HRP20200250T1 - Metoda site-specifično enzimsko obilježavanje nukleinskih kiselina in vitro ugradnjom neprirodnih nukleotida - Google Patents
Metoda site-specifično enzimsko obilježavanje nukleinskih kiselina in vitro ugradnjom neprirodnih nukleotida Download PDFInfo
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- 238000010348 incorporation Methods 0.000 title claims 3
- 238000000034 method Methods 0.000 title claims 3
- 239000002773 nucleotide Substances 0.000 title claims 3
- 125000003729 nucleotide group Chemical group 0.000 title claims 3
- 230000002255 enzymatic effect Effects 0.000 title 1
- 238000000338 in vitro Methods 0.000 title 1
- 238000002372 labelling Methods 0.000 title 1
- 150000007523 nucleic acids Chemical class 0.000 title 1
- 102000039446 nucleic acids Human genes 0.000 title 1
- 108020004707 nucleic acids Proteins 0.000 title 1
- 108091034117 Oligonucleotide Proteins 0.000 claims 29
- 230000000295 complement effect Effects 0.000 claims 23
- 125000005647 linker group Chemical group 0.000 claims 18
- 150000001875 compounds Chemical class 0.000 claims 17
- 239000003153 chemical reaction reagent Substances 0.000 claims 15
- 125000000824 D-ribofuranosyl group Chemical group [H]OC([H])([H])[C@@]1([H])OC([H])(*)[C@]([H])(O[H])[C@]1([H])O[H] 0.000 claims 12
- 238000006243 chemical reaction Methods 0.000 claims 10
- 230000009257 reactivity Effects 0.000 claims 9
- 229910052739 hydrogen Inorganic materials 0.000 claims 7
- 239000001257 hydrogen Substances 0.000 claims 7
- 125000003172 aldehyde group Chemical group 0.000 claims 6
- IVRMZWNICZWHMI-UHFFFAOYSA-N azide group Chemical group [N-]=[N+]=[N-] IVRMZWNICZWHMI-UHFFFAOYSA-N 0.000 claims 6
- 125000002534 ethynyl group Chemical group [H]C#C* 0.000 claims 5
- NINIDFKCEFEMDL-UHFFFAOYSA-N Sulfur Chemical compound [S] NINIDFKCEFEMDL-UHFFFAOYSA-N 0.000 claims 4
- 150000002431 hydrogen Chemical group 0.000 claims 4
- 229910052717 sulfur Inorganic materials 0.000 claims 4
- 239000011593 sulfur Substances 0.000 claims 4
- 125000003396 thiol group Chemical group [H]S* 0.000 claims 4
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical group [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 claims 3
- 125000000217 alkyl group Chemical group 0.000 claims 3
- 229910052799 carbon Inorganic materials 0.000 claims 3
- 239000001177 diphosphate Substances 0.000 claims 3
- XPPKVPWEQAFLFU-UHFFFAOYSA-J diphosphate(4-) Chemical compound [O-]P([O-])(=O)OP([O-])([O-])=O XPPKVPWEQAFLFU-UHFFFAOYSA-J 0.000 claims 3
- 235000011180 diphosphates Nutrition 0.000 claims 3
- 125000004435 hydrogen atom Chemical group [H]* 0.000 claims 3
- 150000004712 monophosphates Chemical class 0.000 claims 3
- 125000002264 triphosphate group Chemical group [H]OP(=O)(O[H])OP(=O)(O[H])OP(=O)(O[H])O* 0.000 claims 3
- IJGRMHOSHXDMSA-UHFFFAOYSA-N Atomic nitrogen Chemical group N#N IJGRMHOSHXDMSA-UHFFFAOYSA-N 0.000 claims 2
- BUGBHKTXTAQXES-UHFFFAOYSA-N Selenium Chemical compound [Se] BUGBHKTXTAQXES-UHFFFAOYSA-N 0.000 claims 2
- 125000003342 alkenyl group Chemical group 0.000 claims 2
- 125000000304 alkynyl group Chemical group 0.000 claims 2
- 125000003277 amino group Chemical group 0.000 claims 2
- KWEDUNSJJZVRKR-UHFFFAOYSA-N carbononitridic azide Chemical group [N-]=[N+]=NC#N KWEDUNSJJZVRKR-UHFFFAOYSA-N 0.000 claims 2
- 238000007306 functionalization reaction Methods 0.000 claims 2
- 229910052736 halogen Inorganic materials 0.000 claims 2
- 150000002367 halogens Chemical class 0.000 claims 2
- MJGXOSYVWHETDC-UHFFFAOYSA-N methoxymethanethiol Chemical group COCS MJGXOSYVWHETDC-UHFFFAOYSA-N 0.000 claims 2
