 3721[109] AAACCGTATAAACAGTTGCCAGAAACCAGTAGATCTAATATT Core staple 3731[130] CTGCAGTGCCTTGAGTATCTGAATACCGTAATCCAGACGCGA Core staple 3743[130] AACACCGGAATCATAATACCTTTTTAACCTCCGG Core staple 3752[167] AAATCATAGGTCTGAGAGACTTACTAGAAAAAGCCTGTTTAG Core staple 3762[188] GAGTCAATAGTGAATTTATCATATCATATGCGTTATACAAAT Core staple 3772[205] GATTAAGACGCTGAGAATCTTACCAGTATAAAGC Core staple 3784[209] TGACAACAACCAGCAGGGAGTTAATGACCCCCAGCGATCATCGCCTG Core staple 379 A

[25] GTGGTTCCGATCCACGCAGAG Core staple 3803 [25] CTGACTATTAAGAAAACAAGT Core staple 3811 [25] CACCCTGAACCATAAAAATTT Core staple 382[166] CTGAGTAGAAGAACTCAAACACGACCAGTA Core staple 383[163] ATTCTGGCCAACAGAGATAAAACAGAG Core staple 384[163] AGTATTAACACCGCCTGCAACAGTCAGAAGATAGAACCCAGT Core staple 385[163] TCTTTAGGAGCACTAACAACTAATAAGGAATGAAA Core staple 386 [142] TTGTTACCTGAAACAAATACTTCTTTGATTAGTAATA Core staple 387[166] GCACGTAAAACAGAAATAAATGAGGAAGGT Core staple 3880[160] AACAAACATCAAGAAGCAAAA Core staple 3892[163] ACATAAATCAATATATGGAACCTACCATAT Core staple 3904[142] CAGAGGGTTATGAGTGATTGAATTACCTTTTTTA Core staple 3914[160] GCGGAACAAAGAAAGAGTAAC Core staple 3928[166] ATTAACATCCAATAAATCATTTTAGAACCC Core staple 3930[163] AAATGCAATGCCTGAGTCAGGTCATTG Core staple 3942[163] GGAGCAAACAAGAGAATCGATGAAAGGCTATAATGTGTAAAA Core staple 3954[163] TGTTAAATCAGCTCATTTTTTAACTATTTTGTGGG Core staple 3966[142] AAGGGTGGAGAATCGGCAGGTGGCATCAATTCTACTA Core staple 397 '— end Sequence Note SEQ ID

NO:6[166] CATTCAGGCTGCGCAACTGTTTAAAATTCG Core staple 3988[160] ACCTCACCGGAAACCCGCCAC Core staple 3990[163] TCTCCGTGGTGAAGGGAGAAACCAGGCAAA Core staple 4002[142] GGGGGTGCCGTAGCTCTAGTCCCGGAATTTGTGA Core staple 4012[160] GGTCACGTTGGTGTATTGACC Core staple 4026[166] ATTATTCATTAAAGGTGAATAAGTTTGCCT Core staple 4038[163] CTGTAGCGCGTTTTCATCTCAGAGCCG Core staple 4040[163] ACCACCAGAGCCGCCGCCAGCATTCACCACCCGGCATTCAGA Core staple 4052[163] GGAGTGTACTGGTAATAAGTTTTAAGCGTCAAAGC Core staple 4064[142] CCATTTCTGTCAGCGGAATTGAGGGAGGGAAGGTAAA Core staple 4074[166] CCCTCATTTTCAGGGATAGCTACATGGCTT Core staple 4086[160] ACTTTCAACAGTTTATGGGAT Core staple 4098[163] TTGAAAATCTCCAAAAAGAACCGCCACCCT Core staple 4100[142] GCGACCCTCAAAAGGCTAGGAATTGCGAATAATA Core staple 4110[160] GGTTTTGCTCAGTAAAGGATT Core staple 412[160] CAAAATTATGA Connector staple 4137[160] GCGCCATTCCA Connector staple 4145[160] CAGAGCCACTA Connector staple 4151[154] GAAGATGATTT Connector staple 4169[154] GGGAACGGACA Connector staple 4177[154] TTTGCTAAAGC Connector staple 418[157] TATCTAAAAAC Connector staple 4195[157] CATTAAATTGA Connector staple 4203 [157] TTGATGATATT Connector staple 421[160] ACATCACTTTT Connector staple 4229[160] ATAGTAGTAGG Connector staple 4237[160] TATTGACGGTA Connector staple 424[157] ATAAAAGGGTA Connector staple 425[157] GTGAGGCGGTC Connector staple 4263[157] ATGGAAACAGT Connector staple 4275[154] ATTATCATTGC Connector staple 4281[157] TCATATATTCA Connector staple 4293 [157] CCTGAGAGTCC Connector staple 4301[157] GAGATAGACCG Connector staple 4313[154] GTAATGGGAAA Connector staple 4329[157] TTAGCGTCATT Connector staple 4331[157] CCACCAGAACT Connector staple 4349[157] ATTTTTTCATT Connector staple 4351[154] AGGATTAGCGC Connector staple 436[12] TTTTTAAACAGGAGGCCGATTAATCAGATCACGGTCACGCTGAACG Vertex staple 437[34] TCGTTAGAAAGGGATTACACTTTTCTTTCGCCATATTTAACAACGCCA Vertex staple 438 ATTTTT

[9] TTTTTAAAAACCGTCTAGCGGGAGCTTTTTT Vertex staple 439[30] TGGGCATCAGTGTGCACGTTTTCATTCCTGTGTGAAATTGTTATTTTT Vertex staple 440[12] TTTTTCAGAATGCGGCGGGCCTCTGTGGCGC Vertex staple 4413[14] TTTTTGTAATGGGTAAAGGGGTGTGTTCAGCTTTTT Vertex staple 4425[16] TTTTTTCCGCTCACAATCGTGCCAGCTGCATTAATGTTTTT Vertex staple 4439[12] TTTTTAGTTTCATTCCATATAAAGTACGGAGAGTACCTTTAAGAA Vertex staple 4448[34] GCAACTAACAGTTGTGAACGGCTGACCAGTCACTGTTGCCCTGCGGC Vertex staple 445 TGTTTTT

1[9] TTTTTAGGTCAGGATTAGTGTCTGGATTTTT Vertex staple 4460[31] CCAGGCTGACCAATAAGGTAAATTGAACTAACGGAACAACATTATTT Vertex staple 447 5'— end Sequence Note SEQ ID

NO:

IT

27[12] TTTTTACACCAGAACGAGTAGCTTGCCCGCA Vertex staple 448

31[14] TTTTTATAAGGGAACCGAATGTACAGACCAGTTTTT Vertex staple 449

33[16] TTTTTTTACAGGTAGAAACGATAAAAACCAAAATAGTTTTT Vertex staple 450

37[12] TTTTTTACATACATAAAGGTGTAGCAAAAGTAAGCAGATAGCATAG Vertex staple 451

36[34] AGTATGTGCAACATGAGAATAAGAGGCAACGAGGCGCAGACGGTCA Vertex staple 452 ATCTTTTT

39[9] TTTTTCTTTTTAAGAAACGTAGAAAATTTTT Vertex staple 453

38[30] CAAAATTCTGAACAAGATAGAAACCCCAATAGCAAGCAAATCATTTT Vertex staple 454 T

45[12] TTTTTCTAATTTACGAGCATGAAAATAAGAG Vertex staple 455

49[14] TTTTTCATGTAATTTAGGCTAAAGTACCGACTTTTT Vertex staple 456

51[16] TTTTTGATATAGAAGGCAATCTTACCAACGCTAACGTTTTT Vertex staple 457

5[9] TTTTTAAAATCCTGTTTCGTCAAAGGGCGTTTTT Vertex staple 458

7[24] GGGGTGGTTTGCCCCAGCAGGCGTTTTT Vertex staple 459

23 [9] TTTTTAAATCAGGTCTTGCAAACTCCAACTTTTT Vertex staple 460

25[24] AAAGGAGAATGACCATAAATCAATTTTT Vertex staple 461

41[9] TTTTTGGGAGAATTAACCTTACCGAAGCCTTTTT Vertex staple 462

43 [24] CCTAACAGGGAAGCGCATTAGACTTTTT Vertex staple 463

7[9] TTTTTAATCGGCCAACGTGCTGCGGCTTCACTAATCTGATGAAAAGG Vertex bundle strand 464 TAAAGTTAGCTATTGAA

25[9] TTTTTCGAGAGGCTTTTTGACGAGAAGCAAAATTCTCATTGAAATCGT Vertex bundle strand 465 TAACGACTCCAAGATG

TTTTTAGCGTCTTTCCATATCCCATC TTCACTAATCTTATGTACT 466

43[9] GCGCATAGGCTGACCGGAATACC Vertex bundle strand 467

CATCAGATTAGTGAA Vertex bundle strand 468

(complementary)

CAATGAGAATTTTGC Vertex bundle strand 469

(complementary)

AGTACATAAGATTAGTGAA Vertex bundle strand 470

(complement-ary)

Table 6. Sequences of the cube with long connector staples.

[81] CGGACGTCAGATGAACTTGTTCTTCCCGGGTACCGAGCAAGC Core staple 489[91] AAATGAATAGAGCCGTCAAAGCTAACTCGAGA Core staple 490[109] ATCCTGCAACAGTGCCATTTTGAAACCCTTCAACA Core staple 491[51] CCGAAGCATAAAGTGTATCGAATTCCAG Core staple 492[114] ACTGTATTAGACTTTACTTTGCGGGATGATGACAT Core staple 493 [65] CAGTTCTTTTTCACCGCCTGGCCCATCA Core staple 494 [60] CACTGCGTTACGTCAGCGTGGTGCCGTG Core staple 495[130] TTCATTTGCACAAATATGGCGGTCAGTATTATAAT Core staple 4961[88] CTTAAAGCGTGGCACAGACAATATCGCTGAGAGCCAAA Core staple 4971[130] TTGAAGGGACCGAACTGATAGCCCGAGGTGACAAA Core staple 4980[37] CCCATCAGAGCGGGAGCCTACAGGTAGGGCGCTGGCAAAACA Core staple 4990[58] TGTGAGGCCGATTAAAGCCCGCCGGGTCACGCTGCGCGTTGA Core staple 5000[65] CCGCGGTGCCTTGTTCCGAATAGCCCGAGATTTGCCCTCACC Core staple 5010[100] CCTATCCTGAGAAGTGTAACTATCAAAACGCTCATGGACCAA Core staple 5020[114] CTCGTTCCGGTCAATATATGTGAGATTCCTGAAAGAAAAAGC Core staple 5030[121] TTTATCAGTGAGGCCACTTGCCTGACATTTTGACGCTCGTAA Core staple 5043 [74] CTGGTGATGAAGGGTAAGAGCACAGTAC Core staple 5053[95] AAACCTTGCTTCTGTAAGTGAGCCAGGTTTAGCGCAGC Core staple 5062[37] TAATAATGGGTAAAGGTTTCTTAATACAAAT Core staple 5072[48] TCTTACCACCGGGGTGTCACTTATTGGGGTTGCAG Core staple 5082[79] TCGCTTTTAGTATCATAGCGTGCCGCAT Core staple 5092[100] TAACGATGCTGATTGCCGTCGCTGACAATAAAGAT Core staple 5102[121] AAACAAACGCGGGATGAAACAAACTTAATGGAAACAGTGCAA Core staple 5115[46] CGGCTTTCCAGTCGGGAGTTTGCGGCGCGCCATGCCGGACAT Core staple 5125[67] CTGTTGCGTTGCGCTCAGTGGTTTACGATCCGCGGTGCGACT Core staple 5135[88] GATAATACATTTGAGGACAGAAGGAGCGGCTCACAGTTTGTA Core staple 5145[109] GAAAACAACTAATAGATAAATCTATTGCGTAGGGAGAAGCAG Core staple 5155[130] AATTAAAATATCTTTAGTGAACCTCGTAAAAGCCTGATCGTT Core staple 5167[134] CAGCAGCAACCGCGGCGGCCTTTAGT Core staple 5176[167] TCCCGTAAAAAAAGCCGCACAAAGAATGCCAACGGCAGCACC Core staple 5186[188] GTGTACATCGACATAAAAAAAGTCGGTGGTGCCATCCCACGC Core staple 5196[209] GCCGCCAGCAGTTGGGCGGTTAACCAGCTTACGGCTGGAGGT Core staple 5206[221] TTCTGCTCATTTGTCCAGCATCAG Core staple 5219[53] CAGTTAATCATAAGGGAGCATAGGAGAC Core staple 5229[84] TTTAGTTAATAAAGCCTCATCATTTTTGTGCGAACAAGA Core staple 5239[116] GGTTCGGAACTCACCCTTCTCACGGAAAAAGCGACGACATCG Core staple 5248[44] AATTTAGAGAGTACCTTGCCCGAACTGG Core staple 5258[65] TGGTCCTTTTGATAAGACATC Core staple 5261[102] ACCTAGCAAAATTAAGCTGACCATCTAC Core staple 5271[144] CTTTAGCATTAACATCCGCTATATATAACCTCACCGAACGAC Core staple 5280[44] TTCCTTTACCCTGACTAGTCATAAAAGAAGTAATT Core staple 5290[65] TTACAGAAGCAAAGCGGAGCGTCCTAATAGTCAGA Core staple 5300[72] AAATAGGGGGATGTGCTAGGACTAGAGTAGA Core staple 5310[93] GAAGATTAAGCTTCGCTTTAGTTTGAGGGGAAGAC Core staple 5320[107] ATTAACCGTTCTAGCTGGAACGGTGCCCCAAAACC Core staple 5330[114] GGTGGTTTTCAAGGGCGAGTATCGGGGCGCATCGTAACGCTT Core staple 5340[135] GCAGTAAAACTCAGGCTGCACTCCATAGGTCACGTTGGGAGC Core staple 5353 [25] TAAATCAAAACCCCTCAAATA Core staple 5363 [60] AGTAGAGGAATAATTGCCTTAGAGCTTAATTATAA Core staple 5373 [123] ATTAGTAATGCCTGTAACATACAGGCAAGGCAAAT Core staple 5382[41] TTGAATCATCAGGTAAATATCGTCAGGAATAATGC Core staple 5392[97] CATGTCAATCATAGACTGGATATGTCAAATCACCATCAATAT Core staple 540 [32] GCGCAACACTGGAACAACATTATTGTTGGGAAACACCAGCCG Core staple 541[60] CCAAGAACCGACCTTCAAGGAAGTTTGATTCCCAATTCCGGA Core staple 542[51] ACGGAAAGATTCATCAGGCTCATTTTGGGCTAGG Core staple 543[72] TACTTAGGAATACCACACTTATGCTTCAACTAACT Core staple 544[90] TCGCGCAACTAATGAAAATGTCAGCTGGCGAAAATGTTT Core staple 545[114] AATTCAACATTAAATGTTGTAGATGCCTCAGGGAT Core staple 546[65] ACAGAGGGGGAATACTGCGGAATCTTAT Core staple 547[86] CGCTTATGTACCCCGGTAAATAAT Core staple 548[107] GTGCAGAAAAAATCGTAAAACTAGGATATTCCAAAAGGTTGT Core staple 549[74] AATGATTTTAAGAACTGTTGAGATATAACGCCAAAAGGTTTG Core staple 550[129] GATCGCGCAACAAGATTGACAAGAGAATCGATATAA Core staple 551[39] GGCACCGAACAAGTTTCATTCCATGCTG Core staple 552[53] CTGGATATTCTAGTAAAATACCAGTCAGGACACAG Core staple 553[88] GGCAGGCCGGAGACATGGGGAGCATAAAGCTAAATCGGGTGA Core staple 554[102] GTAGCAACGGTAGATACATTTCGCAAAGAATAAAAACATTATGACTGT Core staple 555 A

