WO2017143873A1 - Isothermal nucleic acid amplification method - Google Patents

Isothermal nucleic acid amplification method Download PDF

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WO2017143873A1
WO2017143873A1 PCT/CN2017/000188 CN2017000188W WO2017143873A1 WO 2017143873 A1 WO2017143873 A1 WO 2017143873A1 CN 2017000188 W CN2017000188 W CN 2017000188W WO 2017143873 A1 WO2017143873 A1 WO 2017143873A1
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amplification
nucleic acid
polymerase
reaction
acid amplification
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马翠萍
尚凡金
周美玲
张攀松
王一凡
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青岛艾菲生物技术有限公司
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
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    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

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  • PCR Polymerase Chain Reaction
  • the PCR method uses a small amount of double-stranded nucleic acid as a template to achieve exponential amplification, and the amplification result has the advantage of high sensitivity, so the method is widely used as a tool for cloning or nucleic acid amplification.
  • the PCR method clearly has the following problems: each cycle of PCR includes three steps of denaturation, annealing and extension.
  • Strand Displacement Amplification is a method developed by Walker et al. in 1992 to detect double-stranded nucleic acid amplification. This method is mainly based on the interaction of a restriction enzyme and a DNA polymerase. The principle is to first convert a double-stranded DNA into a single strand using a thermal denaturation method, and a primer containing a restriction endonuclease recognition sequence binds to a single-stranded template and is extended by a DNA polymerase.
  • the addition of the outer primer strand replaces the template complementary strand formed, and another primer with a restriction enzyme recognition sequence binds to and extends the complementary strand of the formed template, and a specific base of thio is used in the experiment.
  • the endonuclease cleaves a strand in the double strand to create a nick, the polymerase synthesizes a new strand at the nick and replaces the original strand while filling in the cleavage site, and the replaced strand is complementary to the amplification primer. Cycle amplification.
  • Chain displacement amplification is highly sensitive and can be rapidly amplified to obtain single-stranded DNA, but this method requires an initial thermal denaturation step; the reaction also requires restriction enzymes, which adds additional cost and requires the participation of four primers. It is easy to cause non-specific reactions; the limitations of detection methods limit its application range.
  • Loop Mediated Isothermal Amplification is a new method for in vitro amplification of nucleic acid-specific sequences established by Japanese scholar Notomi et al. in 2000.
  • the method mainly uses four specific primers.
  • the six specific regions of the target DNA are identified, and rapid isothermal amplification of the nucleic acid is achieved by two loop structures and a strand displacement reaction.
  • the LAMP reaction process includes a dumbbell template synthesis stage, a cycle amplification stage, an elongation and a recycle stage.
  • the method is rapid in response and has good sensitivity and specificity.
  • Cross Priming Amplification is a method of constantly amplifying target nucleic acid sequences.
  • the method mainly designs 5 specific primers for 5 regions of the target gene, cross-interleaving sequences at the tail ends of the primers, and DNA aggregation with strand displacement activity.
  • the enzyme is subjected to extension and displacement, and is amplified by linear structure or secondary structure, and multiple primer hybridization sites are generated by repeated hybridization, extension and self-hybrid folding and extension of the amplification product, so that the same template can be used.
  • a plurality of amplification reactions are simultaneously performed to complete the nucleic acid amplification reaction under constant temperature conditions, and the method has the advantages of not requiring thermal denaturation of the template, multiple temperature cycling processes, rapid reaction, and the like.
  • the method has a large number of primers, and is easy to produce a non-specific reaction, and the obtained amplification product is complicated, and can only be qualitatively detected by agarose gel electrophoresis and cannot be quantitatively analyzed.
  • the invention provides a method for isothermal nucleic acid amplification, which solves the problems that the prior art isothermal nucleic acid amplification method requires multiple primers, multiple enzymes, and poor amplification effect on small fragments.
  • the invention establishes a nucleic acid amplification reaction by designing two forward and reverse primers, utilizing the dynamic dissociation principle between the double strands and the action of the strand displacement DNA polymerase under the isothermal condition to complete the nucleic acid amplification reaction.
  • a novel rapid and sensitive method for nucleic acid amplification is established by designing two forward and reverse primers, utilizing the dynamic dissociation principle between the double strands and the action of the strand displacement DNA polymerase under the isothermal condition to complete the nucleic acid amplification reaction.
  • the Bst DNA polymerase has both reverse transcription and strand displacement activities, and the RNA can be reverse transcribed into cDNA under the action of the substrate, and the strand displacement amplification reaction is carried out by using Bst DNA polymerase.
  • the whole system is completely expanded under isothermal conditions without additional reverse transcriptase, which integrates reverse transcription and amplification, reduces the amount of enzyme, and greatly shortens the reaction time and reduces the reaction. the cost of.
  • a method for isothermal nucleic acid amplification comprises the following steps:
  • the forward primer hybridizes with the amplified target nucleic acid sequence, and polymerizes and extends under the action of a polymerase to obtain an amplification product
  • the amplification product obtained in the step (2) is dynamically dissociated at the reaction temperature, so that the reverse primer hybridizes with the amplification product and extends to obtain an amplification product of the two primers;
  • the Tm value of the primer is ⁇ the reaction temperature, and the primer length is between 15-30 nucleotides.
  • the reaction temperature is 55-73 ° C, and the preferred reaction temperature is 65 ° C.
  • the amplified target nucleic acid sequence may be DNA or RNA, and the amplified target nucleotide sequence is ⁇ 100 bp, preferably ⁇ 60 bp.
  • the shortest length of the amplified target nucleotide sequence of the present invention may be the sum of the lengths of amplification of the two primers, and the principle of dynamic dissociation between the double strands under the condition of high reaction temperature during the amplification process is utilized. .
  • the method of the present invention is carried out at a constant temperature.
  • the forward primer is annealed to the target, and then extended by the polymerase to generate an amplification target, and the reverse primer and amplification are simultaneously utilized by the principle of dynamic dissociation between the two strands.
  • the target is annealed and then extended by the polymerase to obtain a double-stranded amplification product, and the resulting double-stranded amplification product can be reused as a substrate for another cycle, and is continuously circulated and amplified, thereby causing exponential amplification. Therefore, the reaction
  • the design of the primer Tm value is especially critical, that is, the designed primer has a Tm value higher than the reaction temperature to ensure that the primer can completely anneal to the target.
  • the polymerase of the present invention is a polymerase which is stable at the reaction temperature, preferably a polymerase having no exonuclease activity.
  • the polymerase has reverse transcription activity or the enzyme reaction temperature of the reverse transcriptase is consistent with the reaction temperature of the polymerase.
  • the method of the present invention can be completed under isothermal conditions, and isothermal means that the reaction temperature of each step in the whole process of the technical solution is constant, and each step is performed at a constant temperature without repeated lifting and lowering.
  • the invention does not need to adjust the temperature up and down in the whole process of nucleic acid amplification, and can be implemented only by using a device capable of maintaining a constant temperature, and the operation is simple;
  • the method of the present invention requires only one polymerase in the amplification process, especially when the RNA is amplified, no additional reverse transcriptase is added, and the reverse transcription and amplification are integrated, and the enzyme is reduced.
  • the method of the invention has good amplification effect on small fragments, and is more suitable for detecting mutated RNA viruses under isothermal conditions.
  • Figure 1 is a schematic diagram of the method of the present invention
  • FIG. 2-a is a fluorescence verification diagram, wherein A indicates that a target, an enzyme, and a primer are added to the reaction system; B indicates that only an enzyme and a primer are added; and C indicates that only a primer is added.
  • Figure 2-b shows the PAGE electrophoresis verification chart.