- 125000000467 secondary amino group Chemical class [H]N([*:1])[*:2] 0.000 claims 2
- 229910052711 selenium Inorganic materials 0.000 claims 2
- 239000011669 selenium Substances 0.000 claims 2
- 230000002194 synthesizing effect Effects 0.000 claims 2
- 239000001226 triphosphate Substances 0.000 claims 2
- 235000011178 triphosphate Nutrition 0.000 claims 2
- UNXRWKVEANCORM-UHFFFAOYSA-N triphosphoric acid Chemical compound OP(O)(=O)OP(O)(=O)OP(O)(O)=O UNXRWKVEANCORM-UHFFFAOYSA-N 0.000 claims 2
- QVGXLLKOCUKJST-UHFFFAOYSA-N atomic oxygen Chemical compound [O] QVGXLLKOCUKJST-UHFFFAOYSA-N 0.000 claims 1
- 125000002887 hydroxy group Chemical group [H]O* 0.000 claims 1
- -1 methaneseleno Chemical class 0.000 claims 1
- 229910052757 nitrogen Chemical group 0.000 claims 1
- 229910052760 oxygen Inorganic materials 0.000 claims 1
- 239000001301 oxygen Substances 0.000 claims 1
- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 claims 1
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
- C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
- C07H19/24—Heterocyclic radicals containing oxygen or sulfur as ring hetero atom
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- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
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- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
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- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
- C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/102—Mutagenizing nucleic acids
- C12N15/1024—In vivo mutagenesis using high mutation rate "mutator" host strains by inserting genetic material, e.g. encoding an error prone polymerase, disrupting a gene for mismatch repair
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- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
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- C12N9/22—Ribonucleases RNAses, DNAses
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- C12P19/00—Preparation of compounds containing saccharide radicals
- C12P19/26—Preparation of nitrogen-containing carbohydrates
- C12P19/28—N-glycosides
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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Claims (19)
1. Spoj koje sadrži analog nukleobaze bilo koje od sljedećih formula:
[image]
naznačeno time, da je R vodik ili reaktivni veznik koji sadrži reaktivni centar prilagođen za vezanje na transportni reagens koji sadrži isporuku i skupinu reaktivnosti komplementarnih reaktivnom centru, ili je R spojen veznik za kojeg je vezana isporuka;
gdje je svaki X ugljik,
gdje je svaki R2 nezavisno vodik, alkil, alkenil, alkinil, metoksi, metantiol, metanseleno, halogen, cijano, azidna skupina, reaktivni veznik koji sadrži reaktivni centar prilagođen za vezivanje za transportni reagens koji sadrži isporuku i skupinu reaktivnosti komplementarnu reaktivnom centru, ili spojeni veznik za kojeg je vezana isporuka,
gdje je svaki Y nezavisno sumpor, selen ili sekundarni amin,
gdje je svako E sumpor,
i valovita linija označava točku vezanja za ribozilni, deoksiribozilni ili dideoksiribozilni ostatak ili njegov analog, pri čemu je ribozilni, deoksiribozilni ili dideoksiribozilni ostatak ili njegov analog u slobodnom obliku, vezan za monofosfatnu, difosfatnu ili trifosfatnu skupinu, koja opcijski sadrži α-tiotrifosfatnu, β-tiotrifosfatnu ili γ-tiotrifosfatnu skupinu ili je uključen u RNA ili DNA ili u analog RNA ili analog DNA.