[130] GTTATGCCTGAATGCCGGAGAGGGGGAGCAATATA Core staple 556[72] CTTATACGTAATTGCAGGGAGTTAGGCTTTGGCAA Core staple 557[93] AGAAAGGCCGGAAACAGCGGATCATTAATCAATTA Core staple 558[121] GCACAATAACCTGTTTAAATAAATTACTTTTGCGGGAGAAAT Core staple 559[37] GGCGAACGAGGCGCAGACGGTCCCTTCGCAC Core staple 560[48] TCAATCCGAACGAGATTACCCTTTGCAAATATTCA Core staple 561[59] CGCTATTAAACGGGTAAATTTCATGTCAAGAGAAGA Core staple 562[79] TAAATCGGGGTCATTGCTGAGATGCTTG Core staple 563[100] GCACTTTTGCGGGATCGGAGGGTAACGCCAGAAAG Core staple 564[121] AGCCAGCAGCGAGAAACAATCGGCTCTCCGTGGTGAAGGAA Core staple 565[46] GTAAGGCATAGTAAGAGAGAGGCTAAATCAAACCA Core staple 566[91] CCTTCCTGTAGCCACGTGCATCTGCCGTGAATTACTTTCTGG Core staple 567[109] TCAAGGAACGCCATCAATGATAATCGGGCCTTTGG Core staple 568[130] GAGTCAGCTCATTTTTTAAACAGGTGTTGGGCCAGTCAGACA Core staple 569[134] GCCACTACGAAGGGGTCGCTGAGGCT Core staple 570[167] CCACGCATAACCGATATATTCCACCAACCTAAAACGAAAGAG Core staple 571[188] GACAATGACAACAACCATCGCGCAAAAGAATACACTAAAACA Core staple 572[209] CTTGATACCGATAGTTGCGCCCTCATCTTTGACCCCCAGCGA Core staple 573[221] TTTCTTAAACAGTTATACCAAGCG Core staple 574[53] AAGTTATTTAGGCAGAGAATTCTGCCCA Core staple 575[84] ATTTTGTCAAAATCACCAGAAC Core staple 576[116] TTTATGTAAAGGCTTAGGAGCCTTTAATTGTGTGTATCACCG Core staple 577[44] CATAGATAGCCGAACAAAGTTAAGTCCAGACGAAC Core staple 578[65] CGGAGAAGGAAACCGAGAGAG Core staple 579[75] GCAATACACGGAAGAGAAAATCTGACCTATCATA Core staple 580[102] CCGGGAATTAGAGCCAGCACAATCCAATCGCGAGACTATATCAGC Core staple 581[144] TCACATTAAAGGTGAATCAAAAGGACAGTTTCAGCGTATCGT Core staple 582[44] ATACCTGAACAAAGTCAAAAAATGAGTTACAAAGA Core staple 583[65] ACAATTGAGCGCTAATAAACGATTATTATTTGAGG Core staple 584[72] ATAACCCTGTAGCATTCAGAACGCTAAGTTT Core staple 585[83] ATCAAAGGATAGCACCATTACCATTAGCGCCA Core staple 586[93] TCTAGCCCTCTTTCGTCGTAGCCCGGAATAGATCG Core staple 587[107] ATTGAACCGCCTCCCTCGGTTGAGGCCAGAACAGT Core staple 588[114] CCCGATCTAACCCATGTACCGTACGCCGTCGAGAGGGTTCGG Core staple 589[135] CATTCCAGACGGATAGCACCGCCACTCAGTACCAGGCGCATG Core staple 590 [25] GAGAATTAACTACAGAGCTTT Core staple 591 [60] GTAAGAATTGAGTTACCAATACCCAAAAGAAATAA Core staple 592 1[123] CCGTTCGGTCGAAACCAGTCACCGACTTGAGATGG Core staple 5930[41] CAGCCTTTGAACACATAAGAGAGTAAGCGATTAAG Core staple 5940[97] TGGCCTTGATATCAAATAAGATCAATCACCGGAACCAGAGCC Core staple 5953[32] CCACCCAGCTCAGATATAGAAGGCATCGTAGGAGCATGCCTG Core staple 5963 [60] AAATAATGCAGACGACAAAATATAAAACGCAAAGACACATAA Core staple 5973[130] GTCCAGCATTGACAGGAAGAG Core staple 5982[51] TTAGTATTCTAAGAACGAAGCAAGTAATCGGCAAC Core staple 5992[72] TTTTTTTAGCGAACCTCAGTACCGCATTCCACGAGGTGAACGAAA Core staple 6002[90] AACAGGACTTGCGGATCCCAACAAACTACAACGATTCCT Core staple 6012[114] GCCCTATTATTCTGAAAGATAAGTTCAGGAGCCAAAAGGTTGGGT Core staple 6024[51] GCGCAATCAACCGTTTTTATTTTCTTAT Core staple 6034[107] TAACATTAAAGCAGGTCAGACGATACCACCGAGCGTTTAAGG Core staple 6045[74] TATCACTCATCGAGAACCGAGGCGTGAAGCCTTAAATCAAAT Core staple 6057[39] AGTGCATTTTAAAGGTGGCAACATCTGG Core staple 6067[102] TTAGCAAATCAATAGAAAATTCATCCATTTGGAAACGTCACCAATATAG Core staple 6077[130] CTTCGGCATTCCACCCTCAGAACCCCGCCGCTCTGAATGGTA Core staple 6086[121] TATACCAGCGCCAAAGATATCACCTCGATAGCAGCACCTTTT Core staple 6099[84] GGTCTGAAAGACAACACAGACTTTCATA Core staple 6109[126] TAGAGTGAGAATAGCCAAAAAAAAGGCTGTTTAGTAAGCCCACGCA Core staple 6118[37] ATATTAACAACGCCAACATGTATTGATTTGT Core staple 6128[48] ATCATCGTAGAAACCCTGTTTATTTGCCAAAATAG Core staple 6138[58] GGAAGTTAATTTCATCTCTTTTTCATAAACAACCC Core staple 6148[69] CAAAGTACTGTCTTGTTCAGCCAGCCATTTTTGTTTAACGTCGAGG Core staple 6158[90] TTGCTTTAGAACGGACCAGTATCTCACAAACAAATCCGTATA Core staple 6168[100] GTTCCTTTTTAACCTCCTGCTGATGCGTAACCCTT Core staple 6170[104] TGATATAAGTATATTAAACCACCTTAATGCCCCCTGCCTATT Core staple 6181 [46] CCGGTTGCTATTTTGCAGAGCCTAATCAACAGTAA Core staple 6191[109] AACTTGAGTAACAGTGCAAATCCTCACTGAGATAG Core staple 6201[130] AAAAGTTTTAACGGGGTTGGAAAGATAGGAAAGTTTTGTAAC Core staple 6213 [134] AATTTAATGGTTTGAATTTATCAAAA Core staple 6222[167] ACGCTGAGAAGAGTCAATAGTGAAATACCGACCGTGTGATAA Core staple 6232[188] ATAGCGATAGCTTAGATTAAGATAAGGCGTTAAATAAGAATA Core staple 6242[209] TCCCTTAGAATCCTTGAAAACAACACCGGAATCATAATTACT Core staple 6252[221] ATTAATTAATTTAGAAAAAGCCTG Core staple 626[137] CCCGGTTATCTCGACAACTCGTATAAGTTTGTAATCCTACCT Core staple 627[151] CTGCAGAAGATAAAACATAAAACAACGACCAAATC Core staple 628[146] TGAGGAATCAATCAACCATATAGTTACATACCTGAAAGAGTC Core staple 6292[142] TTTATCAAGAAAACAAATTTCAATAAATCGCCAGTCAC Core staple 6302[163] ACAATTTCATTTGAATTGATTGTTAGAACCTATAT Core staple 6314[160] GTTATTAATTTTAATAAATCCAAGGAAT Core staple 6325[137] AGCTGTTAAATAACAACCCGTCGGTAATGGGAGCCAGCTAGA Core staple 6335[151] TTGTTGCCTGAGAGTCTTAGCTATATATTTTAAGC Core staple 6344[146] AAATTTTAAATATTTCGCCATGACGGCCGGAACGGTTTCATT Core staple 6350[142] CTTGAAACGTACAGCGCCGCCACGAGTGCCACCCTCAT Core staple 6360[163] CCGGAATTTGTGAGAGATTTCCGGGCGCCATTAAA Core staple 6372[160] CGGCGGATTGACCGATTCTCCTCGCATT Core staple 6383[151] GTAAACCACCACCAGAGGCCACCCTAGCGCGGTAA Core staple 6392[135] ATAGTATTAAGAGGCTGGGTTTTGCCCTCAGAAAA Core staple 6402[146] GTGTACTTTACCGTTTTTCAGGTTAGTAACTTTCAGCGACAT Core staple 6418[142] TCTAAAGGAACAACTAACTAAACAAATGAATCAGACTG Core staple 6428[163] ATAATTTTTTCACGTTGAACCGCCACCCTCATCCA Core staple 6430[160] ATTAGGATTAGCGGAGACTCCTACAGGA Core staple 644 0[160] TTATTCAATTAATTACATTTA Connector staple 6458[160] GTGGAGCCATGTTTACCAGTA Connector staple 6466[160] GATTTTGAGGAATTGCGAATC Connector staple 647[166] TAATGGAAGGGTTTGGATTATACTTCTGAA Connector staple 6486[166] GAAACCAGGCAAACACCGCTTCTGGTGCGG Connector staple 6494[166] CCTCAGAGCCACCACCCTCAGAACCGCCAG Connector staple 650[163] GCAGATTCACGCAGAGGCGAA Connector staple 6510[163] ATTTTTAGAAAGCTTTCAGAC Connector staple 6528[163] CCTTTAGCGTTTTCTGTATCG Connector staple 653[163] GAACCACCAGGTCAGTTGGCAATG Connector staple 6542[163] TATCAGGTCATAAACGTTAATATG Connector staple 6550[163] CCGCCACCAGAGCGTCATACATAA Connector staple 656[147] TCGCCATTAAAAATACCGAAC Connector staple 6573[147] TTTTGAGAGATCTACAAAGAG Connector staple 6581[147] TCAGAGCCACCACCCTCAGGC Connector staple 659[147] TGTCCATTTTGATTTGAAATGGATTATTTACATAT Connector staple 6609[147] TGGGGCGATAGTAGTATTTCAACGCAAGGATAAGG Connector staple 6617[147] TCAACCGAATTATTGTAGCGACAGAATCAAGTTTT Connector staple 662[163] CAACAGTTGATTTGCCCGATT Connector staple 6634[163] TTGTTAAAATGTGGGAACAGT Connector staple 6642[163] CTTTTGATGATCAAGAGAAGC Connector staple 665[166] GTAGCAATACTTCCACGCAAATTAACCGAC Connector staple 6668[166] ATCAATTCTACTACGAGCTGAAAAGGTGGG Connector staple 6676[166] AAATATTGACGGAATTGAGGGAGGGAAGAA Connector staple 668[12] TTTTTCAGAATGCGGCGGGCCTCTGTGGCGC Vertex staple 6695[16] TTTTTTCCGCTCACAATCGTGCCAGCTGCATTAATGTTTTT Vertex staple 6708[30] AAAACAAAAGATAGATAAATTTACGAATCATTACCGCGCCCAATTTTT Vertex staple 6716[34] ACTCCTTCATACATCGAGCCAGCCATATAATTGTGTCGAAATCCGCGAC Vertex staple 6729[14] TTTTTCTTAATTGAGAATCGTAATAAGAGAATTTTT Vertex staple 6735[12] TTTTTAATAATATCCCATCCTAGTCCTGCGA Vertex staple 6741[16] TTTTTTAGCAAGCAAATACAATTTTATCCTGAATCTTTTTT Vertex staple 6757[12] TTTTTGCAAACGTAGAAAATAATTACGCCCCTTTTTAAGAAACAAG Vertex staple 6769[9] TTTTTATCTTACCGAAGAGTATGTTATTTTT Vertex staple 6770[31] TTTTTGTACAGCGTAACAGACGAGAAGAAAAATCTACGTTAATATTTTT Vertex staple 6788[34] TGTAGCTTGTCTGGTGACCAATTAGCCGGCGGTTGCGGTATGAGCCGGG Vertex staple 6791[14] TTTTTCTGCTCCATGTTACCTTTGAAAGAGGTTTTT Vertex staple 6807[12] TTTTTGAATAAGGCTTGCCCTAAGCTGCAAA Vertex staple 6813[16] TTTTTAAACGAACTAACATCATAACCCTCGTTTACCTTTTT Vertex staple 6829[12] TTTTTTGCAACTAAAGTACGGCAACATGGCAAACTCCAACAGGCG Vertex staple 683[12] TTTTTTATAACGTGCTTTCCTTGCTTTGTCAAGCGAAAGGAGAACG Vertex staple 6841[9] TTTTTACCAGACCGGAATTTTAAATATTTTT Vertex staple 685[30] TGGGCATCAGTGTGCACGTTTTCATTCCTGTGTGAAATTGTTATTTTT Vertex staple 686[34] CTATGGTCGTTAGATTACACTCGGCTGGAGCCAACGCTCAACAGTAGG Vertex staple 687 GTTTTT

