CN116024313A - Programmable nucleic acid molecule detection method and platform - Google Patents
Programmable nucleic acid molecule detection method and platform Download PDFInfo
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Abstract
The invention discloses a programmable nucleic acid molecule detection method and a programmable nucleic acid molecule detection platform. According to the programming type nucleic acid molecule detection platform provided by the embodiment of the invention, weak initial signals are greatly improved through the triple signal amplification element RCA-Cas12a-HCR, so that the sensitivity of the detection platform is effectively improved. Compared with the traditional amplification element, the rolling circle amplification element RCA in the triple amplification element can realize the sensitive detection of a plurality of different types of nucleic acid molecules by changing the nucleic acid molecule identification region in the rolling circle probe, and meanwhile, the Cas12a system is adopted as the medium of RCA and HCR, so that the specificity and the robustness of the detection are effectively improved. For DNA detection, the DNA is transcribed into the corresponding RNA by the prior art. The property of the aptamer nucleic acid molecule that it can specifically bind to the target molecule is utilized to allow the aptamer that binds to the target molecule to trigger RCA amplification, which can be further used for sensitive analysis of other substances, such as: proteins, drugs, ions, etc.
Description
Technical Field
The invention relates to the field of nucleic acid detection, in particular to a programmable nucleic acid molecule detection method and a programmable nucleic acid molecule detection platform.
Background
Photoelectrochemical (PEC) biosensing has attracted considerable attention as an emerging technology. Compared with the traditional ELISA, the photoelectrochemistry adopts a unique signal separation mode of 'optical signal excitation and electric signal reception', thereby ensuring the detection sensitivity and low background interference. In addition, photoelectrochemistry is a movable biological detection technology, which is beneficial to developing miniaturized devices to realize point-of-care testing (POCT). However, the conventional single-signal photoelectrochemical sensing platform cannot meet the requirement of people on detection accuracy. Therefore, the development of a detection platform with multi-mode signal transduction has important practical significance.
microRNA (miRNA) is a non-coding short-chain ribonucleic acid widely existing in animals and plants, and has a length of 18-25 ribonucleotides, and plays a key role in the development process and physiological metabolism process of cells. In recent years, a great deal of research shows that miRNA plays an important role in the processes of tumor development, infiltration, diffusion, metastasis and the like. In addition, miRNA has close relation with the differentiation and development process of plants and animals. Therefore, the monitoring of the content of each type of miRNA in plants, animals and human bodies has important practical significance for early lesion screening, disease development progress and disease prognosis diagnosis. Due to the characteristics of low miRNA abundance, high homology similarity and instability, the existing miRNA biological detection method has the problems of complex sample pretreatment, complex operation, expensive equipment and low detection sensitivity, and cannot meet the detection requirements of a large number of complicated and diversified varieties at present. Therefore, there is an urgent need to establish a rapid, accurate, low-cost, programmable detection method for sensitive detection of different types of mirnas.
Rolling Circle Amplification (RCA) is proposed by referring to rolling circle replication of pathogenic organisms, using circular DNA as a template, transforming dNTPs into single-stranded DNA containing hundreds or thousands of repeated template complementary fragments under the catalysis of DNA polymerase by a short DNA primer (complementary to part of circular template), and not only directly amplifying specific DNA and RNA molecules, but also amplifying signals of the target nucleic acids. The rolling circle amplification technology has wide application prospect in the aspects of nucleic acid sequencing, single nucleotide polymorphism genotyping, cell in-situ detection analysis, DNA chip, protein chip analysis and the like.
The CRISPR system is an adaptive immune system found in archaea, bacteria and fungi, for withstanding infection with external nucleic acids. Since the discovery in 1987, CRISPR systems have been widely used in the fields of gene editing, gene therapy, and metabolic regulation. In recent years, CRISPR/Cas12a systems have attracted considerable attention in the field of analytical detection due to their unique trans-cleavage (trans-clean) capabilities. The Cas12a system is not only capable of mediating specific recognition and cis-cleavage (cis-cleavage) of target sequences by crRNA; can also activate the trans-cleavage property and randomly cleave single-stranded DNA. Therefore, researchers combine Cas12a systems with traditional nucleic acid amplification methods, and utilize the unique properties of Cas12a to improve the specificity and sensitivity of biosensors.
The hybridization chain reaction (Hybridization chain reaction, HCR) is a novel signal amplification technique, which initiates hybridization reaction of two stable DNA hairpin probes at constant temperature through single-stranded DNA (ssDNA), thereby amplifying detection signals and realizing the purpose of selectively detecting target molecules.
Although there are various methods for detecting nucleic acid sequences in the prior art, quantitative analysis is achieved by means of specialized instruments, which are often bulky, expensive, and inconvenient to use, and are to be further improved.
Disclosure of Invention
The invention aims to overcome at least one defect of the prior art and provides a programmable nucleic acid molecule detection method and a programmable nucleic acid molecule detection platform.