2. Spoj koje sadrži analog nukleobaze bilo koje od sljedećih formula:
[image]
gdje je svaki X nezavisno ugljik ili dušik,
gdje je svaki R1 nezavisno vodik, alkil skupina, reaktivni linker koji sadrži reaktivni centar prilagođen za vezanje za transportni reagens koji sadrži isporuku i skupinu reaktivnosti komplementarnu reaktivnom centru, ili spojen veznik za koga je vezana isporuka,
gdje je svaki R2 prisutan, kada je X ugljik i nezavisno je vodik, alkil, alkenil, alkinil, metoksi, metantiol, metanseleno, halogen, cijano, azidna skupina, reaktivni veznik koji sadrži reaktivni centar prilagođen za vezanje za transportni reagens koji sadrži isporuku i skupinu reaktivnostu komplementarnu reaktivnom centru, ili spojen veznik za kojeg je vezana isporuka,
gdje je svaki Y nezavisno sumpor, kisik, selen ili sekundarni amin,
gdje je svako E sumpor,
i valovita linija označava točku vezivanja za ribozilnu, deoksiribozilnu ili dideoksiribozilnu skupinu ili njen analog, pri čemu je ribozilni, deoksiribozilni ili dideoksiribozilni ostatak ili njegov analog u slobodnom obliku, vezan za monofosfatnu, difosfatnu ili trifosfatnu skupinu, koja opcijski sadrži α-tiotrifosfatnu, β-tiotrifosfatnu ili γ-tiotrifosfatnu skupina ili je uključen u RNA ili DNA ili u analog RNA ili analog DNA.
3. Spoj sukladno patentnom zahtjevu 1, naznačeno time, da reaktivni centar sadrži amino skupinu, acetilensku skupinu, tiol skupinu, aldehidnu skupinu ili azidnu skupinu.
4. Spoj sukladno patentnom zahtjevu 2, naznačeno time, da reaktivni centar sadrži amino skupinu, acetilensku skupinu, tiol skupinu, aldehidnu skupinu ili azidnu skupinu.
5. Spoj sukladno patentnom zahtjevu 1, naznačeno time, da ribozilni ili deoksiribozilni ostatak nosi trifosfatnu ili α-tiotrifosfatnu skupinu vezanu za njegov 5'-hidroksil.
6. Spoj sukladno patentnom zahtjevu 2, naznačeno time, da ribozilni ili deoksiribosilni ostatak nosi trifosfatnu ili α-tiotrifosfatnu skupinu vezanu za njegov 5'-hidroksil.
7. Spoj sukladno patentnom zahtjevu 1, naznačeno time, da je ribozilni ili deoksiribosilni ostatak inkorporiran u RNA ili DNA oligonukleotidni lanac, respektivno, ili je ribozilni ili deoksiribozilni ostatak ili njegov analog ugrađen u analog RNA ili DNA.
8. Spoj sukladno patentnom zahtjevu 2, naznačeno time, da je ribozilna ili deoksiribozilna grupa ugrađena u RNA ili DNA oligonukleotidni lanac, respektivno, ili je ribozilni ili deoksiribozilni ostatak ili njegov analog ugrađen u analog RNA ili DNA.