3[14] TTTTTTCACTGTTGCCCTGGGTGTGTTCAGCTTTTT Vertex staple 688 [9] TTTTTAAAAACCGTCTAACGAGCACGTTTTT Vertex staple 689[24] GGGGTGGTTTGCCCCAGCAGGCGTTCACTAATCTGATGGAAGCGCATTA Vertex bundle strand 690 GATAGCAATAGCTTTTTT

5[24] CCAAAATGCTTTAAACAGTTCAGGCAAAATTCTCATTGAAAATCCTGTT Vertex bundle strand 691 TCGTCAAAGGGCGTTTTT

3 [24] GCGTAGAATAACATAAAAACAGGAATGTCGATATCTAGAAAACGAGAA Vertex bundle strand 692 TGGCTTCAAAGCGATTTTT

[9] TTTTTAATCGGCCAACGTGCTGCGGCTTCACTAATCTGATGTATAAAGT Vertex bundle strand 693 ACCGCAATGAAACGG 25[9] TTTTTAGACGACGATAATCATTCAGTGCAAAATTCTCATTGAAATCGTT Vertex bundle strand 694 AACGACTCCAAGATG

43[9] TTTTTTACCAACGCTAAAACAAGAAAAATGTCGATATCTAGACAGATG Vertex bundle strand 695 AACGGAATTCGAACCA

CATCAGATTAGTGAA Vertex bundle strand 696

(complement-ary)

CAATGAGAATTTTGC Vertex bundle strand 697

(complement-ary)

CTAGATATCGACATT Vertex bundle strand 698

(complement-ary)

Table 7. Sequences of the cube with short connector staples.

'— end Sequence Note SEQ ID

NO:2[100] TAACGATGCTGATTGCCGTCGCTGACAATAAAGAT Core staple 7382[121] AAACAAACGCGGGATGAAACAAACTTAATGGAAACAGTGCAA Core staple 7395[46] CGGCTTTCCAGTCGGGAGTTTGCGGCGCGCCATGCCGGACAT Core staple 7405[67] CTGTTGCGTTGCGCTCAGTGGTTTACGATCCGCGGTGCGACT Core staple 7415[88] GATAATACATTTGAGGACAGAAGGAGCGGCTCACAGTTTGTA Core staple 7425[109] GAAAACAACTAATAGATAAATCTATTGCGTAGGGAGAAGCAG Core staple 7435[130] AATTAAAATATCTTTAGTGAACCTCGTAAAAGCCTGATCGTT Core staple 7447[134] CAGCAGCAACCGCGGCGGCCTTTAGT Core staple 7456[167] TCCCGTAAAAAAAGCCGCACAAAGAATGCCAACGGCAGCACC Core staple 7466[188] GTGTACATCGACATAAAAAAAGTCGGTGGTGCCATCCCACGC Core staple 7476[209] GCCGCCAGCAGTTGGGCGGTTAACCAGCTTACGGCTGGAGGT Core staple 7486[221] TTCTGCTCATTTGTCCAGCATCAG Core staple 7499[53] CAGTTAATCATAAGGGAGCATAGGAGAC Core staple 7509[84] TTTAGTTAATAAAGCCTCATCATTTTTGTGCGAACAAGA Core staple 7519[116] GGTTCGGAACTCACCCTTCTCACGGAAAAAGCGACGACATCG Core staple 7528[44] AATTTAGAGAGTACCTTGCCCGAACTGG Core staple 7538[65] TGGTCCTTTTGATAAGACATC Core staple 7541[102] ACCTAGCAAAATTAAGCTGACCATCTAC Core staple 7551[144] CTTTAGCATTAACATCCGCTATATATAACCTCACCGAACGAC Core staple 7560[44] TTCCTTTACCCTGACTAGTCATAAAAGAAGTAATT Core staple 7570[65] TTACAGAAGCAAAGCGGAGCGTCCTAATAGTCAGA Core staple 7580[72] AAATAGGGGGATGTGCTAGGACTAGAGTAGA Core staple 7590[93] GAAGATTAAGCTTCGCTTTAGTTTGAGGGGAAGAC Core staple 7600[107] ATTAACCGTTCTAGCTGGAACGGTGCCCCAAAACC Core staple 7610[114] GGTGGTTTTCAAGGGCGAGTATCGGGGCGCATCGTAACGCTT Core staple 7620[135] GCAGTAAAACTCAGGCTGCACTCCATAGGTCACGTTGGGAGC Core staple 7633 [25] TAAATCAAAACCCCTCAAATA Core staple 7643 [60] AGTAGAGGAATAATTGCCTTAGAGCTTAATTATAA Core staple 7653 [123] ATTAGTAATGCCTGTAACATACAGGCAAGGCAAAT Core staple 7662[41] TTGAATCATCAGGTAAATATCGTCAGGAATAATGC Core staple 7672[97] CATGTCAATCATAGACTGGATATGTCAAATCACCATCAATAT Core staple 7685[32] GCGCAACACTGGAACAACATTATTGTTGGGAAACACCAGCCG Core staple 7695[60] CCAAGAACCGACCTTCAAGGAAGTTTGATTCCCAATTCCGGA Core staple 7704[51] ACGGAAAGATTCATCAGGCTCATTTTGGGCTAGG Core staple 7714[72] TACTTAGGAATACCACACTTATGCTTCAACTAACT Core staple 7724[90] TCGCGCAACTAATGAAAATGTCAGCTGGCGAAAATGTTT Core staple 7734[114] AATTCAACATTAAATGTTGTAGATGCCTCAGGGAT Core staple 7746[65] ACAGAGGGGGAATACTGCGGAATCTTAT Core staple 7756[86] CGCTTATGTACCCCGGTAAATAAT Core staple 7766[107] GTGCAGAAAAAATCGTAAAACTAGGATATTCCAAAAGGTTGT Core staple 7777[74] AATGATTTTAAGAACTGTTGAGATATAACGCCAAAAGGTTTG Core staple 7787[129] GATCGCGCAACAAGATTGACAAGAGAATCGATATAA Core staple 7799[39] GGCACCGAACAAGTTTCATTCCATGCTG Core staple 7809[53] CTGGATATTCTAGTAAAATACCAGTCAGGACACAG Core staple 7819[88] GGCAGGCCGGAGACATGGGGAGCATAAAGCTAAATCGGGTGA Core staple 7829[102] GTAGCAACGGTAGATACATTTCGCAAAGAATAAAAACATTATGACTGTA Core staple 7839[130] GTTATGCCTGAATGCCGGAGAGGGGGAGCAATATA Core staple 7848[72] CTTATACGTAATTGCAGGGAGTTAGGCTTTGGCAA Core staple 7858[93] AGAAAGGCCGGAAACAGCGGATCATTAATCAATTA Core staple 7868[121] GCACAATAACCTGTTTAAATAAATTACTTTTGCGGGAGAAAT Core staple 787 '— end Sequence Note SEQ ID

NO:0[37] GGCGAACGAGGCGCAGACGGTCCCTTCGCAC Core staple 7880[48] TCAATCCGAACGAGATTACCCTTTGCAAATATTCA Core staple 7890[59] CGCTATTAAACGGGTAAATTTCATGTCAAGAGAAGA Core staple 7900[79] TAAATCGGGGTCATTGCTGAGATGCTTG Core staple 7910[100] GCACTTTTGCGGGATCGGAGGGTAACGCCAGAAAG Core staple 7920[121] AGCCAGCAGCGAGAAACAATCGGCTCTCCGTGGTGAAGGAA Core staple 7933[46] GTAAGGCATAGTAAGAGAGAGGCTAAATCAAACCA Core staple 7943[91] CCTTCCTGTAGCCACGTGCATCTGCCGTGAATTACTTTCTGG Core staple 7953[109] TCAAGGAACGCCATCAATGATAATCGGGCCTTTGG Core staple 7963[130] GAGTCAGCTCATTTTTTAAACAGGTGTTGGGCCAGTCAGACA Core staple 7975[134] GCCACTACGAAGGGGTCGCTGAGGCT Core staple 7984[167] CCACGCATAACCGATATATTCCACCAACCTAAAACGAAAGAG Core staple 7994[188] GACAATGACAACAACCATCGCGCAAAAGAATACACTAAAACA Core staple 8004[209] CTTGATACCGATAGTTGCGCCCTCATCTTTGACCCCCAGCGA Core staple 8014[221] TTTCTTAAACAGTTATACCAAGCG Core staple 8027[53] AAGTTATTTAGGCAGAGAATTCTGCCCA Core staple 8037[84] ATTTTGTCAAAATCACCAGAAC Core staple 8047[116] TTTATGTAAAGGCTTAGGAGCCTTTAATTGTGTGTATCACCG Core staple 8056[44] CATAGATAGCCGAACAAAGTTAAGTCCAGACGAAC Core staple 8066[65] CGGAGAAGGAAACCGAGAGAG Core staple 8076[75] GCAATACACGGAAGAGAAAATCTGACCTATCATA Core staple 8089[102] CCGGGAATTAGAGCCAGCACAATCCAATCGCGAGACTATATCAGC Core staple 8099[144] TCACATTAAAGGTGAATCAAAAGGACAGTTTCAGCGTATCGT Core staple 8108[44] ATACCTGAACAAAGTCAAAAAATGAGTTACAAAGA Core staple 8118[65] ACAATTGAGCGCTAATAAACGATTATTATTTGAGG Core staple 8128[72] ATAACCCTGTAGCATTCAGAACGCTAAGTTT Core staple 8138[83] ATCAAAGGATAGCACCATTACCATTAGCGCCA Core staple 8148[93] TCTAGCCCTCTTTCGTCGTAGCCCGGAATAGATCG Core staple 8158[107] ATTGAACCGCCTCCCTCGGTTGAGGCCAGAACAGT Core staple 8168[114] CCCGATCTAACCCATGTACCGTACGCCGTCGAGAGGGTTCGG Core staple 8178[135] CATTCCAGACGGATAGCACCGCCACTCAGTACCAGGCGCATG Core staple 8181 [25] GAGAATTAACTACAGAGCTTT Core staple 8191 [60] GTAAGAATTGAGTTACCAATACCCAAAAGAAATAA Core staple 8201[123] CCGTTCGGTCGAAACCAGTCACCGACTTGAGATGG Core staple 8210[41] CAGCCTTTGAACACATAAGAGAGTAAGCGATTAAG Core staple 8220[97] TGGCCTTGATATCAAATAAGATCAATCACCGGAACCAGAGCC Core staple 8233[32] CCACCCAGCTCAGATATAGAAGGCATCGTAGGAGCATGCCTG Core staple 8243 [60] AAATAATGCAGACGACAAAATATAAAACGCAAAGACACATAA Core staple 8253[130] GTCCAGCATTGACAGGAAGAG Core staple 8262[51] TTAGTATTCTAAGAACGAAGCAAGTAATCGGCAAC Core staple 8272[72] TTTTTTTAGCGAACCTCAGTACCGCATTCCACGAGGTGAACGAAA Core staple 8282[90] AACAGGACTTGCGGATCCCAACAAACTACAACGATTCCT Core staple 8292[114] GCCCTATTATTCTGAAAGATAAGTTCAGGAGCCAAAAGGTTGGGT Core staple 8304[51] GCGCAATCAACCGTTTTTATTTTCTTAT Core staple 8314[107] TAACATTAAAGCAGGTCAGACGATACCACCGAGCGTTTAAGG Core staple 8325[74] TATCACTCATCGAGAACCGAGGCGTGAAGCCTTAAATCAAAT Core staple 8337[39] AGTGCATTTTAAAGGTGGCAACATCTGG Core staple 8347[102] TTAGCAAATCAATAGAAAATTCATCCATTTGGAAACGTCACCAATATAG Core staple 8357[130] CTTCGGCATTCCACCCTCAGAACCCCGCCGCTCTGAATGGTA Core staple 8366[121] TATACCAGCGCCAAAGATATCACCTCGATAGCAGCACCTTTT Core staple 8379[84] GGTCTGAAAGACAACACAGACTTTCATA Core staple 8389[126] TAGAGTGAGAATAGCCAAAAAAAAGGCTGTTTAGTAAGCCCACGCA Core staple 839 '— end Sequence Note SEQ ID