The technical scheme adopted by the invention is as follows:
in a first aspect of the invention, there is provided:
a programmable nucleic acid molecule detection platform comprises an amplifying element, a biological load element and a signal conversion element,
the amplification element is formed by sequentially coupling a rolling circle amplification system, a CRISPR/Cas12a system and a hybridization chain reaction system, wherein:
the rolling circle amplification system is used for amplifying the nucleic acid molecules to be detected;
the CRISPR/Cas12a system identifies an amplification product of the rolling circle amplification system, activates trans-cleavage performance of the CRISPR/Cas12a system, and cleaves a trigger probe TS of the hybridization chain reaction system to obtain a degradation product;
the hybridization chain reaction system comprises a hairpin probe H1 fixed on the biological load element, a free hairpin probe H2 modified by a first signal conversion element and a free hairpin probe H1 modified by biological enzyme, wherein the hairpin probe H1 and the hairpin probe H2 can be alternatively opened under the starting of an uncleaved trigger probe TS, and are self-assembled to form a repeated linear double-stranded DNA structure, so that a hybridization chain reaction HCR product is obtained;
the biological enzyme loaded by the HCR product is coupled with a first signal element to generate a first cascade reaction, is coupled with a second signal element to generate a second cascade reaction, and the products of the first cascade reaction and the second cascade reaction are utilized to realize photoelectrochemical detection and colorimetric detection.
In some examples of programmable nucleic acid molecule detection platforms, the bioburden element is CdS/Ag 2 S/B-ZnO NRs photoelectric composite material.
In some examples of programmable nucleic acid molecule detection platforms, the CdS/Ag 2 The preparation method of the S/B-ZnO NRs photoelectric composite material comprises the following steps:
firstly, synthesizing a branched zinc oxide nano rod array B-ZnO NRs, and loading cadmium sulfide/silver sulfide CdS/Ag on the branched zinc oxide nano rod array B-ZnO NRs 2 S layer for preparing CdS/Ag 2 S/B-ZnO NRs photoelectric composite material.
In some examples of programmable nucleic acid molecule detection platforms, the biological enzyme is glucose oxidase.
In some examples of programmable nucleic acid molecule detection platforms, the first signal conversion element is nanogold, which can form a first cascade reaction with glucose oxidase and react with a substrate to realize photoelectrochemical detection; and/or the second signal conversion element is an iron-based material, can form a second cascade reaction with glucose oxidase and reacts with a substrate to realize colorimetric detection.
In some examples of programmable nucleic acid molecule detection platforms, the nanogold is beta-cyclodextrin modified nanogold; and/or the iron-based material is NH 2 -an iron-based organic framework material of MILs-88B (Fe).
In a second aspect of the invention, there is provided:
a method for programmable nucleic acid molecule detection comprising the steps of:
amplifying a nucleic acid molecule sample to be detected by using a rolling circle amplification system to obtain an amplified product;
identifying the amplification product by using a CRISPR/Cas12a system, activating CRISPR/Cas12a trans-cutting performance, and cutting a trigger probe TS to obtain a degradation product;
mixing degradation products, a free hairpin probe H2 modified by a first signal conversion element, a free hairpin probe H1 modified by biological enzyme and a biological load element fixed with the hairpin probe H1, wherein the hairpin probe H1 and the hairpin probe H2 can be alternatively opened under the starting of an uncleaved trigger probe TS, and self-assembled to form a repeated linear double-stranded DNA structure, so as to obtain a hybridization chain reaction HCR product;
based on the first cascade reaction of the biological enzyme of the HCR product and the coupling of the first signal conversion element, quantification of the target nucleic acid molecule is realized;
and based on a second cascade reaction of the biological enzyme of the HCR product and the coupling of the second signal conversion element, the quantification of the target nucleic acid molecule is realized.
In some examples of programmable nucleic acid molecule detection methods, the bioburden element is CdS/Ag 2 S/B-ZnO NRs photoelectric composite material. The biological enzyme is glucose oxidase which can react with a substrate through first cascade reaction with nanometer Jin Ouge to realize photoelectrochemical detection; and/or the second signal conversion element is an iron-based material, and can be coupled with glucose oxidase to form a second cascade reaction to react with a substrate, so that colorimetric detection is realized.
In some examples of programmable nucleic acid molecule detection methods, the nanogold is beta-cyclodextrin modified nanogold; and/or the iron-based material is an iron-based organic framework material of NH2-MIL-88B (Fe).
The beneficial effects of the invention are as follows:
according to the programming type nucleic acid molecule detection platform provided by the embodiment of the invention, weak initial signals are greatly improved through the triple signal amplification element RCA-Cas12a-HCR, so that the sensitivity of the detection platform is effectively improved. Compared with the traditional amplification element, the rolling circle amplification element RCA in the triple amplification element can realize the sensitive detection of a plurality of different types of nucleic acid molecules by changing the nucleic acid molecule identification region in the rolling circle probe, and meanwhile, the Cas12a system is adopted as the medium of RCA and HCR, so that the specificity and the robustness of the detection are effectively improved. The detection platform can be used for detecting DNA or RNA, and can be used for directly replacing RNA with DNA.
The programming type nucleic acid molecule detection platform of some examples of the invention adopts internal cascade reaction formed by glucose oxidase GOx and beta-cyclodextrin modified nanometer Jin-CD@AuNPs and internal cascade reaction formed by glucose oxidase GOx and iron-based metal organic framework nanometer enzyme NH 2 MIL-88B (Fe) forms an external cascade reaction, and a bimodal sensing coupling photoelectrochemical detection and colorimetric detection is constructed. The detection platform based on double-signal reading adopts different conversion mechanisms and signal transmission modes for two signals. Compared with the traditional single signal, the bimodal detection platform can obtain more accurate and reliable detection results. In addition, the detection platform introduces a colorimetric detection mode, so that the detection is more visual and convenient.
