KR20020064896A - Method for synthesizing nucleic acid - Google Patents

Abstract

The present invention is a method for synthesizing oligonucleotides having a novel structure and nucleic acids using the primers. This oligonucleotide has a nucleotide sequence substantially the same as the region synthesized on the 5 'side of the primer using the primer as a synthetic starting point. The present invention realizes the synthesis of nucleic acid based on isothermal reaction with a simple reagent configuration. The present invention also provides a method for synthesizing a nucleic acid having high specificity, based on this nucleic acid synthesis method.

Description

Method for synthesizing nucleic acid

Technical Field

The present invention relates to a method for synthesizing a nucleic acid composed of a specific base sequence, which is useful as a method for amplifying a nucleic acid.

Background

In the analysis method based on the complementarity of nucleic acid base sequences, it is possible to directly analyze genetic characteristics. Therefore, it is a very powerful means for genetic diseases, cancerization, microorganism identification, and the like. In addition, since the gene itself is the detection target, for example, an operation that takes time and labor such as culturing may be omitted.

Nevertheless, detection of a small amount of the target gene present in a sample is generally not easy, and it is necessary to amplify the target gene itself, a detection signal, and the like. PCR (Polymerase Chain Reaction) is known as a method of amplifying a target gene (Science, 230, 1350-1354, 1985). The PCR method is currently the most common method for amplifying nucleic acids in vitro. It settled as an excellent detection method by the high sensitivity based on the exponential amplification effect. Moreover, since the amplification product can be recovered as DNA, it has been widely applied as an important means for supporting genetic engineering methods such as gene cloning and structural determination. However, in the PCR method, a special temperature control device is required for the implementation; Quantitative problems because the amplification proceeds exponentially; Problems such as being susceptible to contamination caused by contamination of a sample or a reaction solution from the outside and erroneously mixed nucleic acids function as a template have been pointed out.

Along with the accumulation of genomic information, the interpretation of single nucleotide polymorphisms (SNPs) is drawing attention. SNPs can be detected by PCR by designing the primers to include SNPs. That is, the presence or absence of the base sequence complementary to the primer can be determined by the presence or absence of the reaction product. However, in PCR, if the complementary chain synthesis is performed by mistake, the product functions as a template for subsequent reactions, which causes a wrong result. In reality, it is said that it is difficult to strictly control PCR only by the difference of one base at the terminal of the primer. Therefore, in order to use PCR for detecting SPNs, specificity needs to be improved.

On the other hand, nucleic acid synthesis methods based on ligase have also been put to practical use. The LCR method (Ligase Chain Reaction, Laffler TG; Carrino JJ; Marshall RL; Ann. Biol. Clin. (Paris), 1993, 51: 9, 821-6) includes two contiguous on the sequence to be detected. The basic principle is the reaction of hybridizing a probe to link both by ligase. Since it is impossible to link two probes when there is no target base sequence, the presence of the linkage product is an index of the target base sequence. The LCR method also has the same problem as the PCR method because temperature control is required for separation between the synthesized complementary chain and the template. As for LCR, a method of improving specificity by providing a gap between adjacent probes and filling them with DNA polymerase has also been reported. However, only the specificity that can be expected by this improvement method remains a problem in terms of requiring temperature control. In addition, since the required enzyme is increased, there is a problem that the cost increases.

As a method for amplifying DNA having a complementary sequence using a sequence to be detected as a template, SDA method (Strand Displacement Amplification) [Proc. Natl. Acad. Sci. USA, 89, 392-396; 1992] Nucleic Acid. Res., 20, 1691-1696; 1992 is also known. In the SDA method, when a complementary chain is synthesized using a primer complementary to the 3 'side of a nucleotide sequence as a synthetic starting point, if there is a double-stranded chain region on the 5' side, the SDA method performs a special synthesis of the complementary chain while replacing the chain. It is a method using DNA polymerase. In addition, below, when expressing simply as 5 'side or 3' side in this specification, all mean the direction in the chain of the side which becomes a template. The double-stranded chain portion on the 5 'side is called the SDA method because it is replaced by a newly synthesized complementary chain. In the SDA method, by inserting a restriction enzyme recognition sequence into a sequence annealed as a primer in advance, it is possible to omit the temperature change step, which is essential in the PCR method. That is, the nicks caused by restriction enzymes give the 3'-OH group, which is the starting point of the complementary chain, and then perform the chain substitution synthesis therefrom, whereby the synthesized complementary chain is released as a single-stranded chain. It is reused as a template of chain synthesis. In this way, the SDA method eliminated the complicated temperature control required for the PCR method.