  • Lane 450 DNA ladder
  • Lane 1 only two primers containing 500 nM
  • Lane 2 Two primers and DNA polymerase containing 500 nM
  • Lane 3 Two primers containing 1 nM HCV-DNA, 500 nM, also added to DNA polymerase
  • Figure 3 is a graph showing amplification results of target nucleotide sequences of different lengths, wherein An amplification map showing the length of the amplified product of 45 bp, --- NTC indicates an amplification map of the template with a length of 45 bp instead of water.
  • An amplification map showing an amplification template length of 66 bp, and -b NTC indicates an amplification map of a template having a length of 66 bp instead of water.
  • An amplification map showing an amplification product of 87 bp in length, --c NTC indicates an amplification map of a template having a length of 87 bp instead of water.
  • Figure 4 is a graph showing the results of amplification of different amounts of PEG-200, wherein Indicates an amplification map of 20% PEG-200 added to the system. Represents an amplification map of 10% PEG-200 added to the system. Indicates the addition of 5% PEG-200 to the system. An amplification plot showing the addition of 0% PEG-200 to the system.
  • Figure 5 is a diagram showing the results of double-stranded DNA amplification, wherein An amplification map showing a target concentration of 10 -8 M, An amplification map showing a target concentration of 10 -9 M, An amplification map showing a target concentration of 10 -10 M, An amplification map showing a target concentration of 10 -11 M, An amplification map showing a target concentration of 0M.
  • Figure 6 is a graph showing the results of amplification of RNA at different concentrations, wherein An amplification map showing a target concentration of 10 -9 M, An amplification map showing a target concentration of 10 -10 M, An amplification map showing a target concentration of 10 -11 M, Indicates an amplification map when the target concentration is 0M.
  • Figure 7 is a graph showing the results of amplification of vent DNA polymerase.
  • Figure 8 is a graph showing the results of anti-interference amplification, wherein An amplification map showing the addition of 10% bovine serum to 16S rRNA with a target concentration of 10 -9 M, An amplification map showing the addition of 10% bovine serum to 16S rRNA with a target concentration of 10 -10 M, An amplification map showing the addition of 10% bovine serum to 16S rRNA with a target concentration of 10 -11 M, Indicates an amplification map when the detection concentration is 0M.
  • Example 1 The feasibility of the verification method and the correctness of its principle.
  • the DNA sequence of the synthesized HCV virus is used as a target nucleotide (sequence is 5'-GCCTGATAGGGTGCTTGCGAGTGCCCCGGGAGGT-3' (SEQ ID NO. 1), and two primers P1 (sequence 5'-ACCTCCCGGGGCACT-3' are utilized. (SEQ ID NO. 2)), P2 (sequence 5'-GCCTGATAGGGTGCTTGCG-3' (SEQ ID NO. 3)) was subjected to constant temperature amplification, and the feasibility and principle of the method were verified by fluorescence signal and electrophoresis results.
  • the 10 ⁇ L reaction system is as follows:
  • the method of the present invention is used to amplify 16S rDNA of Escherichia coli of different lengths, and three pairs of primers are designed, and these primers can amplify DNA product sequences of different lengths (45 bp, 66 bp, 87 bp).
  • the reaction system is:
  • 1 primers P1 and P2 are 10 -6 M, respectively
  • Primer P1 (sequence is 5'-CAAGGCGACGATCCCTAGCT-3' (SEQ ID NO. 5)
  • Primer P2 (sequence is 5'-GTGTGGCTGGTCATCCTCTCAGAC-3' (SEQ ID NO. 6));
  • Primer P1 (sequence is 5'-GTGTGGCTGGTCATCCTCTCAGAC-3' (SEQ ID NO. 8)
  • Primer P2 (sequence is 5'-GTTGGTGGGGTAACGGCTCAC-3' (SEQ ID NO. 9));
  • Primer P1 (sequence is 5'-ACTGCTGCCTCCCGTA-3' (SEQ ID NO. 11)
  • Primer P2 (sequence is 5'-CAAGGCGACGATCCCTAGCT-3' (SEQ ID NO. 12)).
  • PEG promotes the chain exchange reaction in order to verify whether PEG promotes the present invention, in the present example, different ratios of PEG-200 are separately added for verification, and the target nucleotide to be amplified is PBS plasmid (sequence is 5'-ATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGC-3' (SEQ ID NO. 13)), the detection primers were P1 (sequence 5'-GCCGTCGTTTTACAACGTCGTGA-3' (SEQ ID NO. 14)) and primer P2 (sequence 5'-ATTAAGTTGGGTAACGGCAGGGT-3) '(SEQ ID NO. 15)). 10 ⁇ L reaction system;
  • the detection was performed using a Bole CFX96 TM real-time PCR instrument, and the fluorescence signal was collected every minute, and the reaction was carried out at 65 ° C.
  • the amplification results are shown in FIG. 5 .
  • PBS plasmid different concentrations of PBS plasmid were used as target nucleotides (sequence 5'-ATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGC-3' (SEQ ID NO. 16)).
  • Bole CFX96 TM using real-time PCR instruments detect a fluorescent signal collected once every minute, reaction at 65 °C, amplification results shown in Figure 5.
  • results show that the present invention can perform better amplification of the PBS target having a helical double-strand structure, and thus the method can also be applied to the amplification of other double-stranded targets.
  • Escherichia coli 16S rRNA was used as an amplification template (sequence is 5'-GCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCG-3' (SEQ ID NO. 19)), and two primers P1 (sequence 5'-CGCTCGTTGCGGGACTTAACC-3' (SEQ ID NO. 20)), P2 (sequence 5'-GCTGTCGTCAGCTCGTGTTG-3' (SEQ ID NO. 21)) was subjected to constant temperature amplification. 10 ⁇ L reaction system;
  • 16S rRNA (1 ⁇ 10 -8 M, 1 ⁇ 10 -9 M, 1 ⁇ 10 ⁇ 10 M, 1 ⁇ 10 -11 M and 0 M) of different concentrations of Escherichia coli was added, and the reaction system was 10 ⁇ L.
  • Bole CFX96 TM using real-time PCR instruments detect a fluorescent signal collected once every minute, reaction at 65 °C, amplification results shown in Figure 6.
  • the present invention utilizes the characteristic that Bst DNA polymerase has reverse transcription activity, and the extracted Escherichia coli 16S rRNA is used as a target, and is directly reverse transcribed into cDNA for subsequent amplification reaction, that is, reversed under isothermal conditions.
  • the integration of recording and amplification allows the present invention to achieve one-step amplification of RNA.
  • Embodiment 6 Verification of the anti-interference ability of the present invention:
  • Example 5 On the basis of Example 5, 10% bovine serum was added to the reaction system to verify the anti-interference ability of the method of the present invention, and the amplification results are shown in Fig. 8.

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Abstract

Disclosed is an isothermal nucleic acid amplification method, carried out under a constant temperature, wherein a forward primer and a target are annealed and are then extended under the effect of a polymerase to generate an amplification target; meanwhile, a reverse primer and the amplification target are annealed by utilizing the principle of dynamic dissociation between two strands, and are then extended under the effect of the polymerase to generate a double-stranded amplification product. The generated double-stranded amplification product can be reused as a substrate for another circulation to implement cyclic amplification, thereby achieving exponential amplification.