NO:8[37] ATATTAACAACGCCAACATGTATTGATTTGT Core staple 8408[48] ATCATCGTAGAAACCCTGTTTATTTGCCAAAATAG Core staple 8418[58] GGAAGTTAATTTCATCTCTTTTTCATAAACAACCC Core staple 8428[69] CAAAGTACTGTCTTGTTCAGCCAGCCATTTTTGTTTAACGTCGAGG Core staple 8438[90] TTGCTTTAGAACGGACCAGTATCTCACAAACAAATCCGTATA Core staple 8448[100] GTTCCTTTTTAACCTCCTGCTGATGCGTAACCCTT Core staple 8450[104] TGATATAAGTATATTAAACCACCTTAATGCCCCCTGCCTATT Core staple 8461 [46] CCGGTTGCTATTTTGCAGAGCCTAATCAACAGTAA Core staple 8471[109] AACTTGAGTAACAGTGCAAATCCTCACTGAGATAG Core staple 8481[130] AAAAGTTTTAACGGGGTTGGAAAGATAGGAAAGTTTTGTAAC Core staple 8493 [134] AATTTAATGGTTTGAATTTATCAAAA Core staple 8502[167] ACGCTGAGAAGAGTCAATAGTGAAATACCGACCGTGTGATAA Core staple 8512[188] ATAGCGATAGCTTAGATTAAGATAAGGCGTTAAATAAGAATA Core staple 8522[209] TCCCTTAGAATCCTTGAAAACAACACCGGAATCATAATTACT Core staple 8532[221] ATTAATTAATTTAGAAAAAGCCTG Core staple 854[166] GTAGCAATACTTCTTTGATTTGAAATGGAT Core staple 855[163] GCAGATTCACCAGTCACTCGCCATTAA Core staple 856[163] GAACCACCAGCAGAAGATAAAACATAAAACAACGACCAAATC Core staple 857[137] CCCGGTTATCTCGACAACTCGTATAAGTTTGTAATCCTACCT Core staple 858[163] CAACAGTTGAAAGGAATTGAGGAATCAATCAACCATATAGTTACATACC Core staple 859[166] TAATGGAAGGGTTAGAACCTATATCTGGTC Core staple 8600[142] TGAAAGAGTCTGTCCATCACGCA Core staple 8610[160] TTATTCATTTCAATAAATCGC Core staple 8622[142] TTTATCAAGAAAACAAAATT Core staple 8632[163] ACAATTTCATTTGAATTGATTGTTTGGATT Core staple 8644[160] GTTATTAATTTTAATAAATCC Core staple 8658[166] ATCAATTCTACTAATAGTAGTATTTCAACG Core staple 8660[163] ATTTTTAGAACCCTCATTTTTGAGAGA Core staple 8672[163] TATCAGGTCATTGCCTGAGAGTCTTAGCTATATATTTTAAGC Core staple 8685[137] AGCTGTTAAATAACAACCCGTCGGTAATGGGAGCCAGCTAGA Core staple 8694[163] TTGTTAAAATTCGCATTAAATTTTAAATATTTCGCCATGACGGCCGGAA Core staple 8706[166] GAAACCAGGCAAAGCGCCATTAAATTGTAA Core staple 8718[142] CGGTTTCATTTGGGGCGCGAGCT Core staple 8728[160] GTGGAGCCGCCACGAGTGCCA Core staple 8730[142] CTTGAAACGTACAGCGCCAT Core staple 8740[163] CCGGAATTTGTGAGAGATTTCCGGCACCGC Core staple 8752[160] CGGCGGATTGACCGATTCTCC Core staple 8766[166] AAATATTGACGGAAATTATTGTAGCGACAG Core staple 8778[163] CCTTTAGCGTCAGACTGTCAGAGCCAC Core staple 8780[163] CCGCCACCAGAACCACCACCAGAGGCCACCCTAGCGCGGTAA Core staple 8792[135] ATAGTATTAAGAGGCTGGGTTTTGCCCTCAGAAAA Core staple 8802[163] CTTTTGATGATACAGGAGTGTACTTTACCGTTTTTCAGGTTAGTAACTT Core staple 8814[166] CCTCAGAGCCACCACCCTCATCCAGTAAGC Core staple 8826[142] TCAGCGACATTCAACCGATTGAG Core staple 8836[160] GATTTTGCTAAACAAATGAAT Core staple 8848[142] TCTAAAGGAACAACTAAAGG Core staple 8858[163] ATAATTTTTTCACGTTGAACCGCCACCCTC Core staple 8860[160] ATTAGGATTAGCGGAGACTCC Core staple 8873[157] AATTACATTTA Connector 888 staple

1[157] GTTTACCAGTA Connector 889 staple

9[157] AATTGCGAATC Connector 890 staple '— end Sequence Note SEQ ID

NO:

[160] ATACTTCTGAA Connector 891 staple

7[160] TTCTGGTGCGG Connector 892 staple

5[160] AGAACCGCCAG Connector 893 staple

1[154] GCAGAGGCGAA Connector 894 staple

9[154] AGCTTTCAGAC Connector 895 staple

7[154] TTTCTGTATCG Connector 896 staple

[157] AGTTGGCAATG Connector 897 staple

5[157] ACGTTAATATG Connector 898 staple

3 [157] GTCATACATAA Connector 899 staple

[157] AAATACCGAAC Connector 900 staple

3 [157] TCTACAAAGAG Connector 901 staple

1[157] CACCCTCAGGC Connector 902 staple

[157] TATTTACATAT Connector 903 staple

1[157] CAAGGATAAGG Connector 904 staple

9[157] AATCAAGTTTT Connector 905 staple

5[154] TTTGCCCGATT Connector 906 staple

3[154] GTGGGAACAGT Connector 907 staple

1[154] TCAAGAGAAGC Connector 908 staple

[160] AATTAACCGAC Connector 909 staple

9[160] GAAAAGGTGGG Connector 910 staple

7[160] GGAGGGAAGAA Connector 911 staple

[12] TTTTTCAGAATGCGGCGGGCCTCTGTGGCGC Vertex staple 9125[16] TTTTTTCCGCTCACAATCGTGCCAGCTGCATTAATGTTTTT Vertex staple 9138[30] AAAACAAAAGATAGATAAATTTACGAATCATTACCGCGCCCAATTTTT Vertex staple 9146[34] ACTCCTTCATACATCGAGCCAGCCATATAATTGTGTCGAAATCCGCGACTTTTT Vertex staple 9159[14] TTTTTCTTAATTGAGAATCGTAATAAGAGAATTTTT Vertex staple 9165[12] TTTTTAATAATATCCCATCCTAGTCCTGCGA Vertex staple 9171[16] TTTTTTAGCAAGCAAATACAATTTTATCCTGAATCTTTTTT Vertex staple 9187[12] TTTTTGCAAACGTAGAAAATAATTACGCCCCTTTTTAAGAAACAAG Vertex staple 9199[9] TTTTTATCTTACCGAAGAGTATGTTATTTTT Vertex staple 9200[31] TTTTTGTACAGCGTAACAGACGAGAAGAAAAATCTACGTTAATATTTTT Vertex staple 9218[34] TGTAGCTTGTCTGGTGACCAATTAGCCGGCGGTTGCGGTATGAGCCGGGTTTTT Vertex staple 9221[14] TTTTTCTGCTCCATGTTACCTTTGAAAGAGGTTTTT Vertex staple 9237[12] TTTTTGAATAAGGCTTGCCCTAAGCTGCAAA Vertex staple 9243[16] TTTTTAAACGAACTAACATCATAACCCTCGTTTACCTTTTT Vertex staple 9259[12] TTTTTTGCAACTAAAGTACGGCAACATGGCAAACTCCAACAGGCG Vertex staple 926[12] TTTTTTATAACGTGCTTTCCTTGCTTTGTCAAGCGAAAGGAGAACG Vertex staple 9271[9] TTTTTACCAGACCGGAATTTTAAATATTTTT Vertex staple 928[30] TGGGCATCAGTGTGCACGTTTTCATTCCTGTGTGAAATTGTTATTTTT Vertex staple 929[34] CTATGGTCGTTAGATTACACTCGGCTGGAGCCAACGCTCAACAGTAGGGTTTTT Vertex staple 9303[14] TTTTTTCACTGTTGCCCTGGGTGTGTTCAGCTTTTT Vertex staple 931

-ary

Table 8. Sequences of the pentagonal prism.

5'— end Sequence Note SEQ ID

NO:

1 [53] CGCCAACCGCAAGAAAAGTTACCTGTCC Core staple 942

1 [84] AGTGAGGAAAACGCTCATGCGCGTACTAGTGTTTTTGGT Core staple 943

0[44] CGTCCACCACACCCGCCAACAAGAGCAG Core staple 944

3[102] AATCCATTGCAACAGGACCACCGACGGACTTGCGGTCCCTTAGAA Core staple 945

3 [144] CACTATCGGCCTTGCTGGTAGCAAATTAATTACATTGCATTA Core staple 946

2[44] ACTAAAATCCCTTATAATGAGAGACGCCAGGCTGC Core staple 947

2[65] TCCGAATAGCCCGAGATTTGCCCTCACC Core staple 948

2[72] GTGCCAACGGATTCGCCGTCAGCGTATAATC Core staple 949

2[93] GAATTTGAATGTACCTTTCTCATCAATATAAATTT Core staple 950

2[107] CAGAACATCGCCATTAAAAATGAATCTGGTCAATA Core staple 951

2[114] CGTTCGCGCATCAGATGTGTTTGGATTCCTGATTATCAGTAT Core staple 952

2[135] TGAATTTCAACGTAGATTAATGGAAAGGAGCGGAATTACGTT Core staple 953

5[25] GTGGTTCCGATCCACGCAGAG Core staple 954

5 [60] AAAAGTTTGGGCGCTTATTTGACGAGCACGTGGTA Core staple 955

5[123] ACCGCGTAAGTATTTACCCAGAACAATATTACCATCACCATC Core staple 956

4[41] CAAGCGGAATCGGCATTAAAGCGCGTAAGCTTTCC Core staple 957

4[97] ACCTTGCTGAACAACAGCTGAAGTTTAATGCGCGAACTGATA Core staple 958

4[135] CGCCAGTTGAAGATTAGAATTTTAAAAGTTTCCAC Core staple 959

7 [32] GCGAACCTGTTCCACACAACATACTAGCTGTCGGTCATTGAG Core staple 960

7[60] TTTACGATCCGCGGTGCTCAG Core staple 961

7[74] AGTACATTAAGGGTGCCTAATGAGGAGGATCCGCGTCCAAAC Core staple 962 '— end Sequence Note SEQ ID