However, in the SDA method, it is necessary to add a restriction enzyme which causes nicking in addition to the chain substitution type DNA polymerase. The increase in required enzyme is a factor of the increase in cost. In addition, in order to perform nick introduction (that is, cleavage of only one chain) rather than cleavage of double-stranded chains by restriction enzymes used, one substrate, such as αthio dNTP, is used as a substrate during synthesis so as to be resistant to enzymatic digestion. dNTP derivatives must be used. For this reason, the amplification product by SDA has a structure different from a natural nucleic acid, and the use of restriction | strength by restriction enzyme and application to the gene cloning of an amplification product is restrict | limited. In this regard, it can be said that the cost increase is accompanied. In addition, when the SDA method is applied to an unknown sequence, it is impossible to deny the possibility that there is a base sequence identical to the restriction enzyme recognition sequence for nick introduction in the synthesized region. In such cases, there is a fear that the synthesis of the complete complementary chain may be disturbed.

As a nucleic acid amplification method that does not require complicated temperature control, NASBA (Nucleic Acid Sequence-based Amplification, also called TMA / Transcription Mediated Amplification method) is known. NASBA performs DNA synthesis by DNA polymerase with a probe to which a target RNA is used as a template and to which a T7 promoter is added, which is further double stranded with a second probe, and the resulting double stranded DNA is used as a template. It is a reaction system that amplifies a large amount of RNA by causing transcription by RNA polymerase (Nature, 350, 91-92, 1991). NASBA requires several heat denaturation steps to complete the double-stranded DNA, but subsequent transcription by T7 RNA polymerase proceeds isothermally. However, since a combination of plural enzymes called reverse transcriptase, RNaseH, DNA polymerase, and T7 RNA polymerase is essential, it is disadvantageous in terms of cost as well as SDA. Moreover, since the setting of conditions for performing a plurality of enzyme reactions is complicated, it is difficult to spread as a general analysis method. As described above, in the known nucleic acid amplification reaction, a problem of complicated temperature control or a plurality of enzymes remains.

Moreover, few attempts have been made on these known nucleic acid synthesis reactions to further improve the nucleic acid synthesis efficiency without sacrificing specificity or cost. For example, in a method called rolling-circle amplification (RCA), it is possible to continuously synthesize DNA of a single-stranded chain of sequential sequences complementary to a padlock probe in the presence of a target base sequence. (Paul M. Lizardi et al, Nature Genetics 19, 225-232, July, 1998). In RCA, a padlock probe having a special structure in which the 5 'end and the 3' end of the single-stranded oligonucleotide constitute an adjacent probe in the LCR is used. By combining the polymerase catalyzing the chain substitution type complementary chain synthesis reaction, a continuous complementary chain synthesis reaction is triggered by using a padlock probe ligated in the presence of the target base sequence. Regions of the same base sequence are repeated to form single stranded chain nucleic acids having a contiguous structure. The single-stranded nucleic acid is further annealed to synthesize a complementary chain thereof to achieve high amplification. However, the need for multiple enzymes remains a challenge. Moreover, the trigger of complementary chain synthesis depends on the linking reaction of two adjacent regions, and its specificity is in principle the same level as LCR.