Description

一种等温核酸扩增的方法Method for isothermal nucleic acid amplification 背景技术Background technique
近年来,核酸扩增方法已得到广泛的关注。目前,聚合酶链式反应(Polymerase Chain Reaction,PCR)是体外扩增核酸序列最常用的方法。PCR方法使用少量双链核酸为模板实现指数式扩增,扩增结果使其具有高灵敏度的优点,因此该方法被广泛的用作克隆或核酸扩增的工具。然而,PCR方法明显存在以下问题:PCR的每一个循环都包括变性、退火和延伸这三个步骤,因此,必须要用具有精确调控温度的仪器,在医院的床边或户外难以应用;需要优化复性温度以提高特异性,工作较繁琐复杂;反应耗时长;因而满足不了即时检测领域中简单快速的要求。In recent years, nucleic acid amplification methods have received extensive attention. Currently, Polymerase Chain Reaction (PCR) is the most commonly used method for amplifying nucleic acid sequences in vitro. The PCR method uses a small amount of double-stranded nucleic acid as a template to achieve exponential amplification, and the amplification result has the advantage of high sensitivity, so the method is widely used as a tool for cloning or nucleic acid amplification. However, the PCR method clearly has the following problems: each cycle of PCR includes three steps of denaturation, annealing and extension. Therefore, it is necessary to use an instrument with precise temperature regulation, which is difficult to apply at the bedside or outside of the hospital; Refolding temperature to improve specificity, work is more complicated and complicated; reaction takes a long time; thus it can not meet the simple and fast requirements in the field of real-time detection.
为克服PCR方法存在的弊端,自20世纪90年代初以来很多实验室尝试发展一系列无需热变性的等温核酸扩增方法,如链置换扩增(Strand Displacement Amplification,SDA)、环介导等温扩增(Loop Mediated Isothermal Amplification,LAMP)、交叉引物扩增(Cross Priming Amplification,CPA)等,这些方法的共同特点是扩增反应均在一个特定的温度下简单快速反应,从而大大的降低了对仪器的要求。In order to overcome the shortcomings of the PCR method, many laboratories have tried to develop a series of isothermal nucleic acid amplification methods without thermal denaturation since the early 1990s, such as Strand Displacement Amplification (SDA) and ring-mediated isothermal expansion. (Loop Mediated Isothermal Amplification, LAMP), Cross Priming Amplification (CPA), etc. The common feature of these methods is that the amplification reaction is simple and rapid at a specific temperature, which greatly reduces the instrument. Requirements.
链置换扩增(Strand Displacement Amplification,SDA)是由沃克(Walker)等人于1992年开发的一种检测双链核酸扩增的方法。该方法主要是依赖于限制性内切酶和DNA聚合酶共同作用来完成的。其原理是首先使用热变性方法将双链DNA转变为单链,含有限制性内切酶识别序列的引物与单链模板结合,在DNA聚合酶作用下延伸 形成模板的互补链,加入的外引物链置换下形成的模板互补链,另一个带有限制性酶识别序列的引物与形成的模板互补链结合并延伸,实验中采用硫代的特定碱基,使得内切酶切割双链中的一条链产生切口,聚合酶在切口处合成新的链并将原先的链置换下来同时补平酶切位点,被置换的链又与扩增引物互补而开启循环扩增。链置换扩增灵敏性高,可快速扩增获得单链DNA,但是该方法需要初始热变性的步骤;反应还需限制性内切酶,增加了额外的费用,需要四条引物的参与,体系复杂易引起非特异性反应;检测手段的局限,限制了它的应用范围。Strand Displacement Amplification (SDA) is a method developed by Walker et al. in 1992 to detect double-stranded nucleic acid amplification. This method is mainly based on the interaction of a restriction enzyme and a DNA polymerase. The principle is to first convert a double-stranded DNA into a single strand using a thermal denaturation method, and a primer containing a restriction endonuclease recognition sequence binds to a single-stranded template and is extended by a DNA polymerase. Forming a complementary strand of the template, the addition of the outer primer strand replaces the template complementary strand formed, and another primer with a restriction enzyme recognition sequence binds to and extends the complementary strand of the formed template, and a specific base of thio is used in the experiment. The endonuclease cleaves a strand in the double strand to create a nick, the polymerase synthesizes a new strand at the nick and replaces the original strand while filling in the cleavage site, and the replaced strand is complementary to the amplification primer. Cycle amplification. Chain displacement amplification is highly sensitive and can be rapidly amplified to obtain single-stranded DNA, but this method requires an initial thermal denaturation step; the reaction also requires restriction enzymes, which adds additional cost and requires the participation of four primers. It is easy to cause non-specific reactions; the limitations of detection methods limit its application range.
环介导等温扩增(Loop Mediated Isothermal Amplification,LAMP)是由日本学者Notomi等人在2000年建立的一种新的体外扩增核酸特异性序列的方法,该方法主要利用4条特异性引物分别识别目标DNA的6个特定区域,通过2个环状结构和链置换反应实现核酸的快速等温扩增。LAMP反应过程包括哑铃状模板合成阶段、循环扩增阶段、伸长和再循环阶段。该方法反应迅速,有较好的灵敏度和特异性。但是此方法四条引物设计比较困难,需要特殊的设计软件,对设计人员要求高,易引起气溶胶污染而导致假阳性结果,并且在检测中多用于定性而不是定量检测。上述不足在一定程度上限制了该技术的推广应用。Loop Mediated Isothermal Amplification (LAMP) is a new method for in vitro amplification of nucleic acid-specific sequences established by Japanese scholar Notomi et al. in 2000. The method mainly uses four specific primers. The six specific regions of the target DNA are identified, and rapid isothermal amplification of the nucleic acid is achieved by two loop structures and a strand displacement reaction. The LAMP reaction process includes a dumbbell template synthesis stage, a cycle amplification stage, an elongation and a recycle stage. The method is rapid in response and has good sensitivity and specificity. However, the design of the four primers is more difficult, and requires special design software, which requires high requirements for designers, which may cause aerosol contamination and lead to false positive results, and is used for qualitative rather than quantitative detection in testing. The above shortcomings have limited the promotion and application of the technology to some extent.
交叉引物扩增(Cross Priming Amplification,CPA)是一种恒温扩增靶核酸序列的方法。该方法主要针对靶基因的5个区域设计5条特异性引物,引物尾端交叉互换序列,利用具有链置换活性的DNA聚 合酶进行延伸置换,以线性结构或二级结构的方式进行扩增,通过引物的反复杂交、延伸和扩增产物的自我杂交折叠及延伸,产生多个引物杂交位点,使同一模板上可有多个扩增反应同时进行,从而在恒温条件下完成核酸扩增反应,该方法的优点是不需要模板的热变性、多次温度循环过程,反应迅速等。然而,该方法引物比较多,易产生非特异性反应,得到的扩增产物复杂,只能通过琼脂糖凝胶电泳进行定性检测而不能进行定量分析。Cross Priming Amplification (CPA) is a method of constantly amplifying target nucleic acid sequences. The method mainly designs 5 specific primers for 5 regions of the target gene, cross-interleaving sequences at the tail ends of the primers, and DNA aggregation with strand displacement activity. The enzyme is subjected to extension and displacement, and is amplified by linear structure or secondary structure, and multiple primer hybridization sites are generated by repeated hybridization, extension and self-hybrid folding and extension of the amplification product, so that the same template can be used. A plurality of amplification reactions are simultaneously performed to complete the nucleic acid amplification reaction under constant temperature conditions, and the method has the advantages of not requiring thermal denaturation of the template, multiple temperature cycling processes, rapid reaction, and the like. However, the method has a large number of primers, and is easy to produce a non-specific reaction, and the obtained amplification product is complicated, and can only be qualitatively detected by agarose gel electrophoresis and cannot be quantitatively analyzed.
发明内容Summary of the invention
本发明提供一种等温核酸扩增的方法,来解决现有的等温核酸扩增的方法需要多引物、多酶、对小片段扩增效果差等问题。The invention provides a method for isothermal nucleic acid amplification, which solves the problems that the prior art isothermal nucleic acid amplification method requires multiple primers, multiple enzymes, and poor amplification effect on small fragments.