The programming type nucleic acid molecule detection platform has good development application prospect, not only can realize the detection of different types of nucleic acid molecules by utilizing the programmable performance, but also can be developed to the sensitive analysis of other substances by combining with proper ligand nucleic acid molecules, such as: proteins, drugs, ions, etc.
Drawings
FIG. 1 is a schematic diagram of a programmable detection of nucleic acid molecules by a triple signal amplification element.
FIG. 2 is a CdS/Ag diagram 2 S/B-ZnO NRs scanning electron microscope pictures. A: magnification factor: 20000x, b magnification: 80000x.
Fig. 3 is a graph of the response of the photovoltaic performance. a: B-ZnO NRs，b:CdS/B-ZnO NRs，c:Ag 2 S/B-ZnO NRs，d:CdS/Ag 2 S/B-ZnO NRs。
FIG. 4 is a feasibility analysis of the triple amplification element RCA-Cas12 a-HCR. RCA reaction, cas12a cleavage, C: HCR reaction.
FIG. 5 is a possible analysis of a cascade reaction. A: internal cascade reaction formed by glucose oxidase GOx and cyclodextrin modified nanometer Jin-CD@AuNPs, B: and glucose oxidase GOx and iron-based metal organic framework nano enzyme NH 2 MIL-88B (Fe) forms an external cascade.
Detailed Description
In a first aspect of the invention, there is provided:
a programmable nucleic acid molecule detection platform comprises an amplifying element, a biological load element and a signal conversion element,
the amplification element is formed by sequentially coupling a rolling circle amplification system, a CRISPR/Cas12a system and a hybridization chain reaction system, wherein:
the rolling circle amplification system is used for amplifying the nucleic acid molecule sample to be detected;
the CRISPR/Cas12a system identifies an amplification product of the rolling circle amplification system, activates trans-cleavage performance of the CRISPR/Cas12a system, and cleaves a trigger probe TS of the hybridization chain reaction system to obtain a degradation product;
the hybridization chain reaction system comprises a hairpin probe H1 fixed on the biological load element, a free hairpin probe H2 modified by a first signal conversion element and a free hairpin probe H1 modified by biological enzyme, wherein the hairpin probe H1 and the hairpin probe H2 can be alternatively opened under the starting of an uncleaved trigger probe TS, and are self-assembled to form a repeated linear double-stranded DNA structure, so that a hybridization chain reaction HCR product is obtained;
the biological enzyme loaded by the HCR product is coupled with a first signal element to generate a first cascade reaction, is coupled with a second signal element to generate a second cascade reaction, and the products of the first cascade reaction and the second cascade reaction are utilized to realize photoelectrochemical detection and colorimetric detection.
The working principle of the detection platform is shown in fig. 1, and examples are as follows:
the rolling circle amplification system is used for amplifying the nucleic acid molecule sample to be detected to obtain an amplification product;
identifying the amplification product by using a CRISPR/Cas12a system, activating CRISPR/Cas12a trans-cutting performance, and cutting a trigger probe TS to obtain a degradation product;
mixing degradation products, a free hairpin probe H2 modified by a first signal conversion element, a free hairpin probe H1 modified by biological enzyme and a biological load element fixed with the hairpin probe H1, wherein the hairpin probe H1 and the hairpin probe H2 can be alternatively opened under the starting of a trigger probe TS, and self-assembled to form a repeated linear double-stranded DNA structure, namely a hybridization chain reaction HCR, so as to finally obtain a HCR product fixed on the biological load element;
introducing a second signal conversion element to realize multi-mode signal output;
based on the first cascade reaction of the biological enzyme loaded by the HCR product and the coupling of the first signal conversion element, the quantification of the target nucleic acid molecule is realized.
Based on the introduced second signal conversion element, the signal initiation element and the second cascade of second signal conversion element coupling effects quantification of the nucleic acid molecule of interest.
When target nucleic acid molecules exist in a sample to be detected, corresponding amplification products are generated, and the CRISPR/Cas12a system is activated to cut the trigger probe TS. The cleavage degree of TS affects the assembly degree of HCR, and glucose oxidase and nanogold are on the product of HCR, thus insoluble bio-precipitates are generated through cascade reaction, and the precipitates affect the light absorption performance of the photoelectric material. The generation of bioprecipitates can thus lead to a reduction in photocurrent. As the content of nucleic acid molecules increases, cas12a, which is activated in trans-cleavage property, is more, resulting in an increase in the degradation degree of TS, which in turn results in a low degree of assembly of HCR. Finally, the precipitation generated by the cascade reaction is small, and the photocurrent is high. Thus, the higher the concentration of the target nucleic acid molecule, the more positively the intensity of the photocurrent is correlated with the concentration of the nucleic acid molecule. For colorimetric signals, this is achieved by a cascade of coupled glucose oxidase on the HCR product and iron-based material (additionally incorporated). Similarly, the higher the target nucleic acid molecule content, the lower the degree of product assembly of HCR, the less glucose oxidase is supported on the HCR product, resulting in weaker colorimetric signals. Thus, the higher the concentration of the target nucleic acid molecule, the more the colorimetric signal is inversely related to the concentration of the nucleic acid molecule. Through coupling of photoelectrochemistry and colorimetric detection, accuracy and reliability of the detection system can be further improved.