For the problem of supplying 3'-OH, a method is known in which a hairpin loop is formed at the end by having a sequence complementary to the base sequence on the same chain at the 3 'end (Gene 71, 29-40, 1988). . From such a hair pin loop, complementary chain synthesis using the template as a template is carried out to generate a single stranded nucleic acid composed of complementary nucleotide sequences. For example, in PCT / FR95 / 00891, the structure which anneals on the same chain in the terminal part which connected complementary base sequences is implement | achieved. However, in this method, the step of eliminating base pairing with the complementary chain at the terminal and forming a new base pair bond on the same chain is essential. This step is supposed to proceed depending on the delicate equilibrium at the ends of the complementary base sequences with base pair bonds. That is, only the annealing with the base sequence on the same chain using the equilibrium state maintained between the base pair bond with the complementary chain and the base pair bond on the same chain becomes the starting point of the synthesis of the complementary chain. Therefore, in order to achieve a high reaction efficiency, it is considered that exact setting of reaction conditions is required. Moreover, in this prior art, the primer itself is making a loop structure. Therefore, once a primer dimer is produced, an amplification reaction is automatically started with or without the target base sequence to form a nonspecific synthetic product. This is a major problem. Moreover, the consumption of the primers by the production of primer dimers and the nonspecific synthetic reactions accompanying them leads to a decrease in the amplification efficiency of the target reaction.

In addition, there is a report (EP713922) that realizes a 3 'terminal structure that anneals to the same chain using a region that is not a template for DNA polymerase. This report also has the same problems as the previous PCT / FR95 / 00891 in using the dynamic equilibrium at the end and the possibility of nonspecific synthetic reactions accompanied by primer dimer formation. Moreover, special regions that do not serve as templates for DNA polymerase must be prepared as primers.

Also, in various signal amplification reactions applying the principle of NASBA, oligonucleotides having a hairpin structure at the end are often used to supply a promoter region of a double-stranded chain (Japanese Patent Laid-Open No. Hei 5-211873). However, these do not enable the continuous supply of 3'-OH of complementary chain synthesis. Moreover, in Japanese Patent Application Laid-open No. 10-510161 (WO96 / 17079), a hairpin loop structure in which the 3 'end is annealed on the same chain is used for the purpose of obtaining a DNA template that is transcribed by RNA polymerase. In this method, template amplification is carried out using transcription to RNA and reverse transcription from RNA to DNA. However, this method also cannot constitute a reaction system without combining a plurality of enzymes.

Disclosure of the Invention

An object of the present invention is to provide a method for synthesizing nucleic acids based on novel principles. More specifically, the present invention provides a method capable of efficiently and efficiently synthesizing a nucleic acid depending on a sequence at low cost. That is, it is a subject of the present invention to provide a method that can achieve the synthesis and amplification of nucleic acids even under the use of a single enzyme and under isothermal reaction conditions. Further, the present invention has an object to provide a method for synthesizing a nucleic acid capable of realizing high specificity which is difficult to achieve by known nucleic acid synthesis reaction principles, and a nucleic acid amplification method applying the synthesis method.

The present inventors first focused on the use of a polymerase that catalyzes the chain substitution type complementary chain synthesis, which is useful for nucleic acid synthesis that does not depend on complicated temperature control. Such DNA polymerase is an enzyme used also in SDA and RCA. However, even if such an enzyme is used, another enzyme reaction is always required in order to supply 3'-OH, which is a synthetic starting point, for example, SDA, based on known primers.

Therefore, the present inventors examined supply of 3'-OH from an angle completely different from a known approach. As a result, the inventors have found that by using oligonucleotides having a special structure, 3'-OH can be supplied without resorting to additional enzymatic reactions. That is, the present invention relates to a method for synthesizing a nucleic acid described below, further to a nucleic acid amplification method to which the nucleic acid synthesis method is applied, and a novel oligonucleotide which enables these methods.