本发明通过设计正向和反向两条引物,利用双链间的动态解离原理和链置换DNA聚合酶的作用在等温条件下实现信号的多重放大来完成核酸扩增反应,从而建立的一种新型的快速灵敏的核酸扩增方法。The invention establishes a nucleic acid amplification reaction by designing two forward and reverse primers, utilizing the dynamic dissociation principle between the double strands and the action of the strand displacement DNA polymerase under the isothermal condition to complete the nucleic acid amplification reaction. A novel rapid and sensitive method for nucleic acid amplification.
本发明根据专利201510501218.X中提出Bst DNA聚合酶兼有反转录和链置换活性,可使RNA在其作用下首先反转录成cDNA,再利用Bst DNA聚合酶进行链置换扩增反应,使得整个体系完全在等温条件下进行RNA的扩增,无需额外加入反转录酶,使反转录与扩增实现一体化,减少了酶的用量,且大大缩短了反应时间,同时降低了反应的成本。According to the patent 201510501218.X, the Bst DNA polymerase has both reverse transcription and strand displacement activities, and the RNA can be reverse transcribed into cDNA under the action of the substrate, and the strand displacement amplification reaction is carried out by using Bst DNA polymerase. The whole system is completely expanded under isothermal conditions without additional reverse transcriptase, which integrates reverse transcription and amplification, reduces the amount of enzyme, and greatly shortens the reaction time and reduces the reaction. the cost of.
为了实现上述目的,一种等温核酸扩增的方法,包括以下步骤:In order to achieve the above object, a method for isothermal nucleic acid amplification comprises the following steps:
(1)设计正向和反向两条引物; (1) design two forward and reverse primers;
(2)所述正向引物与扩增靶核酸序列杂交,在聚合酶的作用下聚合延伸,得到扩增产物;(2) the forward primer hybridizes with the amplified target nucleic acid sequence, and polymerizes and extends under the action of a polymerase to obtain an amplification product;
(3)步骤(2)得到的扩增产物在反应温度下发生动态解离,使得反向引物与扩增产物杂交并延伸,得到两条引物的扩增产物;(3) The amplification product obtained in the step (2) is dynamically dissociated at the reaction temperature, so that the reverse primer hybridizes with the amplification product and extends to obtain an amplification product of the two primers;
(4)两条引物的扩增产物在反应温度下不断的杂交、延伸,最终得到大量的扩增产物。(4) The amplification products of the two primers are continuously hybridized and extended at the reaction temperature, and finally a large amount of amplification products are obtained.
进一步的,所述引物的Tm值≥反应温度,引物长度在15-30个核苷酸之间。Further, the Tm value of the primer is ≥ the reaction temperature, and the primer length is between 15-30 nucleotides.
所述反应温度为55-73℃,优选的反应温度为65℃。The reaction temperature is 55-73 ° C, and the preferred reaction temperature is 65 ° C.
进一步的,所述扩增的靶核酸序列可以是DNA也可以是RNA,扩增靶核苷酸序列≤100bp,优选的为≤60bp。Further, the amplified target nucleic acid sequence may be DNA or RNA, and the amplified target nucleotide sequence is ≤100 bp, preferably ≤60 bp.
因此,本发明所述扩增靶核苷酸序列的最短长度可以为两条引物扩增的长度之和,扩增过程中利用在反应温度较高的条件下双链间的动态解离的原理。Therefore, the shortest length of the amplified target nucleotide sequence of the present invention may be the sum of the lengths of amplification of the two primers, and the principle of dynamic dissociation between the double strands under the condition of high reaction temperature during the amplification process is utilized. .
本发明所述方法在恒定的温度下进行,首先正向引物与靶标退火,然后在聚合酶的作用下延伸产生扩增靶标,同时利用双链间的动态解离原理使反向引物与扩增靶标退火,再在聚合酶的作用下延伸得到双链扩增产物,产生的双链扩增产物可重新作为另一个循环的底物,不断循环扩增,从而引发指数扩增,因此,本反应引物Tm值的设计尤为关键,即设计的引物的Tm值要高于反应温度以保证引物能与靶标完全退火。 The method of the present invention is carried out at a constant temperature. First, the forward primer is annealed to the target, and then extended by the polymerase to generate an amplification target, and the reverse primer and amplification are simultaneously utilized by the principle of dynamic dissociation between the two strands. The target is annealed and then extended by the polymerase to obtain a double-stranded amplification product, and the resulting double-stranded amplification product can be reused as a substrate for another cycle, and is continuously circulated and amplified, thereby causing exponential amplification. Therefore, the reaction The design of the primer Tm value is especially critical, that is, the designed primer has a Tm value higher than the reaction temperature to ensure that the primer can completely anneal to the target.
进一步的,为了加快反应的速度,我们还加入促进链交换的物质,解链剂,例如:PEG-200、极高热稳定单链结合蛋白(ET SSB)等,保证反应能快速进行。Further, in order to speed up the reaction, we also add substances that promote chain exchange, such as PEG-200, extremely high heat stable single-stranded binding protein (ET SSB), etc., to ensure rapid reaction.
进一步的,本发明所述的聚合酶为在反应温度下稳定的聚合酶,优选的为没有外切酶活性的聚合酶。Further, the polymerase of the present invention is a polymerase which is stable at the reaction temperature, preferably a polymerase having no exonuclease activity.
优选的,当靶核苷酸序列为RNA时,所述聚合酶具有反转录活性或反转录酶的酶反应温度与聚合酶的反应温度一致。Preferably, when the target nucleotide sequence is RNA, the polymerase has reverse transcription activity or the enzyme reaction temperature of the reverse transcriptase is consistent with the reaction temperature of the polymerase.
本发明的有益效果主要体现在以下几个方面:The beneficial effects of the present invention are mainly embodied in the following aspects:
1)本发明所述方法可在等温条件下完成,等温是指技术方案中全过程的每个步骤的反应温度是不变的,每步都是在恒定的温度下进行,不需要反复升降温,本发明在核酸扩增全过程无需对温度进行上下调节,仅仅利用可保持恒定温度的设备就可得以施行,操作简便;1) The method of the present invention can be completed under isothermal conditions, and isothermal means that the reaction temperature of each step in the whole process of the technical solution is constant, and each step is performed at a constant temperature without repeated lifting and lowering. The invention does not need to adjust the temperature up and down in the whole process of nucleic acid amplification, and can be implemented only by using a device capable of maintaining a constant temperature, and the operation is simple;
2)本发明所述方法实施扩增过程中只需一种聚合酶,尤其是对RNA进行扩增时,无需额外加入反转录酶,使反转录与扩增实现一体化,减少了酶的用量,且大大缩短了反应时间,同时降低了反应的成本;2) The method of the present invention requires only one polymerase in the amplification process, especially when the RNA is amplified, no additional reverse transcriptase is added, and the reverse transcription and amplification are integrated, and the enzyme is reduced. The amount of use, and greatly shorten the reaction time, while reducing the cost of the reaction;
3)本发明技术方案实施扩增过程中仅需正向和反向两条引物,无需现有技术中LAMP法所述的四条引物,实验设计简单,投入成本较低。3) The technical solution of the present invention requires only two forward and reverse primers in the amplification process, and does not need the four primers described in the prior art LAMP method, and the experimental design is simple and the input cost is low.
4)本发明所述方法对小片段扩增效果好,更适用于在等温条件下对易变异的RNA病毒进行检测。4) The method of the invention has good amplification effect on small fragments, and is more suitable for detecting mutated RNA viruses under isothermal conditions.