The bioburden element may be selected accordingly based on the detected signal. In some examples of programmable nucleic acid molecule detection platforms, the bioburden element is CdS/Ag 2 S/B-ZnO NRs photoelectric composite material. This is advantageous for realizing high-precision photoelectric detection.
In some examples of programmable nucleic acid molecule detection platforms, the CdS/Ag 2 The preparation method of the S/B-ZnO NRs photoelectric composite material comprises the following steps:
firstly, synthesizing a branched zinc oxide nano rod array B-ZnO NRs, and sequentially loading silver sulfide layers Ag on the branched zinc oxide nano rod array B-ZnO NRs 2 S and cadmium sulfide layer CdS to prepare CdS/Ag 2 S/B-ZnO NRs photoelectric composite material.
The type of biological enzyme may be selected accordingly depending on the nature of the signal conversion element. In some examples of programmable nucleic acid molecule detection platforms, the biological enzyme is glucose oxidase. The substrate of the glucose oxidase is easy to obtain,
the signal conversion element may be a conventional optical, electrical, or the like conversion element. In some examples of programmable nucleic acid molecule detection platforms, the first signal conversion element is nanogold, which can form a first cascade reaction with glucose oxidase and react with a substrate to realize photoelectrochemical detection; and/or the second signal conversion element is an iron-based material, can form a second cascade reaction with glucose oxidase and reacts with a substrate to realize colorimetric detection.
In some examples of programmable nucleic acid molecule detection platforms, the nanogold is beta-cyclodextrin modified nanogold; and/or the iron-based material is NH 2 -an iron-based organic framework material of MILs-88B (Fe).
In a second aspect of the invention, there is provided:
a method for programmable nucleic acid molecule detection comprising the steps of:
amplifying a nucleic acid molecule sample to be detected by using a rolling circle amplification system to obtain an amplified product;
identifying the amplification product by using a CRISPR/Cas12a system, activating CRISPR/Cas12a trans-cutting performance, and cutting a trigger probe TS to obtain a degradation product;
mixing degradation products, a free hairpin probe H2 modified by a first signal conversion element, a free hairpin probe H1 modified by biological enzyme and a biological load element fixed with the hairpin probe H1, wherein the hairpin probe H1 and the hairpin probe H2 can be alternatively opened under the starting of an uncleaved trigger probe TS, and self-assembled to form a repeated linear double-stranded DNA structure, so as to obtain a hybridization chain reaction HCR product;
based on the first cascade reaction of the biological enzyme of the HCR product and the coupling of the first signal conversion element, quantification of the target nucleic acid molecule is realized;
and based on a second cascade reaction of the biological enzyme of the HCR product and the coupling of the second signal conversion element, the quantification of the target nucleic acid molecule is realized.
In some examples of programmable nucleic acid molecule detection methods, the bioburden element is CdS/Ag 2 S/B-ZnO NRs photoelectric composite material. The biological enzyme is glucose oxidase which can react with a substrate through first cascade reaction with nanometer Jin Ouge to realize photoelectrochemical detection; and/or the second signal conversion element is an iron-based material, and can be coupled with glucose oxidase to form a second cascade reaction to react with a substrate, so that colorimetric detection is realized.
In some examples of programmable nucleic acid molecule detection methods, the nanogold is beta-cyclodextrin modified nanogold; and/or the iron-based material is NH 2 -an iron-based organic framework material of MILs-88B (Fe).
The technical scheme of the invention is further described below by combining examples.
Reference will now be made in detail to the specific embodiments of the present invention, examples of which are illustrated in the accompanying drawings. All other embodiments, which can be made by a person skilled in the art without making any inventive effort, are intended to be within the scope of the present invention.
The nucleic acid sequences designed in the examples of the present invention are as follows:
example 1
1. Photoelectric active material CdS/Ag 2 Preparation of S/B-ZnO NRs
Adding 50mL of pure water into a beaker, adding 0.15g of zinc nitrate and 0.07g of urotropine under vigorous stirring to obtain a mixed solution, heating the mixed solution to 80 ℃ and keeping stirring at a low speed to obtain an electrochemical deposition precursor; the FTO conductive glass is used as a load substrate, the platinum wire electrode is used as a counter electrode, the Ag/AgCl electrode is used as a reference electrode, and the B-ZnO NRs is obtained by depositing for 40 minutes under the initial voltage of-1.3V in an electrochemical workstation in a current-time mode. Immersing B-ZnO NRs in an aqueous solution containing 30mM thioacetamide, and standing at 90 ℃ for 2 hours to form a vulcanized layer; immersing the vulcanized B-ZnO NRs into a solution containing 100mM silver nitrate, and reacting for 30 minutes at 25 ℃ to obtain Ag 2 S/B-ZnO NRs; ag with 2 S/B-ZnO NRs are immersed in a mixed solution containing 10mM cadmium nitrate and 10mM thioacetamide, and reacted in an oven at 75 ℃ for 30 minutes to obtain CdS/Ag 2 S/B-ZnO NRs composite material.