NO:

[109] ATAAAATCTAAAGCATCGCCCTAAACAATATGCTC Core staple 963[51] CCGAAGCATAAAGTGTATCGAATTCCAG Core staple 964[90] ACTTTAGCTAACTCGAGACGGGGGAGAAACAATCTTGTTCTTCCCGG Core staple 965 GT

[114] CATATCCTTTGCCCGAATCATCATATTATACGTAA Core staple 966 [65] CAGTTCTTTTTCACCGCCTGGCCCATCA Core staple 967 [60] CACCGCTCAACACCGTCGGTGATGGGTCTGGCGGTGCCTTGT Core staple 968[130] GAATTTCAGGAAATCAATGAGAGCCAGCAGCAAAT Core staple 9691 [39] CGGACATCCCTTTTAGACAGGAACATAA Core staple 9701 [53] CCAAGCGCAGGTTTCTGCGTAATCATGGTCAGAGC Core staple 9711[88] TGCTGGCTATTAGTCGGGGGAAATACCTACATTTTGACTTTT Core staple 9721[130] TTCCCTGAAAGAACGAACCACCAGGCCA Core staple 9730[58] CAGCAGAATCCTGAGAATGGTTGCATGCGCCGCTACAGTTGA Core staple 9740[72] GCTCTGATTGCCGTTCCGGCAAACGTAGAACTGAT Core staple 9750[100] TGCGTAAAAGAGTCTGTCCGCCAGCGTCTGAAATGGATAATA Core staple 9760[114] CTCTCGCTGGGTCGCTATTAATTATCCTGATAATATACATCA Core staple 9770[121] GCAGCAAATTAACCGTTGTAATATATTGGCAGATTCACCTTC Core staple 9782[37] AATGCTCGTCATTGCCAACGGCAGCAGTAGG Core staple 9792[48] GCTTAATACCGGGGTGTCACTTATTGGGGTTGCAG Core staple 9802[79] ATAGCGATAGCTTACAAGCGTGCCGCAT Core staple 9812[90] TCCTTGAGTGAGCCTTACATCGCCTCAAATATCAAGTATTAG Core staple 9822[100] TCCGTTTTTTCGTCTCGATAACGGTACAAAAGGCA Core staple 9832[121] ATCCAGCCTCCGTAACAATTTCATATAACCTTGCTTCTTTCT Core staple 9844[69] ACCGAGCAAGCCTGTTGCGTTGCGCTCAGTGG Core staple 9855[46] CGGCTTTCCAGTCGGGAGTTTGCGGCGCGCCATGC Core staple 9865[98] ACAACTCGATGATGGCAATCTCACAGTTTGACAAACAATTCG Core staple 9875[109] TAATTGAGGATTTAGAAACCCTCAAGTAACAACCAAGTAACG Core staple 9885[130] ATTAGCCGTCAATAGATAGTTGGCTTTAACGGAGGCGACAGA Core staple 9897[130] GTGCCATCCCACGCAACAAGGGTAAAGTTAAACG Core staple 9906[167] CACAGGCGGCCTTTAGTGATGCAGCTTACGGCTGGAGGTGTC Core staple 9916[188] AAAATCCCGTAAAAAAAGCCGCAGCATCAGCGGGGTCATTGC Core staple 9926[205] GTGTACATCGACATAAAAGGCGCTTTCGCACTCA Core staple 9939[53] GAGCACCAACCTAAAGAAGAGTAATCGA Core staple 9949[84] TCGCAAAAAATCGGTTGTATTAATTGCTCCATTAGTACG Core staple 9958[44] TTTTTTTGATAAGAGGTTTTTAATTCTT Core staple 9961[102] TACCAGAGCATAAAGCTTGGTCAAGTTTCCAACAGCATTCTGCTC Core staple 9971[144] ATTACAGGCAAGGCAAAGCTGAAAGAAACGTACAGCTTGCCA Core staple 9980[44] GCTAAGCAAAGCGGATTCTCAAATTAGTAAACACT Core staple 9990[65] AAAAAAGATTAAGAGGAATAAATATAGC Core staple 10000[72] AGACAAGTTGGGTAACGGGTAAAAATACATT Core staple 10010[93] CCATTTCCCAAAGGGGGAACGGCCTCAGGAATTAA Core staple 10020[107] AGAGCCGGAGAGGGTAGGTCAATCAAGCAAATAAT Core staple 10030[114] AGGAAACGACCGCTATTCTCCAGCCCAGTTTGAGGGGACGAG Core staple 10040[135] AAATTTCAGAGGCGATCCGCTTCTCGCATCGTAACCGTCTCC Core staple 10053 [25] CTGACTATTAAGAAAACAAGT Core staple 10063 [60] CAATATCGCGCATTTTTATGCTGTAGCTCAAGAAC Core staple 10073 [123] TTTAAGGGTGCCTTTATCAAAATTAAGCAATATATTTTTAAA Core staple 10082[41] ACAGTTCTAGTCAGTCAAAGCTTGCTCCTAAATAT Core staple 10092[97] TGATAATCAGAAGGAATCGTCAGTCAACCGTTCTAGCTGATA Core staple 10102[135] AATACGTTAACAATAGGGGAACAAACGGCGGAGAT Core staple 10115[32] TTTCCAGACGAGATTCATCAGTTGTAAAACGGGCTTGAGAGC Core staple 1012 '— end Sequence Note SEQ ID

NO:5[60] TTATCAACGTAAGAACCACGA Core staple 10135[74] GTCTACGAGGGCAGATACATAACGCATTATACCTTATGGCCA Core staple 10144[51] ATCGGAATACCACATTCGGGAAGAAACT Core staple 10154[90] GCTTTAAAAGGAATCAATACTGCAAGGCGATTATTTGAATTACCAGT Core staple 1016 CA

4[114] TCGCAACCCGTCGGATTGCATCTGCAGCTTTCGCA Core staple 10176[65] AAAGACTGGATTCATTGAATCCCCGCAT Core staple 10186[107] CAGATTGTATATATGTACCCCGGTAATTAATCAGTCAAGTAA Core staple 10197[60] TTACGCCGGGAAAGAATACACGATTGCCACTGGATATTCTTC Core staple 10207[129] GCACGGTGCGGATTGTAACGTAAAACTAGCATCTAT Core staple 10219[39] TCAGGACAGAATTCCCAATTCTGCCATG Core staple 10229[53] GACAACAAAGTAATTTCAAAATCTACGTTAAAGAT Core staple 10239[88] GGTTCAATATGATATCCGCCCAAAAACATTATGACCCTATCA Core staple 10249[130] AGCGATTCAATGAGAGATCTACAACGGT Core staple 10258[58] AGGTAGATTTAGTTTGAGAATATAGCGGATGGCTTAGACGAA Core staple 10268[72] TAACGTCACCCTCAGCAGCGAAAGTTAAACGCCAG Core staple 10278[100] GAATAACCTGTTTAGCTAAAGCCTTTTTGCGGGAGAAGAGAA Core staple 10288[114] GACCAACGGCACAGCGGATCAAACGATCGCAACGC Core staple 10298[121] GACCATTTGGGGCGCGAGAATTAGTTCAACGCAAGGATAGGT Core staple 10300[37] CGGACTTTGAAAACGAAAGAGGCACGCGGTT Core staple 10310[48] GCGGTATGATGGTTCTGCTCAGGGGTAAGCTTTAA Core staple 10320[79] GCAGTTGGGCGGTTATCATCATTGACCC Core staple 10330[90] ATTTGCCCGATTTTATGTGCTGCAAGCCCCAAAAAGTAGCCA Core staple 10340[100] ATTCGGAACGAGGGTAGTTTTTCACGTTGTACCGG Core staple 10350[121] GAATACAGAGGCGCCATGTTTACCCACGGAAAAAGAGACCG Core staple 10362[69] GGACGTTAACTAATCATAGTAAGAGCAAATGT Core staple 10373[46] TTAATAACCCTCGTTTAGCCAGAGTTCAGTGTTCA Core staple 10383[98] ATGTGAGCGACGACAGTATGAACTGGCTCCCATCAACATTAA Core staple 10393[109] TAACGTCTGGCCTTCCTCAGGAAGCTGGCGAGTCACGATGAG Core staple 10403[130] GTGAACGCCATCAAAAATATTTAAGCCTCTTGGCCAGTTGAG Core staple 10415[132] TAAAACACTCATCTTAGGCCGCTTTTGCGG Core staple 10424[224] TAGTTGCGCCGACAATAAATTGTGTCGAAA Core staple 10437[53] CACCGACCGTGTGATCAGACGACACAAG Core staple 10447[84] AATAGAAGCACCATTACCAGGAATACCCATTTTGTAAAT Core staple 10456[44] CTTAGTTACCAGAAGGAATAAGAGATAA Core staple 10466[65] GAAGAAACGCAATAATAAGAA Core staple 10479[102] AATCAAAATCACCAGTAAATTCATGTTAATTTGTAAATCGAGGTG Core staple 10489[144] ATCTATCACCGTCACCGTCAACCGGTGAGAATAGAAACGTTA Core staple 10498[44] AAAGAGGGTAATTGAGCCAGCCTTCAGCCATTTTT Core staple 10508[65] AAGTCAGAGAGATAACCTAACGTCTCCA Core staple 10518[72] TTGTGCAGACAGCCCTCCTGACCTCACAATC Core staple 10528[93] AAAGCGTAACCAAACTAACGTATCACCGTACTTGC Core staple 10538[107] TCTAGAGCCGCCACCCTAGACGATCGCAGTCACAG Core staple 10548[114] TTTTCGTCTTCACTGAGGTTTAGTTGATATAAGTATAGTCTG Core staple 10558[135] GTCAATGAATATAGGAAAACCGCCGATAAGTGCCGTCGGAGG Core staple 10561 [25] CACCCTGAACCATAAAAATTT Core staple 10571 [60] ATACCCAATAAACCGAGCTGGCATGATTAAGAAGA Core staple 10581[123] ACCCCTTATTCAGCACCCCATTTGGGAATTACCAAAGAAACT Core staple 10590[41] AGAATAAAAAGTCACAATGAACGAACAAATTACGC Core staple 10600[97] ACAAACAAATAATTTTTTGTTCAGAGCCACCACCGGAACCGC Core staple 10610[135] GGATCCAGTAACGGGGTAGACTCCTCAAGAGCCAG Core staple 1062 '— end Sequence Note SEQ ID

NO:3[32] GCCTATCCTGTTATCCGGTATTCTTACCGCGCAATCAAAGCC Core staple 10633 [60] TTTCCTGTTTACATGTTGAAA Core staple 10643 [74] AATTTAAATCCCGACTTGCGGGAGCGAGAACGTATTAATAAA Core staple 10652[51] GCACGAGGCGTTTTAGCTATTTTCTCCT Core staple 10662[90] CCTGCTTTGAAGCCAAGAAACTGTAGCATTCCACAAGAACGGAAGCA Core staple 1067 AG