附图说明DRAWINGS
图1为本发明所述方法原理图; Figure 1 is a schematic diagram of the method of the present invention;
图2为本发明所述方法原理验证图;其中,图2-a为荧光验证图,其中A表示反应体系中加入靶标、酶和引物;B表示只加入酶和引物;C表示只加入引物。图2-b为PAGE电泳验证图,2 is a schematic diagram of the principle of the method of the present invention; wherein, FIG. 2-a is a fluorescence verification diagram, wherein A indicates that a target, an enzyme, and a primer are added to the reaction system; B indicates that only an enzyme and a primer are added; and C indicates that only a primer is added. Figure 2-b shows the PAGE electrophoresis verification chart.
其中泳道M:20bp DNA ladder;Lane 450: DNA ladder;
泳道1:只含500nM的两条引物;Lane 1: only two primers containing 500 nM;
泳道2:含有500nM的两条引物和DNA聚合酶Lane 2: Two primers and DNA polymerase containing 500 nM
泳道3:含有1nM HCV-DNA,500nM的两条引物,还加入DNA聚合酶Lane 3: Two primers containing 1 nM HCV-DNA, 500 nM, also added to DNA polymerase
图3为不同长度的靶核苷酸序列扩增结果图,其中,
Figure PCTCN2017000188-appb-000001
表示扩增产物的长度为45bp的扩增图,--a NTC表示以水代替长度为45bp的模板的扩增图,
Figure PCTCN2017000188-appb-000002
表示扩增模板长度为66bp的扩增图,--b NTC表示以水代替长度为66bp的模板的扩增图,
Figure PCTCN2017000188-appb-000003
表示扩增产物的长度为87bp的扩增图,--c NTC表示以水代替长度为87bp的模板的扩增图。
Figure 3 is a graph showing amplification results of target nucleotide sequences of different lengths, wherein
Figure PCTCN2017000188-appb-000001
An amplification map showing the length of the amplified product of 45 bp, --- NTC indicates an amplification map of the template with a length of 45 bp instead of water.
Figure PCTCN2017000188-appb-000002
An amplification map showing an amplification template length of 66 bp, and -b NTC indicates an amplification map of a template having a length of 66 bp instead of water.
Figure PCTCN2017000188-appb-000003
An amplification map showing an amplification product of 87 bp in length, --c NTC indicates an amplification map of a template having a length of 87 bp instead of water.
图4为PEG-200不同用量的扩增结果图,其中,
Figure PCTCN2017000188-appb-000004
表示在体系加入20%PEG-200的扩增图,
Figure PCTCN2017000188-appb-000005
表示在体系加入10%PEG-200的扩增图,
Figure PCTCN2017000188-appb-000006
表示在体系中加入5%PEG-200的扩增图,
Figure PCTCN2017000188-appb-000007
表示在体系中加入0%PEG-200的扩增图。
Figure 4 is a graph showing the results of amplification of different amounts of PEG-200, wherein
Figure PCTCN2017000188-appb-000004
Indicates an amplification map of 20% PEG-200 added to the system.
Figure PCTCN2017000188-appb-000005
Represents an amplification map of 10% PEG-200 added to the system.
Figure PCTCN2017000188-appb-000006
Indicates the addition of 5% PEG-200 to the system.
Figure PCTCN2017000188-appb-000007
An amplification plot showing the addition of 0% PEG-200 to the system.
图5为双链DNA扩增结果图,其中,
Figure PCTCN2017000188-appb-000008
表示靶标浓度为10-8M的扩增图,
Figure PCTCN2017000188-appb-000009
表示靶标浓度为10-9M的扩增图,
Figure PCTCN2017000188-appb-000010
表示靶标浓度为10-10M的扩增图,
Figure PCTCN2017000188-appb-000011
表示靶标浓度为10-11M的扩增图,
Figure PCTCN2017000188-appb-000012
表示靶标浓度为0M的扩增图。
Figure 5 is a diagram showing the results of double-stranded DNA amplification, wherein
Figure PCTCN2017000188-appb-000008
An amplification map showing a target concentration of 10 -8 M,
Figure PCTCN2017000188-appb-000009
An amplification map showing a target concentration of 10 -9 M,
Figure PCTCN2017000188-appb-000010
An amplification map showing a target concentration of 10 -10 M,
Figure PCTCN2017000188-appb-000011
An amplification map showing a target concentration of 10 -11 M,
Figure PCTCN2017000188-appb-000012
An amplification map showing a target concentration of 0M.
图6为不同浓度RNA扩增结果图,其中,
Figure PCTCN2017000188-appb-000013
表示靶标浓度为10-9M的扩增图,
Figure PCTCN2017000188-appb-000014
表示靶标浓度为10-10M的扩增图,
Figure PCTCN2017000188-appb-000015
表示靶标浓度为10-11M的扩增图,
Figure PCTCN2017000188-appb-000016
表示靶标浓度为0M时的扩增图。
Figure 6 is a graph showing the results of amplification of RNA at different concentrations, wherein
Figure PCTCN2017000188-appb-000013
An amplification map showing a target concentration of 10 -9 M,
Figure PCTCN2017000188-appb-000014
An amplification map showing a target concentration of 10 -10 M,
Figure PCTCN2017000188-appb-000015
An amplification map showing a target concentration of 10 -11 M,
Figure PCTCN2017000188-appb-000016
Indicates an amplification map when the target concentration is 0M.
图7为vent DNA聚合酶的扩增结果图。Figure 7 is a graph showing the results of amplification of vent DNA polymerase.
图8为抗干扰扩增结果图,其中,
Figure PCTCN2017000188-appb-000017
表示靶标浓度为10-9M的16S rRNA中加入10%的牛血清的扩增图,
Figure PCTCN2017000188-appb-000018
表示靶标浓度为10-10M的16S rRNA中加入10%的牛血清的扩增图,
Figure PCTCN2017000188-appb-000019
表示靶标浓度为10-11M的16S rRNA中加入10%的牛血清的扩增图,
Figure PCTCN2017000188-appb-000020
表示检测浓度为0M时的扩增图。
Figure 8 is a graph showing the results of anti-interference amplification, wherein
Figure PCTCN2017000188-appb-000017
An amplification map showing the addition of 10% bovine serum to 16S rRNA with a target concentration of 10 -9 M,
Figure PCTCN2017000188-appb-000018
An amplification map showing the addition of 10% bovine serum to 16S rRNA with a target concentration of 10 -10 M,
Figure PCTCN2017000188-appb-000019
An amplification map showing the addition of 10% bovine serum to 16S rRNA with a target concentration of 10 -11 M,
Figure PCTCN2017000188-appb-000020
Indicates an amplification map when the detection concentration is 0M.
具体实施方式detailed description
实施例1:验证方法的可行性及其原理的正确性。Example 1: The feasibility of the verification method and the correctness of its principle.
本实施例是利用合成的HCV病毒的DNA序列为靶核苷酸(序列为5’-GCCTGATAGGGTGCTTGCGAGTGCCCCGGGAGGT-3’(SEQ ID NO.1),利用2条引物P1(序列为5’-ACCTCCCGGGGCACT-3’(SEQ ID NO.2))、P2(序列为5’-GCCTGATAGGGTGCTTGCG-3’(SEQ ID NO.3))进行恒温扩增,通过荧光信号和电泳结果验证方法的可行性和原理的正确性。In this example, the DNA sequence of the synthesized HCV virus is used as a target nucleotide (sequence is 5'-GCCTGATAGGGTGCTTGCGAGTGCCCCGGGAGGT-3' (SEQ ID NO. 1), and two primers P1 (sequence 5'-ACCTCCCGGGGCACT-3' are utilized. (SEQ ID NO. 2)), P2 (sequence 5'-GCCTGATAGGGTGCTTGCG-3' (SEQ ID NO. 3)) was subjected to constant temperature amplification, and the feasibility and principle of the method were verified by fluorescence signal and electrophoresis results.