2. Hairpin probe H1 modified CdS/Ag 2 Preparation of S/B-ZnO NRs
CdS/Ag 2 The S/B-ZnO NRs composite material is immersed in 0.3M L-cysteine hydrochloride solution for 90 minutes at 25 ℃ to obtain carboxylated CdS/Ag 2 S/B-ZnO NRs composite material; carboxylated CdS/Ag 2 S/B-ZnO NRs were immersed in a mixture of 10mg/mL (1- (3-dimethylaminopropyl) -3-ethylcarbodiimide hydrochloride) and 10mg/mL N-hydroxysuccinimide, and incubated at 37℃for 1 hour to give activated CdS/Ag 2 S/B-ZnO NRs composite material; 30 mu L2Mu M hairpin probe H1 solution was added dropwise to activated CdS/Ag 2 On the S/B-ZnO NRs composite material, incubating for 1 hour at 37 ℃ to obtain hairpin probe H1 modified CdS/Ag 2 S/B-ZnO NRs composite material, then using 5% skimmed milk powder solution to seal the surface active site, cleaning the surface of the composite material with water and preserving at 4 ℃ for standby.
FIG. 2 is a CdS/Ag diagram 2 S/B-ZnO NRs scanning electron microscope pictures. A: magnification factor: 20000x, b magnification: 80000x. Photoactive material CdS/Ag 2 S/B-ZnO NRs are successfully prepared and have obvious branched structures, have larger specific surface area and are favorable for loading biomolecules.
3. Preparation of glucose oxidase modified Probe GOx-H1
15. Mu.L of N-hydroxysuccinimide 3- (2-pyridinedimercapto) propionate SPDP at a concentration of 10mM was added to 1mL of glucose oxidase GOx at a concentration of 1mg/mL, and stirred at 25℃for 3 hours. The activated glucose oxidase was then concentrated to 10mg/mL using a 30kD ultrafiltration tube, with a volume of 200. Mu.L. Then, 200. Mu.L of the annealed thiol-modified hairpin probe H2 was added to the above solution at a concentration of 2. Mu.M, incubated at 25℃for 2 hours, and finally the GOx-H2 probe was purified by using a 30kD ultrafiltration tube. The prepared GOx-H2 is placed at 4 ℃ for standby.
4. Preparation of cyclodextrin-modified nano-gold-modified probe beta-CD@AuNPs-H2
Adding 35mL of pure water into a double-neck flask, heating to boil, sequentially adding 5mL of 100mM phosphate buffer (pH 7.4), 1mL of 10mM chloroauric acid solution and 10mL of 10mM beta-cyclodextrin solution, reacting for 40 minutes to obtain a wine red solution, and centrifuging for 10 minutes at 8000 revolutions per minute to obtain a precipitate; the precipitate was redispersed in 2mL of purified water and kept at 4℃until use. EDC/NHS coupling method is adopted to prepare beta-CD@AuNPs-H1. 1mg/mL of β -CD@AuNPs was added to 10mg/mL of 1- (3-dimethylaminopropyl) -3-ethylcarbodiimide hydrochloride and 10mg/mL of N-hydroxysuccinimide mixture (EDC/NHS), incubated at 37℃for 2 hours, centrifuged at 6000 rpm to give activated β -CD@AuNPs and reconstituted with 200. Mu.L purified water. Subsequently, 200. Mu.L of 2. Mu.M annealed aminated hairpin probe H1 (annealing treatment is specifically heating 2. Mu.M hairpin probe solution to 95℃and incubating for 5 minutes, followed by rapid cooling to 25℃at maximum rate of 1 ℃/s and incubating for 2 hours) was added to the above solution and incubated at 37℃for 2 hours, followed by adding 20. Mu.L of 6-mercaptohexanol MCH to block the remaining active sites on the surface. Finally, 6000 rpm centrifugal separation is carried out, the supernatant is removed, then the mixture is resuspended in 1mL of pure water, and the mixture is placed at 4 ℃ for standby.
5. Iron-based metal organic framework nano enzyme NH 2 Preparation of MIL-88B (Fe)
Adding 15mL of pure water into a beaker, adding 0.16g of poloxamer and 0.18g of ferric nitrate under strong stirring, and continuously stirring for 60 minutes to obtain a mixed solution A; then adding 150 mu L of glacial acetic acid into the mixed solution A, and continuously and strongly stirring to obtain a mixed solution B; finally, adding 0.06g of 2-amino terephthalic acid into the mixed solution B, and slightly stirring to obtain a precursor solution; transferring the precursor solution into a 50mL reaction kettle, and reacting at 110 ℃ for 16 hours to obtain crude NH 2 MIL-88B (Fe), followed by centrifugation at 11000 rpm for 15 min to give a precipitate, which was washed three times with water to give purified NH 2 -MILs-88B (Fe); purified NH 2 Dispersing MIL-88B (Fe) nano enzyme into pure water, and standing at room temperature for standby.