2[114] TGCCATGAAAGTATTAAAGAGGGTACCGCCATAAT Core staple 10684[65] GCGATCCCAAAAAAATGAAAATAGGCTA Core staple 10694[107] GTCTGGAAAGTGGCCTTGATATTCCTCCCTCTTTCATACACC Core staple 10705[60] TATGCGACCTAAATAAGAATACTTATGGTTTCAGCTAAAGTT Core staple 10715[129] TCAGCCCATGTTTACCGTGGTTGAGGCAGGTCCAGA Core staple 10727[39] GACGTAATAAATAAAAGAAACGCAACTC Core staple 10737[53] ACAATCAACACTGTCTTATCGTAGGAATCATAAGA Core staple 10747[88] TTATCACCGGAACCACAACTTAGCAAGGCCGGAAACGTATCA Core staple 10757[130] GTAATAGCCCGCCACCCTCAGAGCGACA Core staple 10766[58] TACCACGGAATAAGTTTAAAA Core staple 10776[72] TTAAGGTTGGGTTATATAACTATATCATCTTATAG Core staple 10786[100] TTAATGGTTTACCAGCGGAGCCAGGAAACCATCGATAGAGCG Core staple 10796[114] TTTAATCGCAATCGGTTTATCAGCTCAGGAGTTTC Core staple 10806[121] GAACAAAAGGGCGACATACTTGAGGTAATCAGTAGCGATTCG Core staple 10818[37] GGATTTTCGAGCAAATAAGGCGTTGCTCCAT Core staple 10828[48] GTTACTTTAATCGGATAGATAAAATAAATACAGAG Core staple 10838[79] CAGCTTGATACCGATCCCATTCCAGAAC Core staple 10848[90] AATTTCTACCAAGTCAACGCCGAATCCTCATTAAAAATGCCC Core staple 10858[100] TTTGCTGATGCAAATCCTCAAATAAGTTTTGGCCA Core staple 10868[121] TGTAGACAAAGAAGGAACAACTAACCAAAAGGAGCCTTCCC Core staple 10870[69] CCGTTTTGAACCTCAAGATTAGTTGCTAATTA Core staple 10881 [46] ACGCCCAGCTACAATTTAGTTACAAGTCCTGTCCA Core staple 10891 [98] CTATTATCCCGGAATAGGTCGCACTCATGTCTATTTCGGAAC Core staple 10901[109] AAACCGTATAAACAGTTGCCAGAAACCAGTAGATCTAATATT Core staple 10911[130] CTGCAGTGCCTTGAGTATCTGAATACCGTAATCCAGACGCGA Core staple 10923[130] AACACCGGAATCATAATACCTTTTTAACCTCCGG Core staple 10932[167] AAATCATAGGTCTGAGAGACTTACTAGAAAAAGCCTGTTTAG Core staple 10942[188] GAGTCAATAGTGAATTTATCATATCATATGCGTTATACAAAT Core staple 10952[205] GATTAAGACGCTGAGAATCTTACCAGTATAAAGC Core staple 10964[167] CTGAGGCTTGCAGGGAGTTAATGACCCCCAGCGATTATACCA Core staple 10974[188] CATAACCGATATATTCGGTCGAGCGCGAAACAAAGTACAACG Core staple 10984[209] TGACAACAACCATCGCCCACGGAGATTTGTATCATCGCCTGA Core staple 1099[25] GTGGTTCCGATCCACGCAGAG Core staple 11003 [25] CTGACTATTAAGAAAACAAGT Core staple 11011 [25] CACCCTGAACCATAAAAATTT Core staple 1102[166] CTGAGTAGAAGAACTCAAACACGACCAGTA Core staple 1103[163] ATTCTGGCCAACAGAGATAAAACAGAG Core staple 1104[163] AGTATTAACACCGCCTGCAACAGTCAGAAGATAGAACCCAGT Core staple 1105[163] TCTTTAGGAGCACTAACAACTAATAAGGAATGAAA Core staple 1106 [142] TTGTTACCTGAAACAAATACTTCTTTGATTAGTAATA Core staple 1107[166] GCACGTAAAACAGAAATAAATGAGGAAGGT Core staple 11080[160] AACAAACATCAAGAAGCAAAA Core staple 11092[163] ACATAAATCAATATATGGAACCTACCATAT Core staple 11104[142] CAGAGGGTTATGAGTGATTGAATTACCTTTTTTA Core staple 11114[160] GCGGAACAAAGAAAGAGTAAC Core staple 1112 '— end Sequence Note SEQ ID

NO:8[166] ATTAACATCCAATAAATCATTTTAGAACCC Core staple 11130[163] AAATGCAATGCCTGAGTCAGGTCATTG Core staple 11142[163] GGAGCAAACAAGAGAATCGATGAAAGGCTATAATGTGTAAAA Core staple 11154[163] TGTTAAATCAGCTCATTTTTTAACTATTTTGTGGG Core staple 11166[142] AAGGGTGGAGAATCGGCAGGTGGCATCAATTCTACTA Core staple 11176[166] CATTCAGGCTGCGCAACTGTTTAAAATTCG Core staple 11188[160] ACCTCACCGGAAACCCGCCAC Core staple 11190[163] TCTCCGTGGTGAAGGGAGAAACCAGGCAAA Core staple 11202[142] GGGGGTGCCGTAGCTCTAGTCCCGGAATTTGTGA Core staple 11212[160] GGTCACGTTGGTGTATTGACC Core staple 11226[166] ATTATTCATTAAAGGTGAATAAGTTTGCCT Core staple 11238[163] CTGTAGCGCGTTTTCATCTCAGAGCCG Core staple 11240[163] ACCACCAGAGCCGCCGCCAGCATTCACCACCCGGCATTCAGA Core staple 11252[163] GGAGTGTACTGGTAATAAGTTTTAAGCGTCAAAGC Core staple 11264[142] CCATTTCTGTCAGCGGAATTGAGGGAGGGAAGGTAAA Core staple 11274[166] CCCTCATTTTCAGGGATAGCTACATGGCTT Core staple 11286[160] ACTTTCAACAGTTTATGGGAT Core staple 11298[163] TTGAAAATCTCCAAAAAGAACCGCCACCCT Core staple 11300[142] GCGACCCTCAAAAGGCTAGGAATTGCGAATAATA Core staple 11310[160] GGTTTTGCTCAGTAAAGGATT Core staple 1132[160] CAAAATTATGA Connector staple 11337[160] GCGCCATTCCA Connector staple 11345[160] CAGAGCCACTA Connector staple 11351[154] GAAGATGATTT Connector staple 11369[154] GGGAACGGACA Connector staple 11377[154] TTTGCTAAAGC Connector staple 1138[157] TATCTAAAAAC Connector staple 11395[157] CATTAAATTGA Connector staple 11403 [157] TTGATGATATT Connector staple 1141[160] ACATCACTTTT Connector staple 11429[160] ATAGTAGTAGG Connector staple 11437[160] TATTGACGGTA Connector staple 11443[157] ATGGAAACAGT Connector staple 11451[157] GAGATAGACCG Connector staple 11469[157] ATTTTTTCATT Connector staple 1147[157] ATAAAAGGGTA Connector staple 1148[157] GTGAGGCGGTC Connector staple 11495[154] ATTATCATTGC Connector staple 11501[157] TCATATATTCA Connector staple 11513 [157] CCTGAGAGTCC Connector staple 11523[154] GTAATGGGAAA Connector staple 11539[157] TTAGCGTCATT Connector staple 11541[157] CCACCAGAACT Connector staple 11551[154] AGGATTAGCGC Connector staple 1156[12] TTTTTAAACAGGAGGCCGATTAATCAGATCACGGTCACGCTGAACG Vertex staple 1157[34] TCGTTAGAAAGGGATTACACTTTTCTTTCGCCATATTTAACAACGCCA Vertex staple 1158 ATTTTT

[9] TTTTTAAAAACCGTCTAGCGGGAGCTTTTTT Vertex staple 1159[30] TGGGCATCAGTGTGCACGTTTTCATTCCTGTGTGAAATTGTTATTTTT Vertex staple 1160[12] TTTTTCAGAATGCGGCGGGCCTCTGTGGCGC Vertex staple 11613[14] TTTTTGTAATGGGTAAAGGGGTGTGTTCAGCTTTTT Vertex staple 1162 5'— end Sequence Note SEQ ID

NO:

15[16] TTTTTTCCGCTCACAATCGTGCCAGCTGCATTAATGTTTTT Vertex staple 1163

19[12] TTTTTAGTTTCATTCCATATAAAGTACGGAGAGTACCTTTAAGAA Vertex staple 1164

18[34] GCAACTAACAGTTGTGAACGGCTGACCAGTCACTGTTGCCCTGCGGC Vertex staple 1165 TGTTTTT

21[9] TTTTTAGGTCAGGATTAGTGTCTGGATTTTT Vertex staple 1166

20[31] CCAGGCTGACCAATAAGGTAAATTGAACTAACGGAACAACATTATTT Vertex staple 1167 TT

27[12] TTTTTACACCAGAACGAGTAGCTTGCCCGCA Vertex staple 1168

31[14] TTTTTATAAGGGAACCGAATGTACAGACCAGTTTTT Vertex staple 1169

33[16] TTTTTTTACAGGTAGAAACGATAAAAACCAAAATAGTTTTT Vertex staple 1170

37[12] TTTTTTACATACATAAAGGTGTAGCAAAAGTAAGCAGATAGCATAG Vertex staple 1171

36[34] AGTATGTGCAACATGAGAATAAGAGGCAACGAGGCGCAGACGGTCA Vertex staple 1172 ATCTTTTT

39[9] TTTTTCTTTTTAAGAAACGTAGAAAATTTTT Vertex staple 1173

38[30] CAAAATTCTGAACAAGATAGAAACCCCAATAGCAAGCAAATCATTTT Vertex staple 1174 T

45[12] TTTTTCTAATTTACGAGCATGAAAATAAGAG Vertex staple 1175

49[14] TTTTTCATGTAATTTAGGCTAAAGTACCGACTTTTT Vertex staple 1176

51[16] TTTTTGATATAGAAGGCAATCTTACCAACGCTAACGTTTTT Vertex staple 1177

5[9] TTTTTAAAATCCTGTTTCGTCAAAGGGCGTTTTT Vertex staple 1178

7[24] GGGGTGGTTTGCCCCAGCAGGCGTTTTT Vertex staple 1179

23 [9] TTTTTAAATCAGGTCTTGCAAACTCCAACTTTTT Vertex staple 1180

25[24] AAAGGAGAATGACCATAAATCAATTTTT Vertex staple 1181

41[9] TTTTTGGGAGAATTAACCTTACCGAAGCCTTTTT Vertex staple 1182

43 [24] CCTAACAGGGAAGCGCATTAGACTTTTT Vertex staple 1183

7[9] TTTTTAATCGGCCAACGTGCTGCGGCTTCACTAATCTGATGAAAAGGT Vertex bundle strand 1184 AAAGTTAGCTATTGAA

25[9] TTTTTCGAGAGGCTTTTTGACGAGAAGCAAAATTCTCATTGAAATCGT Vertex bundle strand 1185 TAACGACTCCAAGATG

43[9] TTTTTAGCGTCTTTCCATATCCCATCAGTGGCGATATCGCGCATAGGC Vertex bundle strand 1186 TGACCGGAATACC

CATCAGATTAGTGAA Vertex bundle strand 1187

(complementary)

CAATGAGAATTTTGC Vertex bundle strand 1188

(complementary)

GATATCGCCACT Vertex bundle strand 1189

(complementary)

Table 9. Sequences of the hexagonal prism.

5'— end Sequence Note SEQ ID

NO:

1 [53] CCGAGCGTGGTGCTGAAGTTACCTGTCC Core staple 1190

1 [84] GTACTATTCCATCACGCAAGACGGGGAACCGCTACGTGC Core staple 1191

0[44] AGGAATCGGAACCCTAAAACAAGAGCAG Core staple 1192

3[102] TTTAGTAAAAGAGTCTGGGTTGCTAGCACATGATGCTGAAACATC Core staple 1193

3 [144] AACCCAGAATCCTGAGAATCAGAGCTTTTACATCGGTTAAAT Core staple 1194

2[44] ACTAAAATCCCTTATAATGAGAGACGCCAGGCTGC Core staple 1195

2[65] TCCGAATAGCCCGAGATTTGCCCTCACC Core staple 1196

2[72] GTGCCGAATAATGGAAGACGGAACAGGGCGC Core staple 1197

2[93] AATACCTACCATCCTGATCGACAACTCGTATATGA Core staple 1198

2[107] ACATCACACGACCAGTATCTTTAACCAGCAGTTGC Core staple 1199

2[114] AATTGCACGTTGATGGCTTTGCCCGAAGTATTAGACTTTCAA Core staple 1200

2[135] AACGAAATTGATCATATTTAAAAGGATAATACATTTGAGGAA Core staple 1201

5[25] GTGGTTCCGATCCACGCAGAGGCGAACCTGTTCCACACAACATACTAG Core staple 1202

5[39] GGCATTAAAGAGCACTAGAAGAAAGCGAAAGGTCACGCTTAC Core staple 1203 [60] AAAAGTTTGGAGGGAGCGAACGTGGCGAGAAACAC Core staple 1204[123] AAGACGCTCATCACTTGTTATAATCAGTGAGTAACGTGTCGC Core staple 1205[97] GCCCTAAAACATAACAGCTGAAGATTATTTACATTGGCAGAT Core staple 1206[135] TTTGTGAGGCTGAAAAATATCTAAAATATCTGTCA Core staple 1207[60] TTTACGATCCGCGGTGCGAAC Core staple 1208[74] AGTACATTAAGGGTGCCTAATGAGGAGGATCCGCGTCCCAAA Core staple 1209[109] CCATGCGCGAACTGATATCACCAGTTTTGACCTTC Core staple 1210[51] CCGAAGCATAAAGTGTATCGAATTCCAG Core staple 1211[90] ATCAAAGCTAACTCGAGACGGGATTATACTTCTCTTGTTCTTCCCGGGT Core staple 1212[114] TGATTGAAAGGAATTGAGGATTTAGAACGTTTTAC Core staple 1213 [65] CAGTTCTTTTTCACCGCCTGGCCCATCA Core staple 1214 [60] CACTGATAAAGCAACCGCAAGTAGACTTGTACGGTGCCTTGT Core staple 1215[130] ATTTCCTGATAACAGAGTGAATGGCTATTAGATAA Core staple 12161 [39] CGGACATCCCTGCGCGTAACCACCAGGA Core staple 12171 [53] CCAAGCGCAGGTTTCTGCGTAATCATGGTCAGAGC Core staple 12181[88] AGACGTCTGAAATGGGGTTATTAACCGTTGTAGCAATAGCTC Core staple 12191[130] AAAAGGAAAAGGACATTCTGGCCAATAT Core staple 12200[58] GTCCCGCGCTTAATGCGAGCCGGCCCCCGATTTAGAGCTTGA Core staple 12210[72] CGGTGATGAAGGGTAAAGTTAAACCCTCATAGGTT Core staple 12220[100] CAGTTGACGAGCACGTAGCCACCGGATTAGTAATAACATGGA Core staple 12230[114] TGGAAACGCGAGCAAAAGAAGATGTAAATCCAATTCATCGAA Core staple 12240[121] TCGCTTTCCTCGTTAGAAGTGTTTCCTGAGTAGAAGAATTGC Core staple 12252[48] TTAAATAACCGGGGTGTCACTTATTGGGGTTGCAGCAAGCGGAATC Core staple 12262[79] ATTAATTACATTTAGTGGCGTGCCGCAT Core staple 12272[90] AAGAAAAGTGAGCCTTGTTTGGCCGCCATTAAAAAACCCTCA Core staple 12282[100] AACATTGCCGTTCCGGCCAGCCTCAATTATTACCT Core staple 12292[121] CTGGTCCGTTTTGAGAAACAATAAATTATTCATTTCAAATTA Core staple 12304[38] CTGTCGGTCATAGAATAAGCTCGTCATGTCTGGTCAGCATAAGGCG Core staple 12314[69] ACCGAGCAAGCCTGTTGCGTTGCGCTCAGTGG Core staple 12325[46] CGGCTTTCCAGTCGGGAGTTTGCGGCGCGCCATGC Core staple 12335[98] TGGCAAATACAAACAATTCCTCACAGTTTGTATCTGGTCAGT Core staple 12345[109] CAGACCTCAAATATCAATACCGAACAATATAATATCAACGGC Core staple 12355[130] GGTTCTAAAGCATCACCAAGATAATATCAGAAAAACAGCGTC Core staple 12367[91] AATGCCAACGGCAGGCACAGGCGGCCTT Core staple 12377[105] CACCGTCGGTGCATCCCAAAAATCCCGTAAAGCC Core staple 12387[126] ACGCAACCAGCTTACGGCTGGCGGTTGTGTACATCGACATAA Core staple 12397[147] AGGTGTCCAGCGCGGGGCATTTGCCGCCGTTGGG Core staple 12406[181] CTTAAATTTCTGCTTCATTGCAGGCGCT Core staple 12419[53] GTTCTTTGAGGACTAACGGTGTACTAAG Core staple 12429[84] TCTGCGAATTAGCAAAATTTCCTTTTGAAGTTGATGGGT Core staple 12438[44] TAGCTCCAACAGGTCAGAAAAGATAGAC Core staple 12441[102] AAGAGGCAAGGCAAAGAACGAGTACGAAAGAATATATTCGGAAAA Core staple 12451[144] CTTATTCTACTAATAGTGTCAATAGCCGCCACGGGACCAGGG Core staple 12460[44] AGGAAATCAAAAATCAGCCAATACCGAGAGGACAT Core staple 12470[65] GATCCCTGACTATTATAAATGTTTGTTT Core staple 12480[72] CAATGACGCCAGCTGGCGGAACGATCCCAAT Core staple 12490[93] AGAGGATGTGCGATCGGATTAACCGTGCATCGCTC Core staple 12500[107] TAACATCAATATGATATAAACAAGGTTGATAAATC Core staple 12510[114] GCCAGTTGGGCTGCGCATTGAGGGTCACGTTGGTGTAGGGCC Core staple 12520[135] CTCTCCCAGTAAGCGCCCGGCCTCGATTGACCGTAATGCATC Core staple 12533 [25] AAAACGAGAAAAATATTCGACGATCGAGGCAAATAAAACGAACTATTA Core staple 12543[39] CATAAGCCCGAAGCAAAAGCTTAATTGCTGATGCAACTCATA Core staple 1255 [60] TTATGCATCAGATTAGATCATTTTTGCGGATGGAA Core staple 1256 [123] CCGTTAAATGCCAAAAATTAACATCCAATAAATTAGATCGGG Core staple 1257[97] GTAATCGTAAAATAATAGTAAGTAGAAAGGCCGGAGACAGTC Core staple 1258[135] GCCAAAAACAATTCGCAATTAAATGTGAGCGAACG Core staple 1259[60] TGCAAGAGTAGCGCATAACAG Core staple 1260[74] TGCCCACATTATTCATCAGTTGAGAATCATTCTTGAGACAGA Core staple 1261[51] AACAACATTATTACAGGGCGATTTCAGA Core staple 1262[90] CGCCATTAGGAATACAGAGGGCTCTTCGCTATTACAATTGGGGTGAATT Core staple 1263[114] AGCCTGTAGCCAGCTTTGGATAGGGACGACGTTTC Core staple 1264[65] ATCAAAAGAAAGACTGGATAGCGTGTCT Core staple 1265[107] TTGTACCCCGAGAATCGATGAACGAAATCACTGTGTAGCATA Core staple 1266[60] ACGGCACTCATGAGGAAGTTTACAAACGGCTGGCTGGCAGCG Core staple 1267[129] GTATATTCGCCAAGCCCCTGAGAGTCTGGAGCTCAA Core staple 1268[39] AACGGTCAATAAAGTACGGTGTCTGGCT Core staple 1269[53] CAGATCTTGAGAAACACTAAGAACTGGCTCAACGG Core staple 1270[88] GGGTTCAAAAGGGTGCAGCAAGCAATAAAGCCTCAGAGGTAA Core staple 1271[130] TTTATATATTTTCTAGCTGATAAACATT Core staple 1272[58] AGGTCATTCCATATAACTAAGAGGGAGTACCTTTAATTGAAG Core staple 1273[72] AGCACCATCGCCCACGCATAACCGCAGCATCGAAA Core staple 1274[100] CAGGATTTAGTTTGACCATCATACCTAAATCGGTTGTACAAT Core staple 1275[114] ATCTGCAGGGGTGGTGAAGGGATATGCCAGTACTG Core staple 1276[121] TTGACATTTCGCAAATGAGTAGCACATTATGACCCTGTAACC Core staple 1277[48] GGGCGCGCTGACGACAAGAACAAAATAGTGCGGAATCGTCATTGAC Core staple 1278[79] AACAGCGGATCAAATTCAGTAGTACTTC Core staple 1279[90] AGAGACGTGGTTTATGCGGGCGGCTAGCATGTCAAATAGGAA Core staple 1280[100] TCACGGTCGCTGAGGCTGTCACCCGCGATTATGAG Core staple 1281[121] TCCAGTTAAAGGACGGATAACCTCTGTGAGAGATAGACACA Core staple 1282[38] TACCGCTTGCCGTTGCGGGAGGCGCAGAAGACTTTTTCAATCCGCC Core staple 1283[69] ACCTTATTAGAAAGCAACTAATGCAGATCTTT Core staple 1284[46] AACGCCAAAAGGAATTAAAAAACCCGGATATGATG Core staple 1285[98] CGCGTCTATGGGCGCATCGTTCAACTTTATTCAAAAATAATT Core staple 1286[109] TTCTCATTTTTTAACCATCATATGGGAAGGGCTGCAAGTCAG Core staple 1287[130] AACTTAAATTTTTGTTAATCAGAAATTCAGGTAACGCCGCTT Core staple 1288[131] CCATTAAACGGGTAAATGCGCCGACAATGACA Core staple 1289[147] ATACGTAATGCCACTACGAAGAAACAGCTTGATACCGATAGT Core staple 1290[168] GCACCAACCTAAAACGAAAAAGAATACACTAAAAC Core staple 1291[209] AATTGTATCGGTTTATCTTTCGAGGTGAATTTCTT Core staple 1292[230] AAGGCTCCAAAAGGAGCCTTTACTCATCTTTGACCCCCAGCG Core staple 1293[246] GAAAATCTCCAAAAAAATTATACCAAGCGCGA Core staple 1294[53] AGATATATAACTATATATAACAACGAAT Core staple 1295[84] CAGTATGGAAGGTAAATATATAGCAATAGACTCCTAACC Core staple 1296[44] GAATGAGTTAAGCCCAAGACGGGAGCCA Core staple 1297[65] TCTAGCAAGAAACAATGTAAA Core staple 1298[102] TGACCGATTGAGGGAGGTTAGCAAGGTCTGATGAAAACAAAGGAA Core staple 1299[144] GCCCATATGGTTTACCAAAAAGAAAGCGTAACGATCAGAGTT Core staple 1300[44] TAATCAAAAATGAAAATAGAGCCTTAGTTGCTAGA Core staple 1301[65] AAGTTTACAGAGAGAATAACGCTACTAC Core staple 1302[72] AACAGACCCTCATTTTCCCTTTTTTATTACG Core staple 1303[93] GAAGCAAGCCTCAGAACAATCCTCAAGAGAAAACA Core staple 1304[107] AATATCGGCATTTTCGGCTCAGAAAGCCGCCTCTC Core staple 1305[114] GCAGTACCGTCCACCCTGATTAGCACATGAAAGTATTAGAGT Core staple 1306[135] CCATCACCAGTACTCAGTACCAGGTTCGGAACCTATTATAAC Core staple 1307 1 [25] CGATTTTTTGAAAATAATTTGAAGTAAGAACCAAGTACCGCACTCGCT Core staple 13081[39] ACGCTGAACACAAGAATAAGTAAGCAGATAGACGCAATAAAG Core staple 13091 [60] GCCCGCATTATAATAAGTACCGAAGCCCTTTCAAA Core staple 13101[123] AGCCATCGATCGACTTGAGACAAAAGGGCGATACATAAAGTG Core staple 13110[97] GCCACCACCCTCAATCTTACCAATTAGCGTCAGACTGTAGCG Core staple 13120[135] CCCGAGGTTGAAGCCAGGTCAGTGCCTTGAGTGCC Core staple 13133 [60] TTGAGCCAGTTGTAATTGTTG Core staple 13143 [74] AATCAATAGCTCATCGTAGGAATCCCCATCCAAGTCCTTAAT Core staple 13152[51] AGGACAAGCAAGCCGTTGTAGAAAGCCT Core staple 13162[90] CATACTACCGCGCCTTTATCCCTCAGAGCCACCGCAATAGATTAATTTA Core staple 13172[114] TGACTGGTAATAAGTTTTTCTGAAGGGGTTTAGCG Core staple 13184[65] TCGCACCCAGACGAGCGTCTTTCCAGCA Core staple 13194[107] ACCCCACCAGCCGCCACCCTCAGACGTTTTCCAGTAGCAAGG Core staple 13205[60] GTTAAAGTACTGCAAATCCAATAAGGCTTAGTAGGCAGAGGG Core staple 13215[129] TCAGGAGGTTTTTGACAGTCAGAGCCGCCACCTCAT Core staple 13227[39] ATTCCAGTATAATAACGGAATACCTTAA Core staple 13237[53] ACAAATAAGAAGAACGCCCAATCAATAATCGATCG Core staple 13247[88] ATATCAAGTTTGCCTCAAATGACGGAAATTATTCATTAGACA Core staple 13257[130] TCGATGAAACCCCCTTATTAGCGTGCCT Core staple 13266[58] GGTACTGGCATGATTAAGCTA Core staple 13276[72] TCCTTAATTTTCCCTTAGAATCCTGAGACTAAGGG Core staple 13286[100] ATAACGTAGAAAATACACATTCAAATTATCACCGTCACAGCA Core staple 13296[114] AATGATTAAGTGAGAATAGAAAGGGGATTAGCAGA Core staple 13306[121] AATAGGTGGCAACATATGCGCCAAAGCCATTTGGGAATGTCA Core staple 13318[48] ATTTGTACTAATGCGAATATATCAAGATAATTTGCCAGTTACTTTA Core staple 13328[79] AATTTTTTCACGTTAACTATCAACATTT Core staple 13338[90] TTGCGAAGAACAAGCGCCACCTGAGAGCCGCCACCTAAGCGT Core staple 13348[100] ACTATAGCGATAGCTTATTATCAAAACCCATCCGT Core staple 13358[121] GAGACGCTGAGATAAAGTTTTGTCCTTTCAACAGTTTCTGC Core staple 13360[38] GTCTTGTTCAGTCATCGCACAAATTCTTGTAAATGCTGAAACGGAG Core staple 13370[69] CGAGCATTTTATTTAAGCAAATCAGATATATT Core staple 13381 [46] AGACTTATCCGGTATTCCCTTAAAAAGTACCCCAT Core staple 13391 [98] GATACAGAGAGGCTGAGACAAATAATATATATGGCTTTTGAT Core staple 13401[109] GTAATTTACCGTTCCAGAGAACCAGCCACCCCAATAGGAATC Core staple 13411[130] GGGAATGGAAAGCGCAGGCCAGCAAGTACCGAACACTGAGTC Core staple 13423[91] TCGCAAGACAAAGATAAATCGTCGCTAT Core staple 13433 [105] ACGCGAGAAAATTCAAAGAGTGAATAACCTTCTG Core staple 13443 [126] TATATTTTAGTTAATTTCATCAGTACATAAATCAATATATGT Core staple 13453[147] TTCTGACCTAAAATGGTATTACCTTTTTGGAAAC Core staple 13462[181] ACAATTTCATTTGATTGAAATACCGACC Core staple 1347[166] TTTTAGACAGGAACGGTACGTATCGGCCTT Core staple 1348[163] CCAGAACAATATTACCGTAGAACCCTT Core staple 1349[163] GCGTAAGAATACGTGGCACAGACAACAGAGACCAGCCACTCA Core staple 1350[163] GCCACGCTGAGAGCCAGCAGCAAAGGTCAGTAATT Core staple 1351 [142] ATCCGTAGATACAGTACCGGGAGCTAAACAGGAGGCC Core staple 1352[166] GAAACCACCAGAAGGAGCGGATTAACACCG Core staple 13530[160] ATGAATATACAGTATTTCAGG Core staple 13542[163] AGTTACAAAATCGCGCAAACATTATCATTT Core staple 13554[142] ATATTTGAGTGAGGCGACGGATTCGCCTGATTGC Core staple 13564[160] AATAGATTAGAGCCTTAGGAG Core staple 13578[166] GAGCTGAAAAGGTGGCATCATTGCGGGAGA Core staple 13580[163] CAACGCAAGGATAAAAACGGAGAGGGT Core staple 1359 2[163] AGAGATCTACAAAGGCTATCAGGTTTAATGCTTTTTAGAATA Core staple 13604[163] TGTAAACGTTAATATTTTGTTAAAGGAAGATCCAG Core staple 13616[142] GCACACGACGAGGTGGAACCTGTTTAGCTATATTTTC Core staple 13626[166] ACCGCTTCTGGTGCCGGAAATGTATAAGCA Core staple 13638[160] TGCCAAGCTTTCAGTTGTAAA Core staple 13640[163] GCCATGTTTACCAGTCCTCGCACTCCAGCC Core staple 13652[142] GCGAGGAAGACGGAATTACCGGAAACAATCGGCG Core staple 13662[160] TCTCCGTGGGAACAAGTAACA Core staple 13676[166] GTCACAATCAATAGAAAATTAGCAAAATCA Core staple 13688[163] ATTACCATTAGCAAGGCCTTTTCATAA Core staple 13690[163] GGAACCAGAGCCACCACCGGAACCTTGCCATCGGAAACTAGA Core staple 13702[163] TCACAAACAAATAAATCCTCATTAAGGCAGGATCA Core staple 13714[142] CCGTACAAACCATAGTTACGCAAAGACACCACGGAAT Core staple 13724[166] GTATAGCCCGGAATAGGTGTTCAGACGATT Core staple 13736[160] CCACAGACAGCCCTTACAACG Core staple 13748[163] TCTGTATGGGATTTTGCGTGCCGTCGAGAG Core staple 13750[142] TATCGGATAATAAACAAGTCTTTCCAGACGTTAG Core staple 13760[160] CAGTTAATGCCCCCTAACAGT Core staple 13773[157] TTTGAATACCA Connector staple 13781[157] AAACGTACATT Connector staple 13799[157] TAAATGAATGC Connector staple 1380[160] TGCGGAACAAG Connector staple 13817[160] AGCTTTCCGTT Connector staple 13825[160] GGTTGATATAG Connector staple 13831[154] TTTAACGTCAA Connector staple 13849[154] ACGACGGCCAA Connector staple 13857[154] CCTGTAGCAGC Connector staple 1386[160] GATTAAAGGCT Connector staple 1387[157] GCTGGTAATGT Connector staple 1388[157] CTGACCTGAAA Connector staple 1389[157] CCTGCAACAAT Connector staple 13905[154] CACTAACAAGA Connector staple 13919[160] ATTTGGGGCAA Connector staple 13921[157] AGCCTTTATAT Connector staple 13933 [157] AGCTATTTTCC Connector staple 13945[157] AATATTTAACC Connector staple 13953[154] ACCCGTCGGTT Connector staple 13967[160] AAGTTTATTAT Connector staple 13979[157] CCAGTAGCAAT Connector staple 13981[157] TCAAAATCATG Connector staple 13993 [157] GGCCTTGATTT Connector staple 14001[154] GCCCGTATAGC Connector staple 1401[12] TTTTTGCTGGCAAGTGTAGCGGAGCGGGTCAAGGTGCCGTAAAACG Vertex staple 1402 [9] TTTTTAAAAACCGTCTACGCTAGGGCTTTTT Vertex staple 1403[30] TGGGCATCAGTGTGCACGTTTTCATTCCTGTGTGAAATTGTTATTTTT Vertex staple 1404[12] TTTTTCAGAATGCGGCGGGCCTCTGTGGCGC Vertex staple 14050[30] ACTTTTCTTTACACCGGAATCATAATTACTAGAAAATTTTT Vertex staple 14063[9] TTTTTGGCTGGTAATGGGTAAAGGGGTGTGTTCAGCTTTTT Vertex staple 14075[16] TTTTTTCCGCTCACAATCGTGCCAGCTGCATTAATGTTTTT Vertex staple 14089[12] TTTTTCAACATGTTTTAAATAATATAATGCGAACCAGACCGGAAA Vertex staple 14091[9] TTTTTTCGAGCTTCAAAGCTGTAGCTTTTTT Vertex staple 14100[31] GACTGAGGACATCATTACGAATAAGAGTCAGGACGTTGGGAAGATTTTT Vertex staple 1411 7[12] TTTTTAAGCTGCTCATTCAGTCCAAATCTAC Vertex staple 14128[30] AGGCCGGAACTATGAGCCGGGTCACTGTTGCCCTGCTTTTT Vertex staple 14131 [9] TTTTTCCTGCTCCATGTTACTTAGGAACCGAACTGATTTTT Vertex staple 14143[16] TTTTTAAAATCTACGTTTAGTAAGAGCAACACTATCTTTTT Vertex staple 14157[12] TTTTTGAAGGAAACCGAGGAACCGAACAAGAGAGATAACCCACCCT Vertex staple 14169[9] TTTTTAGCGCTAATATCAAGTTACCATTTTT Vertex staple 14178[30] GAAAGAATCGGACAAAAAACAACATTCCTTATCATTCCAAGAATTTTT Vertex staple 14185[12] TTTTTCCAGACGACGACAATAGGTAAAGGGG Vertex staple 14196[30] CCAGCGTTATCTGATAAATTGTGTCGAAATCCGCGATTTTT Vertex staple 14209[9] TTTTTAGCCTGTTTAGTATCATATACGCTCAACAGTTTTTT Vertex staple 14211[16] TTTTTCGGGTATTAAACGCGAGGCGTTTTAGCGAACTTTTT Vertex staple 1422[24] GGGGTGGTTTGCCCCAGCAGGCGACAGTTAAAATTCTCATTGCAATCCAA Vertex bundle strand 1423 ATAAAGAGGGTAATTGTTTTT