10μL反应体系如下:The 10 μL reaction system is as follows:
①引物P1和P2分别为5×10-7M1 Primers P1 and P2 are 5×10 -7 M, respectively
②dNTPs(10mM):0.5μL2dNTPs (10mM): 0.5μL
③1×ThermoPol Reaction Buffer反应缓冲液: 31×ThermoPol Reaction Buffer Reaction Buffer:
(20mM Tris-HCl,10mM KCl,10mM(NH4)2SO4,2mM MgSO4,0.1%Triton X-100,pH8.8@25℃)(20 mM Tris-HCl, 10 mM KCl, 10 mM (NH4) 2 SO 4 , 2 mM MgSO 4 , 0.1% Triton X-100, pH 8.8 @ 25 ° C)
④Eva Green(20×):0.25μL4Eva Green (20×): 0.25 μL
⑤Bst 2.0 WarmStartTM DNA polymerase(8U/μL):0.1μL5Bst 2.0 WarmStart TM DNA polymerase (8U/μL): 0.1μL
再加入终浓度为1×10-9M的HCV-DNA靶标,利用伯乐CFX96TM实时荧光定量PCR仪进行检测,每分钟采集一次荧光信号,65℃下进行反应,扩增结果见图2a。Then added to a final concentration of 1 × 10 -9 M of HCV-DNA target using the BioRad CFX96 TM real-time PCR instrument to detect the fluorescence signal collected once every minute, reaction at 65 ℃, amplification results shown in Figure 2a.
以上反应1h后,产物跑17.5%的PAGE电泳,点样5μL电压135V,电泳55min,EB染色,结果见图2b。After the above reaction for 1 h, the product was subjected to 17.5% PAGE electrophoresis, and a 5 μL voltage of 135 V was applied, and electrophoresis was performed for 55 min, and EB staining was performed. The results are shown in Fig. 2b.
结果表明该方法只有在靶标、聚合酶和引物的作用下才会发生反应并得到相应的扩增产物,从而验证了本方法的可行性与正确性。The results showed that the method could only react under the action of target, polymerase and primers and obtain the corresponding amplification products, thus verifying the feasibility and correctness of the method.
实施例2:不同长度的靶核苷酸序列的扩增Example 2: Amplification of target nucleotide sequences of different lengths
本实例利用本发明所述方法扩增不同长度的大肠杆菌16S rDNA,设计3对引物,这些引物可以扩增出不同长度的DNA产物序列(45bp、66bp、87bp)。In this example, the method of the present invention is used to amplify 16S rDNA of Escherichia coli of different lengths, and three pairs of primers are designed, and these primers can amplify DNA product sequences of different lengths (45 bp, 66 bp, 87 bp).
反应体系为:The reaction system is:
①引物P1和P2分别为10-6M1 primers P1 and P2 are 10 -6 M, respectively
②dNTPs(10mM):0.5μL2dNTPs (10mM): 0.5μL
③1×ThermoPol Reaction Buffer反应缓冲液:31×ThermoPol Reaction Buffer Reaction Buffer:
(20mM Tris-HCl,10mM KCl,10mM(NH4)2SO4,2mM MgSO4,0.1%Triton X-100,pH8.8@25℃)(20 mM Tris-HCl, 10 mM KCl, 10 mM (NH4) 2 SO 4 , 2 mM MgSO 4 , 0.1% Triton X-100, pH 8.8 @ 25 ° C)
④Eva Green(20×):0.25μL 4Eva Green (20×): 0.25 μL
⑤Bst 2.0 WarmStartTM DNA polymerase(8U/μL):0.1μL5Bst 2.0 WarmStart TM DNA polymerase (8U/μL): 0.1μL
再加入1×10-10M的16S rDNA靶标1μL,反应终体系10μL。利用伯乐CFX96TM实时荧光定量PCR仪进行检测,每分钟采集一次荧光信号,65℃下进行反应,扩增结果见图3。Further, 1 μL of 1×10 -10 M 16S rDNA target was added, and 10 μL of the final reaction system was added. Bole CFX96 TM using real-time PCR instrument to detect the fluorescence signal collected once every minute, reaction at 65 ℃, amplification results shown in Figure 3.
1)其中扩增长度45bp的16S rDNA(序列为5’-CAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACAC-3’(SEQ ID NO.4)),1) wherein 16S rDNA of 45 bp in length (sequence 5'-CAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACAC-3' (SEQ ID NO. 4)),
引物P1(序列为5’-CAAGGCGACGATCCCTAGCT-3’(SEQ ID NO.5)),Primer P1 (sequence is 5'-CAAGGCGACGATCCCTAGCT-3' (SEQ ID NO. 5)),
引物P2(序列为5’-GTGTGGCTGGTCATCCTCTCAGAC-3’(SEQ ID NO.6));Primer P2 (sequence is 5'-GTGTGGCTGGTCATCCTCTCAGAC-3' (SEQ ID NO. 6));
2)其中扩增长度66bp的16S rDNA(序列为5’-GTTGGTGGGGTAACGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACAC-3’(SEQ ID NO.7)),2) 16S rDNA of a length of 66 bp (sequence 5'-GTTGGTGGGGTAACGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACAC-3' (SEQ ID NO. 7)),
引物P1(序列为5’-GTGTGGCTGGTCATCCTCTCAGAC-3’(SEQ ID NO.8)),Primer P1 (sequence is 5'-GTGTGGCTGGTCATCCTCTCAGAC-3' (SEQ ID NO. 8)),
引物P2(序列为5’-GTTGGTGGGGTAACGGCTCAC-3’(SEQ ID NO.9));Primer P2 (sequence is 5'-GTTGGTGGGGTAACGGCTCAC-3' (SEQ ID NO. 9));
3)其中扩增长度87bp的16S rDNA(序列为5’-CAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGT-3’(SEQ ID NO.10)),3) Amplification of a 16 bp length 16S rDNA (sequence 5'-CAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGT-3' (SEQ ID NO. 10)),
引物P1(序列为5’-ACTGCTGCCTCCCGTA-3’(SEQ ID NO.11)), Primer P1 (sequence is 5'-ACTGCTGCCTCCCGTA-3' (SEQ ID NO. 11)),
引物P2(序列为5’-CAAGGCGACGATCCCTAGCT-3’(SEQ ID NO.12))。Primer P2 (sequence is 5'-CAAGGCGACGATCCCTAGCT-3' (SEQ ID NO. 12)).
结果表明:随着扩增产物长度的不断增大,扩增效率逐渐降低,从扩增结果图中可看出,3组不同长度序列中产物45bp的扩增效果最好,说明本发明对小片段扩增效果好,更适用于在等温条件下对易变异的RNA病毒进行检测。The results showed that as the length of the amplified product increased, the amplification efficiency decreased gradually. It can be seen from the amplification results that the amplification effect of the 45 bp product in the three different length sequences is the best, indicating that the invention is small. The fragment amplification effect is good, and it is more suitable for detecting the susceptible RNA virus under isothermal conditions.
实施例3PEG-200不同用量的扩增:Example 3 Amplification of PEG-200 in different amounts:
由于PEG对链交换反应有促进作用,为了验证PEG对本发明是否有促进作用,在本实施实例中分别加入不同比例的PEG-200进行验证,其扩增的靶核苷酸为PBS质粒(序列为5’-ATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGC-3’(SEQ ID NO.13)),检测引物为P1(序列为5’-GCCGTCGTTTTACAACGTCGTGA-3’(SEQ ID NO.14))和引物P2(序列为5’-ATTAAGTTGGGTAACGGCAGGGT-3’(SEQ ID NO.15))。10μL反应体系;Since PEG promotes the chain exchange reaction, in order to verify whether PEG promotes the present invention, in the present example, different ratios of PEG-200 are separately added for verification, and the target nucleotide to be amplified is PBS plasmid (sequence is 5'-ATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGC-3' (SEQ ID NO. 13)), the detection primers were P1 (sequence 5'-GCCGTCGTTTTACAACGTCGTGA-3' (SEQ ID NO. 14)) and primer P2 (sequence 5'-ATTAAGTTGGGTAACGGCAGGGT-3) '(SEQ ID NO. 15)). 10 μL reaction system;
①引物P1和P2分别为1.0×10-6M1 Primers P1 and P2 are 1.0×10 -6 M, respectively.