Example 2
1. Capture of miR-21
1nM miR-21 (SEQ ID NO. 2), 1. Mu.M PP-miR-21 probe (SEQ ID NO. 1) and 1 xT 4DNA Ligase Buffer are mixed, incubated at 95℃for 10 minutes, and then slowly cooled to room temperature to complete the annealing capture process.
RCA reaction
40U T4DNA ligase was added to the annealed product of the captured miRNA and incubated at 25℃for 2 hours. Subsequently, 20. Mu.L of the above product was taken out and added to 1 Xphi 29 DNA polymerase Buffer, 10U of phi29 DNA polymerase, 3. Mu.L of deoxyribonucleotide at a concentration of 10mM, incubated at 30℃for 2 hours, and heated at 65℃for 10 minutes to terminate the reaction, yielding a miR-21-triggered production of RCA product.
Cas12a System activation
The crRNA reaction solution (SEQ ID NO. 4), 2U DNase I and 1 XDNase I reaction buffer obtained by 5. Mu. L T7RNA polymerase-mediated in vitro transcription were added to DEPC treated water in a total volume of 100. Mu.L. The reaction solution was incubated at 37℃for 30 minutes, then warmed to 80℃for 20 minutes to terminate the reaction, and the template-removed crRNA was placed at-20℃for use.
2U of Cas12a nuclease, 30nM crRNA were mixed and incubated at 25℃for another 30 minutes to form the Cas12a/crRNA structure. Subsequently, 30 μl of RCA product was added to a solution of Cas12a/crRNA complex and primer TS of hybridization chain reaction HCR (SEQ ID No. 3), and incubated at 37 ℃ for 30 minutes to obtain cleavage solution a;
HCR reaction
mu.L of the cleavage solution A was added dropwise to CdS/Ag 2 The S/B-ZnO NRs composite surface was incubated at 37℃for 1 hour, followed by washing the composite surface with a phosphate-Tween buffer at pH 7.4 and a concentration of 0.01M; then 20. Mu.L of a probe solution (specifically, a mixed solution of 10. Mu.L of GOx-H1 and 10. Mu.L of beta. -CD@AuNPs-H2) was dropped onto the electrode surface and incubated at 37℃for 2 hours to complete the HCR reaction, followed by washing the electrode surface with a phosphate-Tween buffer and drying the surface with nitrogen gas.
5. Detection of miR-21
The dual-mode signal output is realized through the two-stage cascade reaction mediated by glucose oxidase GOx immobilized on the hybrid chain reaction HCR product; the reacted CdS/Ag 2 The S/B-ZnO NRs composite material is immersed into 350 mu L of glucose solution with the concentration of 1.5mM for hatching reaction, the final reaction solution is divided into two parts, 100 mu L of each part is added, 200 mu L of 4-chloro-1-naphthol 4-CN solution with the concentration of 3mM is added into one part, and the mixture is mixed with CdS/Ag 2 Incubating the S/B-ZnO NRs composite material for 20 minutes at 37 ℃, oxidizing 4-chloro-1-naphthol by beta-CD@AuNPs nano enzyme fixed on a hybridization chain reaction HCR product to generate insoluble bio-precipitate BCP to realize photoelectrochemical detection, sequentially adding 200 mu L of 0.2M acetic acid-sodium acetate buffer solution (pH 5.0) into the other part, sequentially adding 30 mu L of 30mM 3,3', 5' -tetramethyl benzidine TMB and 20 mu L of 2mg/mL iron-based metal-organic frame nano enzyme NH 2 MIL-88B (Fe) followed by incubation at 25℃for 15 min and observation of the dissolutionThe color of the liquid changes and the change of peak intensity at 652nm is recorded by an ultraviolet absorption spectrometer to realize colorimetric detection.
At the photoelectrochemical detection end, cdS/Ag 2 S/B-ZnO NRs as high-performance photoelectric composite materials have larger specific surface area, excellent electron conduction performance and excellent photoelectric conversion efficiency, and can be used as a good photoelectrochemical substrate material to improve the robustness of a detection system. Specifically, silver sulfide Ag 2 S is used as a shielding layer, and can effectively inhibit the rapid recombination of photo-generated electrons and photo-generated holes on the cadmium sulfide CdS layer. When CdS/Ag 2 After S/B-ZnO NRs are irradiated by illumination, the cadmium sulfide CdS layer is excited by photons to generate photo-generated electrons and photo-generated holes, and then the photo-generated holes can be quickly transferred to silver sulfide Ag 2 The S layer realizes effective separation of photo-generated electrons and photo-generated holes, thereby improving CdS/Ag 2 Photocurrent stability of S/B-ZnO NRs. Meanwhile, ascorbic acid AA is adopted as a sacrificial agent, so that CdS/Ag is effectively avoided 2 And the stability of the substrate is further improved by the photo-etching of S/B-ZnO NRs. Furthermore, more importantly, in CdS/Ag 2 HCR product formed by triple amplification reaction on S/B-ZnO NRs, which is formed by alternate assembly of a hairpin probe GOx-H1 modified with glucose oxidase and a hairpin probe β -cd@aunps-H2 modified with cyclodextrin reduced nanogold. In the HCR product, glucose oxidase GOx and cyclodextrin reduced nano Jin-cd@aunps form an internal cascade reaction that catalyzes the oxidation of 4-chloro-1-naphthol (4-CN) to insoluble bio-precipitate BCP that can deposit onto the electrode material surface and this deposition is irreversible. Thus, by catalyzing the internal cascade reactions to produce BCP effects, the photocurrent intensity can be reduced in proportion to the increase in the degree of assembly of HCR products, thus constituting PEC detection in which the photoelectrochemical signal decreases with decreasing target concentration.