9. Spoj sukladno patentnom zahtjevu 1, naznačeno time, da najmanje jedan R2 nezavisno sadrži: skupinu odabranu iz skupine sastavljene od -C≡C-CH2NHR3 skupine, gdje je R3 vodonik ili je amino-zaštitna skupinu; acetilensku skupinu pogodnu za uporabu u reakciji brave s transportnim reagensom koji sadrži punjenje i acetilen-reaktivnu skupinu; tiol skupinu pogodnu za uporabu u reakciji s transportnim reagensom koji sadrži isporuku i tiol-reaktivnu skupinu; aldehidnu skupinu pogodnu za uporabu u reakciji s transportnim reagensom koji sadrži isporuku i aldehidnu reaktivnu skupinu; azidnu skupinu pogodnu za uporabu u reakciji s transportnim reagensom koji sadrži isporuku i azidnu reaktivnu skupinu; i -C≡C-(CH2)n-C≡CH, gde n je 1, 2, 3, 4, 5 ili 6; i -C≡C-(CH2)n1-O-(CH2)n2-C≡CH, gdje su n1 i n2 svaki nezavisno 1, 2 ili 3.
10. Spoj sukladno patentnom zahtjevu 2, naznačeno time, da najmanje jedan R2 nezavisno sadrži: skupinu odabranu od skupinu koja se sastoji od -C≡C-CH2NHR3 grupe, gdje je R3 vodonik ili je amino-zaštitna skupinu; acetilensku skupinu pogodnu za upotrebu u reakciji brave sa transportnim reagensom koji sadrži isporuku i acetilensku reaktivnu skupinu; tiol skupinu pogodnu za upotrebu u reakciji s transportnim reagensom koji sadrži isporuku i tiol-reaktivnu skupinu; aldehidnu skupinu pogodnu za uporabu u reakciji s transportnim reagensom koji sadrži isporuku i aldehidnu reaktivnu skupinu; azidnu skupinu pogodnu za uporabu u reakciji s transportnim reagensom koji sadrži isporuku i azidnu reaktivnu skupinu; i -C≡C-(CH2)n-C≡CH, gdje n je 1, 2, 3, 4, 5 ili 6; i -C≡C-(CH2)n1-O-(CH2)n2-C≡CH, gdje su n1 i n2 svaki nezavisno 1, 2 ili 3.
11. Nukleobazni par koji sadrži prvi analog nukleobaze koji sadrži formulu
[image]
i drugi analog nukleobaze koji ima bilo koju od formula
[image]
gdje je R nezavisno vodik, ili spojen veznik koji sadrži reaktivni centar prilagođen za vezanje za transportni reagens koji sadrži isporuku i skupinu reaktivnosti komplementarnu reaktivnom centru, ili je R spojen veznik za kojeg je vezana isporuka;
i valovita linija označava točku vezanja za ribozilnu, deoksiribozilnu ili dideoksiribozilnu skupinu ili njen analog, pri čemu je ribozilni, deoksiribozilni ili dideoksiribozilni ostatak ili njegov analog u slobodnom obliku, vezan za monofosfatnu, difosfatnu ili trifosfatnu skupinu, koja opcijski sadrži α-tiotrifosfatnu, β-tiotrifosfatnu ili γ-tiotrifosfatnu skupinu ili je uključen u RNA ili DNA ili u analog RNA ili analog DNA.
12. Dvolančani oligonukleotidni dupleks, naznačen time, da prvi oligonukleotidni lanac sadrži spoj sukladno patentnom zahtjevu 1, a drugi komplementarni oligonukleotidni lanac sadrži komplementarnu nukleobazu za uparivanje baze na njegovom komplementarnom položaju uparivanja baze.
13. Dvolančani oligonukleotidni dupleks, naznačen time, da prvi oligonukleotidni lanac sadrži spoj sukladno patentnom zahtjevu 2, a drugi komplementarni oligonukleotidni lanac sadrži komplementarnu nukleobazu za uparivanje baze na njegovom komplementarnom položaju za uparivanje baze.
14. Dvolančani oligonukleotidni dupleks sukladno patentnom zahtjevu 12, naznačen time, da prvi lanac sadrži nukleobazu koja ima formulu
[image]
a drugi lanac sadrži komplementarnu nukleobazu za uparivanje baze odabranu iz
[image]
na komplementarnom mjestu spajanja baze.