5[24] CAGACATTGAATCCCCCTCAAATAATAGTAGTCTAATCTATGAAAATCCT Vertex bundle strand 1424 GTTTCGTCAAAGGGCGTTTTT

3 [24] AGGTACAGCCATATTATTTATCCCACTAATCTTATGTAGCTTTAAACAGT Vertex bundle strand 1425 TCGCGTTTTAATTTTTT

[9] TTTTTAATCGGCCAACGTGCTGCGGCCACA AGTT AAAGAT TCGTC Vertex bundle strand 1426 ATTGAAGGGCTTAATTGCAAAGTCGAAA

5[9] TTTTTATAACCCTCGTTAACGTAACAGTAA TAGT AGTCTA CATCT Vertex bundle strand 1427 ATGGCAAATCGTTAACGACTCCAAGATG

3[9] TTTTTCTCCCGACTTGCTAATTCTGTTAA TCT TAT Vertex bundle strand 1428 GTACCAACTTTGAAATCAAATATCAG

CAATGAGAATTTTAACTGT Vertex bundle strand 1429

(complementary)

CATAGATTAGACTACTATT Vertex bundle strand 1430

(complementary)

TACATAAGATTAGTG Vertex bundle strand 1431

(complementary)

TCAAT GACGA ATCTTT AACT TGTG Vertex bundle strand 1432

(complementary)

GCCAT AGATG TAGACT ACTA TTAC Vertex bundle strand 1433

(complementary)

TAC ATA AGA TTA Vertex bundle strand 1434

(complementary)

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Claims

CLAIMS What is claimed is:

1. A nucleic acid structure comprising

a first (x), a second (y), and a third (z) nucleic acid arm, each connected at one end to the other arms to form a vertex, and

a first, a second, and a third nucleic strut, wherein the first nucleic acid strut connects the first (x) nucleic arm to the second (y) nucleic arm, the second nucleic acid strut connects the second (y) nucleic arm to the third (z) nucleic arm, and the third nucleic acid strut connects the third (z) arm to the first (x) nucleic acid strut.

2. A nucleic acid structure comprising

three nucleic acid arms radiating from a vertex at fixed angles.

3. A nucleic acid structure comprising

N nucleic acid arms radiating from a vertex, wherein N is the number of nucleic acid arms and is 3 or more, and

M nucleic acid struts, each strut connecting two nucleic acid arms to each other, wherein M is the number of nucleic acid struts and is 3 or more.

4. The nucleic acid structure of claim 3, wherein N is equal to M.

5. The nucleic acid structure of claim 3, wherein N is less than M.

6. The nucleic acid structure of claim 1, wherein the nucleic acid structure comprises 4 nucleic acids and at least 4 nucleic acid struts, or 5 nucleic acid arms and at 5 nucleic acid struts.

7. The nucleic acid structure of claim 1, wherein the nucleic acid arms are equally spaced apart from each other (or the arms are separated from each other by the same angle).

8. The nucleic acid structure of claim 1, wherein the nucleic acid arms are not equally separated from each other (or the arms are separated from each other by different angles).

9. The nucleic acid structure of claim 1, further comprising a vertex nucleic acid.

10. The nucleic acid structure of claim 1, further comprising a connector nucleic acid.

11. The nucleic acid structure of claim 1, wherein the nucleic acid arms, nucleic acid struts, and/or vertex nucleic acid are comprised of parallel double helices.

12. The nucleic acid structure of claim 1, wherein nucleic acid arms are of identical length.

13. The nucleic acid structure of claim 1, wherein the nucleic acid struts are of identical length.

14. The nucleic acid structure of claim 1, wherein the nucleic acid struts are of different lengths.

15. The nucleic acid structure of claim 1, wherein at least one nucleic acid arm comprises a blunt end.

16. The nucleic acid structure of claim 1, wherein at least one nucleic acid arm comprises a connector nucleic acid at its free (non-vertex) end that is up to 16 nucleotides in length.

17. The nucleic acid structure of claim 1, wherein at least one nucleic acid arm comprises a connector nucleic acid at its free (non-vertex) end, thereby comprising a 1 or 2 nucleotide overhang.

18. The nucleic acid structure of claim 1, wherein the nucleic acid structure is up to 5 megadaltons (MD) in size.

19. The nucleic acid structure of claim 1, wherein the nucleic acid arms are 50 nm in length.

20. The nucleic acid structure of claim 1, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 60° - 60° - 60° (tetrahedron).

21. The nucleic acid structure of claim 1, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 60° - 90° - 90° (triangular prism).

22. The nucleic acid structure of claim 1, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 90° - 90° - 90° (cube).

23. The nucleic acid structure of claim 1, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 108° - 90° - 90° (pentagonal prism).

24. The nucleic acid structure of claim 1, wherein the nucleic acid structure comprises three nucleic acid arms separated from each other by 120° - 90° - 90° (hexagonal prism).

25. A composite nucleic acid structure comprising L nucleic acid structures selected from the nucleic acid structures of claim 1, wherein L is an even number of nucleic acid structures, and wherein the L nucleic acid structures are connected to each other at free (non-vertex) ends of the nucleic acid arms.

26. The composite nucleic acid structure of claim 25, wherein the two more nucleic acid structures are two, four, six, eight, ten, twelve or more nucleic acid structures.

27. The composite nucleic acid structure of claim 25, wherein the composite nucleic acid structure is a tetrahedron, a triangular prism, a cube, a pentagonal prism, or a hexagonal prism.

28. The composite nucleic acid structure of claim 25, wherein the composite nucleic acid structure is 20 megadaltons (MD), 30 MD, 40 MD, 50 MD, or 60 MD in size.

29. The composite nucleic acid structure of claim 25, wherein the composite nucleic acid structure has edge widths, comprised of two nucleic acid arms from adjacent nucleic acid structures, of 100 nm.