Fig. 3 is a graph of the response of the photovoltaic performance. a: B-ZnO NRs, B: cdS/B-ZnO NRs, c: ag 2 S/B-ZnO NRs，d:CdS/Ag 2 S/B-ZnO NRs. As shown in fig. 3, B-ZnO NRs (curve a) exhibits a lower photocurrent response due to rapid recombination of photogenerated electrons and holes; when Ag is deposited on ZnO surface 2 After S layer, ag 2 S/B-ZnO NRs photocurrent (Curve)Line c) is enhanced compared to pure B-ZnO NRs; finally, cdS is deposited to Ag 2 After S/B-ZnO NRs, the photocurrent is further enhanced (curve d); in addition, cdS/Ag 2 S/B-ZnO NRs and no Ag 2 Compared with CdS/B-ZnO NRs (curve B) of the S layer, the photocurrent has obvious difference, which shows Ag 2 The S layer can effectively inhibit the rapid recombination of photo-generated electrons and holes, provide stable photocurrent and improve the stability of a detection system.
At the colorimetric detection end, glucose oxidase GOx on an HCR product and iron-based metal organic framework nano enzyme NH are adopted 2 MIL-88B (Fe) forms an external cascade. Due to NH 2 MIL-88B (Fe) is a hydrogen peroxide-sensitive peroxidase capable of utilizing hydrogen peroxide H produced by glucose oxidase 2 O 2 Realizes the high-efficiency oxidation of the contrast color substrate 3,3', 5' -tetramethyl benzidine TMB.
And carrying out bimodal sensitive detection on miR-21 on the basis of a programmed detection platform prepared by the triple amplification element. At the photoelectrochemical detection end, with the increase of miR-21, less HCR product is in CdS/Ag 2 S/B-ZnO NRs were generated, demonstrating that only a small amount of GOx-H1 and beta-CD@AuNPs-H2 were immobilized on the substrate, and that less BCP was generated by internal cascade reactions, thereby achieving higher photoelectrochemical signal response. The miR-21 concentration shows a good linear relation between the concentration logarithmic value and the current change value (delta I) within the range of 1fM-100nM, and a linear regression equation is as follows: Δi=68.6+4.1 [ lgc ] miR-21 (mol·L -1 )](wherein ΔI is the difference in signal in the presence and absence of miR-21). At the same time, the colorimetric detection end was achieved by recording the absorbance intensity at 652 nm. With the decrease of miR-21, a large amount of GOx-H1 is immobilized on an electrode substrate through HCR reaction, and then is reacted with NH through GOx 2 External cascade of MIL-88B (Fe) catalyzes the oxidation of TMB (colorless) to TMB + (blue), producing a pronounced blue color. The blue color deepens along with the reduction of the miR-21 concentration, and the absorbance change value at 652nM and the miR-21 concentration logarithmic value show good linear relation in the range of 1fM-100 nM. The linear regression equation is: Δabs=3.9+0.2 [ lgc ] miR-21 (mol·L -1 )](wherein Δabs. Is absentAnd signal difference in the presence of miR-21).
FIG. 4 is a feasibility analysis of the triple amplification element RCA-Cas12 a-HCR. RCA reaction, cas12a cleavage, C: HCR reaction. As shown in fig. 4A, as the microRNA concentration increases, the brightness of the band at the top gradually increases (red dashed box), indicating that the rolling circle amplification reaction and the microRNA concentration show a good correspondence; then, the trans-cleavage performance of Cas12a is analyzed by fluorescence experiments, and only in the presence of RCA products, the trans-cleavage performance of Cas12a can be activated, and cleavage of the fluorescent probe generates a distinct fluorescent signal (fig. 4B); as microRNA concentration increases, the rolling circle amplification product increases, thereby resulting in better activation of trans-cleavage performance of Cas12a, thereby cleaving more TS probes, reducing assembly of HCR products (fig. 4C). The figure effectively demonstrates that the amplification elements were successfully constructed.
FIG. 5 is a possible analysis of a cascade reaction. A: first cascade reaction of glucose oxidase GOx with cyclodextrin reduced nano Jin-CD@AuNPs, B: and glucose oxidase GOx and iron-based metal organic framework nano enzyme NH 2 MIL-88B (Fe) forms a second cascade. Only in the presence of glucose oxidase GOx and cyclodextrin modified nano Jin-cd@aunps, the substrate was oxidized to produce a significant change in uv absorbance, indicating that the first cascade reaction was successfully constructed (fig. 5A); hydrogen peroxide generated by glucose oxidase GOx can activate iron-based material NH 2 The peroxidase-like properties of MIL-88B (Fe), in turn, oxidize the substrate, producing a distinct color signal (FIG. 5B). Thus, the experiment demonstrates a first cascade reaction of glucose oxidase GOx with cyclodextrin reduced nano Jin-CD@AuNPs and a nano-enzyme NH of glucose oxidase GOx with an iron-based metal-organic framework 2 The formation of the second cascade of MIL-88B (Fe) was successfully constructed. The photoelectrochemistry end and the colorimetric detection end can be in a linear range of 1fM-100nM, so that quantitative detection of microRNA is realized. Therefore, the detection platform is successfully constructed and has good applicability.