15. Postupak izvođenja funkcionalizacije specifične za položaj dvostruko lančanog oligonukleotidnog dupleksa, koji obuhvaća: ugradnju neprirodne nukleobaze koja sadrži reaktivni veznik koji sadrži reaktivni centar, nukleobaze koja je odabrana iz spoja sukladno patentnom zahtjevu 1, u prvi oligonukleotidni lanac; zatim, sintetiziranje drugog oligonukleotidnog lanca komplementarno prvom oligonukleotidnom lancu, drugi oligonukleotidni lanac koji sadrži nukleobazu komplementarnu neprirodnoj nukleobazi na mjestu specifičnom komplementarnom položaju u njemu, pod uvjetom da prvi oligonukleotidni lanac i drugi oligonukleotidni lanac oblikuju dvolančani oligonukleotidni dupleks; zatim, dovođenje u kontakt dvolančanog oligonukleotidnog dupleksa koji inkorporira neprirodnu nukleobazu koja sadrži reaktivnu skupinu veznika s transportnim reagensom koji sadrži isporuku i skupinu komplementarne reaktivnosti, pod uvjetima podobnim za reakciju reaktivnog veznika i skupine komplementarne reaktivnosti da bi se došlo do spojenog veznika; da bi se osigurao funkcionalni dvolančani oligonukleotidni dupleks s isporukom vezanom za njega putem spojenog veznika
16. Postupak provođenja funkcionalizacije dvostrukog lanca oligonukleotidnog dupleksa specifične za položaj, koji uključuje: ugrađivanje neprirodne nukleobaze koja sadrži reaktivni linker koji sadrži reaktivni centar, nukleobaze koja je odabrana iz spoja sukladno patentnom zahtjevu 2, u prvi oligonukleotidni lanac; zatim, sintetiziranje drugog oligonukleotidnog lanca komplementarno prvom oligonukleotidnom lancu, drugi oligonukleotidni lanac koji sadrži nukleobazu komplementarnu s neprirodnom nukleobazom na mjesto-specifičnom komplementarnom položaju u njemu, pod uvjetima da prvi oligonukleotidni lanac i drugi oligonukleotidni lanac oblikuju dvolančani oligonukleotidni dupleks; zatim, kontaktiranje dvolančanog oligonukleotidnog dupleksa koji uključuje neprirodnu nukleobazu koja sadrži reaktivni dio veznika s transportnim reagensom koji sadrži isporuku i skupinu komplementarne reaktivnosti, pod uvjetom pogodnim za reakciju reaktivnog veznika i skupine komplementarne reaktivnosti kako bi se dobio spojeni veznik; da bi se osigurao funkcionalizirani dvolančani oligonukleotidni dupleks s teretom povezanom za njega spojenim veznikom.
17. Struktura koja sadrži formulu:
N1-Zx-N2,
gdje je N1 nukleotid ili njegov analog, ili terminalna fosfatna skupina; gdje je N2 nukleotid ili njegov analog, ili terminalna hidroksilna skupina; gdje je Z spoj sukladno patentnom zahtjevu 1 ili patentnom zahtjevu 2 i gdje je x cijeli broj od 1 do 20.
18. Spoj sukladno patentnom zahtjevu 1, koje ima formulu odabranu od:
[image]
ili njegovih derivata ili analoga,
[image]
19. Spoj sukladno patentnom zahtjevu 2, odabrano iz skupine sastavljene od:
[image]
i njihovih derivata ili analoga.
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201361863649P | 2013-08-08 | 2013-08-08 | |
EP14834827.9A EP3041854B1 (en) | 2013-08-08 | 2014-08-08 | A method for the site-specific enzymatic labelling of nucleic acids in vitro by incorporation of unnatural nucleotides |
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