②dNTPs(10mM):0.5μL2dNTPs (10mM): 0.5μL
③1×ThermoPol Reaction Buffer反应缓冲液:31×ThermoPol Reaction Buffer Reaction Buffer:
(20mM Tris-HCl,10mM KCl,10mM(NH4)2SO4,2mM MgSO4,0.1%Triton X-100,pH8.8@25℃)(20 mM Tris-HCl, 10 mM KCl, 10 mM (NH4) 2 SO 4 , 2 mM MgSO 4 , 0.1% Triton X-100, pH 8.8 @ 25 ° C)
④Eva Green(20×):0.25μL4Eva Green (20×): 0.25 μL
⑤Bst 2.0 WarmStartTM DNA polymerase(8U/μL):0.1μL 5Bst 2.0 WarmStart TM DNA polymerase (8U/μL): 0.1μL
⑥1×10-8M的PBS模板61×10 -8 M PBS template
再向体系中加入0%、5%、10%、20%的PEG,加水使反应终体系为10μL。Then, 0%, 5%, 10%, and 20% PEG was added to the system, and water was added to make the reaction system 10 μL.
利用伯乐CFX96TM实时荧光定量PCR仪进行检测,每分钟采集一次荧光信号,65℃下进行反应,扩增结果见图5。The detection was performed using a Bole CFX96 TM real-time PCR instrument, and the fluorescence signal was collected every minute, and the reaction was carried out at 65 ° C. The amplification results are shown in FIG. 5 .
结果表明:加入不同比例的PEG-200对反应有一定的影响,从扩增结果图中可以看出,加入10%的PEG-200能明显的加快反应速率,因此,本发明将10%的PEG-200作为促进剂来加快反应的速率。The results showed that the addition of different proportions of PEG-200 had a certain effect on the reaction. It can be seen from the amplification results that the addition of 10% PEG-200 can significantly accelerate the reaction rate. Therefore, the present invention will 10% PEG. -200 acts as a promoter to speed up the reaction.
实施例4、双链核酸扩增:Example 4, Double-stranded nucleic acid amplification:
本实施例是利用不同浓度的PBS质粒为靶核苷酸(序列为5’-ATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGC-3’(SEQ ID NO.16))。利用2条引物P1(序列为5’-GCCGTCGTTTTACAACGTCGTGA-3’(SEQ ID NO.17))、P2(序列为5’-ATTAAGTTGGGTAACGCCAGGGT-3’(SEQ ID NO.18))进行恒温扩增。In this example, different concentrations of PBS plasmid were used as target nucleotides (sequence 5'-ATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGC-3' (SEQ ID NO. 16)). The two primers P1 (sequence 5'-GCCGTCGTTTTACAACGTCGTGA-3' (SEQ ID NO. 17)) and P2 (sequence 5'-ATTAAGTTGGGTAACGCCAGGGT-3' (SEQ ID NO. 18)) were subjected to constant temperature amplification.
10μL反应体系;10 μL reaction system;
①引物P1和P2分别为1.0×10-6M1 Primers P1 and P2 are 1.0×10 -6 M, respectively.
②dNTPs(10mM):0.5μL2dNTPs (10mM): 0.5μL
③1×ThermoPol Reaction Buffer反应缓冲液:31×ThermoPol Reaction Buffer Reaction Buffer:
(20mM Tris-HCl,10mM KCl,10mM(NH4)2SO4,2mM MgSO4,0.1%Triton X-100,pH8.8@25℃)(20 mM Tris-HCl, 10 mM KCl, 10 mM (NH4) 2 SO 4 , 2 mM MgSO 4 , 0.1% Triton X-100, pH 8.8 @ 25 ° C)
④10%PEG-200 410% PEG-200
⑤Eva Green(20×):0.25μL5Eva Green (20×): 0.25 μL
⑥Bst 2.0 WarmStartTM DNA polymerase(8U/μL):0.1μL6Bst 2.0 WarmStart TM DNA polymerase (8U/μL): 0.1μL
再加入不同浓度的PBS靶标(1×10-8M、1×10-9M、1×10-10M、1×10-11M及0M),反应终体系10μL。Further, different concentrations of PBS target (1 × 10 -8 M, 1 × 10 -9 M, 1 × 10 -10 M, 1 × 10 -11 M and 0 M) were added, and the reaction system was 10 μL.
利用伯乐CFX96TM实时荧光定量PCR仪检测,每分钟采集一次荧光信号,65℃下进行反应,扩增结果见图5。Bole CFX96 TM using real-time PCR instruments detect a fluorescent signal collected once every minute, reaction at 65 ℃, amplification results shown in Figure 5.
结果表明:本发明可以对具有螺旋双链结构的PBS靶标进行较好的扩增,因此该方法也可以应用于其他双链靶标的扩增。The results show that the present invention can perform better amplification of the PBS target having a helical double-strand structure, and thus the method can also be applied to the amplification of other double-stranded targets.
实施例5、为不同浓度RNA扩增:Example 5: Amplification of RNA at different concentrations:
本实验利用大肠杆菌16S rRNA作为扩增模板(序列为5’-GCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCG-3’(SEQ ID NO.19)),利用2条引物P1(序列为5’-CGCTCGTTGCGGGACTTAACC-3’(SEQ ID NO.20))、P2(序列为5’-GCTGTCGTCAGCTCGTGTTG-3’(SEQ ID NO.21))进行恒温扩增。10μL反应体系;In this experiment, Escherichia coli 16S rRNA was used as an amplification template (sequence is 5'-GCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCG-3' (SEQ ID NO. 19)), and two primers P1 (sequence 5'-CGCTCGTTGCGGGACTTAACC-3' (SEQ ID NO. 20)), P2 (sequence 5'-GCTGTCGTCAGCTCGTGTTG-3' (SEQ ID NO. 21)) was subjected to constant temperature amplification. 10 μL reaction system;
①引物P1和P2分别为1.0×10-6M1 Primers P1 and P2 are 1.0×10 -6 M, respectively.
②dNTPs(10mM):0.5μL2dNTPs (10mM): 0.5μL
③1×ThermoPol Reaction Buffer反应缓冲液:31×ThermoPol Reaction Buffer Reaction Buffer:
(20mM Tris-HCl,10mM KCl,10mM(NH4)2SO4,2mM MgSO4,0.1%Triton X-100,pH8.8@25℃)(20 mM Tris-HCl, 10 mM KCl, 10 mM (NH4) 2 SO 4 , 2 mM MgSO 4 , 0.1% Triton X-100, pH 8.8 @ 25 ° C)
④10%PEG-200410% PEG-200
⑤Eva Green(20×):0.25μL 5Eva Green (20×): 0.25 μL
⑥Bst 2.0 WarmStartTM DNA polymerase(8U/μL):0.1μL6Bst 2.0 WarmStart TM DNA polymerase (8U/μL): 0.1μL
再加入不同浓度的大肠杆菌的16S rRNA(1×10-8M、1×10-9M、1×10-10M、1×10-11M及0M),反应终体系10μL。Further, 16S rRNA (1×10 -8 M, 1×10 -9 M, 1×10 −10 M, 1×10 -11 M and 0 M) of different concentrations of Escherichia coli was added, and the reaction system was 10 μL.