The property of the aptamer nucleic acid molecule that it can specifically bind to the target molecule is utilized to allow the aptamer that binds to the target molecule to trigger RCA amplification, which can be further used for sensitive analysis of other substances, such as: proteins, drugs, ions, etc.
The above description of the present invention is further illustrated in detail and should not be taken as limiting the practice of the present invention. It is within the scope of the present invention for those skilled in the art to make simple deductions or substitutions without departing from the concept of the present invention.
Claims (10)
1. The programmable nucleic acid molecule detection platform comprises an amplification element, a biological load element and a signal conversion element, and is characterized in that the amplification element is formed by sequentially coupling a rolling circle amplification system, a CRISPR/Cas12a system and a hybridization chain reaction system, wherein:
the rolling circle amplification system is used for amplifying the nucleic acid molecules to be detected;
the CRISPR/Cas12a system identifies an amplification product of the rolling circle amplification system, activates trans-cleavage performance of the CRISPR/Cas12a system, and cleaves a trigger probe TS of the hybridization chain reaction system to obtain a degradation product;
the hybridization chain reaction system comprises a hairpin probe H1 fixed on the biological load element, a free hairpin probe H2 modified by a first signal conversion element and a free hairpin probe H1 modified by biological enzyme, wherein the hairpin probe H1 and the hairpin probe H2 can be alternatively opened under the starting of an uncleaved trigger probe TS, and are self-assembled to form a repeated linear double-stranded DNA structure, so that a hybridization chain reaction HCR product is obtained;
the biological enzyme loaded by the HCR product is coupled with a first signal element to generate a first cascade reaction, is coupled with a second signal element to generate a second cascade reaction, and the products of the first cascade reaction and the second cascade reaction are utilized to realize photoelectrochemical detection and colorimetric detection.
2. The programmable nucleic acid molecule detection platform of claim 1, wherein the bioburden element is CdS/Ag 2 S/B-ZnO NRs photoelectric composite material.
3. The programmable nucleic acid molecule detection platform of claim 2, wherein the CdS/Ag 2 The preparation method of the S/B-ZnO NRs photoelectric composite material comprises the following steps:
firstly, synthesizing a branched zinc oxide nano rod array B-ZnO NRs, and loading cadmium sulfide/silver sulfide CdS/Ag on the branched zinc oxide nano rod array B-ZnO NRs 2 S layer for preparing CdS/Ag 2 S/B-ZnO NRs photoelectric composite material.
4. The programmable nucleic acid molecule detection platform of claim 1, wherein the biological enzyme is glucose oxidase.
5. The programmable nucleic acid molecule detection platform of claim 4, wherein the first signal conversion element is nanogold, which can form a first cascade reaction with glucose oxidase and react with a substrate to realize photoelectrochemical detection; and/or
The second signal conversion element is an iron-based material, can form a second cascade reaction with glucose oxidase and reacts with a substrate to realize colorimetric detection.
6. The programmable nucleic acid molecule detection platform of claim 5, wherein the nanogold is beta-cyclodextrin modified nanogold; and/or
The iron-based material is NH 2 -an iron-based organic framework material of MILs-88B (Fe).
7. A method for programmable nucleic acid molecule detection comprising the steps of:
amplifying a nucleic acid molecule sample to be detected by using a rolling circle amplification system to obtain an amplified product;
identifying the amplification product by using a CRISPR/Cas12a system, activating CRISPR/Cas12a trans-cutting performance, and cutting a trigger probe TS to obtain a degradation product;
mixing degradation products, a free hairpin probe H2 modified by a first signal conversion element, a free hairpin probe H1 modified by biological enzyme and a biological load element fixed with the hairpin probe H1, wherein the hairpin probe H1 and the hairpin probe H2 can be alternatively opened under the starting of an uncleaved trigger probe TS, and self-assembled to form a repeated linear double-stranded DNA structure, so as to obtain a hybridization chain reaction HCR product;
based on the first cascade reaction of the biological enzyme of the HCR product and the coupling of the first signal conversion element, quantification of the target nucleic acid molecule is realized;
and based on a second cascade reaction of the biological enzyme of the HCR product and the coupling of the second signal conversion element, the quantification of the target nucleic acid molecule is realized.
8. The method of claim 7, wherein the bioburden element is CdS/Ag 2 S/B-ZnO NRs photoelectric composite material.
9. The method of claim 7, wherein the biological enzyme is glucose oxidase, which reacts with the substrate in a first cascade reaction with nanometer Jin Ouge to realize photoelectrochemical detection; and/or the second signal conversion element is an iron-based material, and can be coupled with glucose oxidase to form a second cascade reaction to react with a substrate, so that colorimetric detection is realized.
10. The method of claim 9, wherein the nanogold is beta-cyclodextrin modified nanogold; and/or
The iron-based material is NH 2 -an iron-based organic framework material of MILs-88B (Fe).
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