利用伯乐CFX96TM实时荧光定量PCR仪检测,每分钟采集一次荧光信号,65℃下进行反应,扩增结果见图6。Bole CFX96 TM using real-time PCR instruments detect a fluorescent signal collected once every minute, reaction at 65 ℃, amplification results shown in Figure 6.
结果表明:本发明利用Bst DNA聚合酶具有反转录活性这一特点,以提取的大肠杆菌16S rRNA为靶标,直接反转录成cDNA进行后续的扩增反应,即在等温条件下实现反转录与扩增一体化,因此本发明可以实现对RNA的一步法扩增。The results showed that the present invention utilizes the characteristic that Bst DNA polymerase has reverse transcription activity, and the extracted Escherichia coli 16S rRNA is used as a target, and is directly reverse transcribed into cDNA for subsequent amplification reaction, that is, reversed under isothermal conditions. The integration of recording and amplification allows the present invention to achieve one-step amplification of RNA.
实施例6、其他聚合酶的扩增Example 6. Amplification of other polymerases
10μL反应体系:10 μL reaction system:
①引物P1和P2分别为1.0×10-6M1 Primers P1 and P2 are 1.0×10 -6 M, respectively.
②dNTPs(10mM):0.5μL2dNTPs (10mM): 0.5μL
③1×ThermoPol Reaction Buffer反应缓冲液:31×ThermoPol Reaction Buffer Reaction Buffer:
(20mM Tris-HCl,10mM KCl,10mM(NH4)2SO4,2mM MgSO4,0.1%Triton X-100,pH8.8@25℃)(20 mM Tris-HCl, 10 mM KCl, 10 mM (NH4) 2 SO 4 , 2 mM MgSO 4 , 0.1% Triton X-100, pH 8.8 @ 25 ° C)
④Eva Green(20×):0.25μL4Eva Green (20×): 0.25 μL
⑤VentR(exo-)DNA聚合酶(0.4U)5Vent R (exo-) DNA polymerase (0.4U)
再加入1×10-7M的HCV-DNA靶标1μL,反应终体系10μL。利用伯乐CFX96TM实时荧光定量PCR仪进行检测,每分钟采集一次荧光信号,65℃下进行反应,扩增结果见图7。Further, 1 μL of 1×10 -7 M HCV-DNA target was added, and 10 μL of the final reaction system was added. The detection was performed using a Bole CFX96 TM real-time PCR instrument, and the fluorescence signal was collected every minute, and the reaction was carried out at 65 ° C. The amplification results are shown in FIG. 7 .
结果表明:在反应温度下稳定的其他酶即可以应用于本发明所述 的方法进行核酸扩增。The results show that other enzymes which are stable at the reaction temperature can be applied to the present invention. The method of nucleic acid amplification.
实施例6、本发明的抗干扰能力的验证:Embodiment 6. Verification of the anti-interference ability of the present invention:
在实施例5的基础上,在反应体系中加入10%的牛血清来验证本发明所述方法的抗干扰能力,扩增结果见图8。On the basis of Example 5, 10% bovine serum was added to the reaction system to verify the anti-interference ability of the method of the present invention, and the amplification results are shown in Fig. 8.
结果表明:加入10%牛血清并没有抑制扩增反应,其扩增结果与加入反应buffer中的一样,都表现出良好的扩增曲线,说明本发明在复杂的反应环境下具有良好的抗干扰能力,可以很好的应用在实际样品的检测中。 The results showed that the addition of 10% bovine serum did not inhibit the amplification reaction, and the amplification results showed good amplification curves as in the reaction buffer, indicating that the invention has good anti-interference in complex reaction environments. Ability, can be well applied in the detection of actual samples.

Claims (10)

  1. 一种等温核酸扩增的方法,包括以下步骤:A method of isothermal nucleic acid amplification comprising the steps of:
    (1)设计正向和反向两条引物;(1) design two forward and reverse primers;
    (2)所述正向引物与扩增靶核酸序列杂交,在聚合酶的作用下聚合延伸,得到扩增产物;(2) the forward primer hybridizes with the amplified target nucleic acid sequence, and polymerizes and extends under the action of a polymerase to obtain an amplification product;
    (3)步骤(2)得到的扩增产物在反应温度下发生动态解离,使得反向引物与扩增产物杂交并延伸,得到两条引物的扩增产物;(3) The amplification product obtained in the step (2) is dynamically dissociated at the reaction temperature, so that the reverse primer hybridizes with the amplification product and extends to obtain an amplification product of the two primers;
    (4)步骤(2)、(3)反复循环,最终得到大量的扩增产物。(4) Steps (2) and (3) are repeatedly cycled to finally obtain a large amount of amplification product.
  2. 如权利要求1所述的一种等温核酸扩增的方法,其特征在于:所述正向和反向引物的Tm值≥反应温度,引物长度在15-30个核苷酸之间。A method of isothermal nucleic acid amplification according to claim 1, wherein said forward and reverse primers have a Tm value ≥ a reaction temperature, and a primer length of between 15 and 30 nucleotides.
  3. 如权利要求1或2所述的一种等温核酸扩增的方法,其特征在于:整个过程反应温度恒定不变,所述反应温度范围为55-73℃。A method of isothermal nucleic acid amplification according to claim 1 or 2, wherein the reaction temperature is constant throughout the process, and the reaction temperature ranges from 55 to 73 °C.
  4. 如权利要求3所述的一种等温核酸扩增的方法,其特征在于:所述反应温度为65℃。A method of isothermal nucleic acid amplification according to claim 3, wherein the reaction temperature is 65 °C.
  5. 如权利要求1所述的一种等温核酸扩增的方法,其特征在于:所述扩增的靶核酸序列可以是DNA序列或RNA序列。A method of isothermal nucleic acid amplification according to claim 1, wherein the amplified target nucleic acid sequence can be a DNA sequence or an RNA sequence.
  6. 如权利要求1或5所述的一种等温核酸扩增的方法,其特征在于:所述靶核苷酸序列长度≤100bp。A method of isothermal nucleic acid amplification according to claim 1 or 5, wherein the target nucleotide sequence is ≤ 100 bp in length.
  7. 如权利要求1所述的一种等温核酸扩增的方法,其特征在于:所述方法还包括在反应体系中添加促进链交换反应的物质,所述促进链交换反应的物质为PEG-200或极高热稳定单链结合蛋白。A method of isothermal nucleic acid amplification according to claim 1, wherein the method further comprises adding a substance which promotes a chain exchange reaction to the reaction system, and the substance for promoting the chain exchange reaction is PEG-200 or Very high heat stable single-stranded binding protein.
  8. 如权利要求1所述的一种等温核酸扩增的方法,其特征在于:所述聚合酶为在反应温度下稳定的聚合酶。 A method of isothermal nucleic acid amplification according to claim 1, wherein said polymerase is a polymerase which is stable at the reaction temperature.
  9. 如权利要求1或8所述的一种等温核酸扩增的方法,其特征在于:所述聚合酶为没有外切酶活性的聚合酶。A method of isothermal nucleic acid amplification according to claim 1 or 8, wherein the polymerase is a polymerase having no exonuclease activity.
  10. 如权利要求1或8所述的一种等温核酸扩增的方法,其特征在于:当靶核苷酸序列为RNA时,所述聚合酶具有反转录活性或反转录酶的酶反应温度与聚合酶的反应温度一致。 A method for isothermal nucleic acid amplification according to claim 1 or 8, wherein when the target nucleotide sequence is RNA, the polymerase has a reverse transcription activity or an enzyme reaction temperature of reverse transcriptase The reaction temperature with the polymerase is the same.
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