[1] A method for synthesizing nucleic acids in which complementary nucleotide sequences are alternately linked on a single-stranded chain comprising the following steps.

a) a step of providing a nucleic acid capable of forming a loop comprising a region F2c capable of base pair binding by having a region F1 that can anneal to some F1c on the same chain at the 3 'end and the region F1 annealed to F1c

b) A step of performing complementary chain synthesis using the 3 'end of F1 annealed to F1c as a synthetic starting point.

c) annealing the oligonucleotide comprising the F2 having the sequence complementary to the region F2c at the 3 'end, and synthesizing the complementary chain by a polymerase which catalyzes the chain substitution complementary chain synthesis reaction using the synthesis starting point; Substituting the complementary chain synthesized in b)

d) annealing polynucleotides comprising a sequence complementary to any region in the complementary chain substituted in step c) to enable base pair bonding at the 3 'end, and the chain substitution complement using the 3' end as a synthetic starting point. A step of substituting the complementary chain synthesized in step c) by performing a complementary chain synthesis by a polymerase catalyzing the chain synthesis reaction

[2] In the step [1], in step d), the synthetic starting point is a region R1 present at the 3 'end of the same chain that can be annealed to the region R1c, and R1 is a region R2c capable of base pair bonding by annealing to R1c. How the loop comprising is formed.

[3] An oligonucleotide consisting of at least two regions X2 and X1c below and linked to X1c on the 5 'side of X2.

X2: region having a nucleotide sequence complementary to any region X2c of a nucleic acid having a specific nucleotide sequence

X1c: region having a base sequence substantially the same as region X1c located on the 5 'side of region X2c in a nucleic acid having a specific base sequence

[4] The method of [1], wherein the nucleic acid in step a) is a second nucleic acid provided by the following step.

i) annealing the region F2c of the nucleic acid having the region F2 of the oligonucleotide of [3], in which region X2 is region F2 and region X1c is region F1c,

ii) a step of synthesizing a first nucleic acid having a nucleotide sequence complementary to a template using F2 of the oligonucleotide as a synthetic starting point;

iii) allowing any pair of the first nucleic acid synthesized in step ii) to be capable of base pair binding,

iv) An oligonucleotide having a nucleotide sequence complementary to the region that enables base pair binding of the first nucleic acid in step iii) is annealed, and a second nucleic acid is synthesized using the synthesis starting point and F1 at the 3 'end. To make base-pair binding possible

[5] The region [3], wherein the region allowing base pair bonding in step iii) is R2c, and in the oligonucleotide in step iv), region X2c is region R2c, and region X1c is region R1c. ] Oligonucleotide.

[6] An outer primer according to [4] or [5], which anneals to the 3 'side of F2c in the mold, wherein the step of allowing base pair bonding in steps iii) and iv) is possible. Chain substitution complement chain by polymerase which catalyzes the chain substitution complement chain chain synthesis reaction using the outer primer annealed on the 3 'side of the region as the starting point of the synthesis in step iv) and the first nucleic acid. How to do it by synthesis.

[7] The method of [6], wherein the melting temperature of each oligonucleotide used for the reaction and its complementary region in the template is in the following relationship under the same stringency.

(Region on the 3 'side in the outer primer / template) ≤ (F2c / F2 and R2c / R2) ≤ (F1c / F1 and R1c / R1)

[8] The method according to any one of [4] to [7], wherein the nucleic acid serving as a template is RNA, and the complementary chain synthesis in step ii) is performed with an enzyme having reverse transcriptase activity.

[9] Amplification of nucleic acids in which complementary nucleotide sequences are alternately linked on a single-stranded chain by repeating the following steps.

A) At the 3 'end and the 5' end, a loop having a base sequence complementary to the terminal region on the same chain and allowing base pair bonding between both when the complementary base sequences are annealed Process of providing the mold to be formed

B) a step of performing complementary chain synthesis using the 3 'end of the template annealed in the same chain as a synthetic starting point,

C) A polymer which anneals an oligonucleotide comprising a complementary base sequence at the 3 'end in the loop located at the 3' end side of the loop at the loop portion, and catalyzes the chain substitution complementary chain synthesis reaction using this as a synthetic starting point. Synthesizing the complementary chain by laase, replacing the complementary chain synthesized in step B), and leaving the 3 'end in a state capable of base pair bonding; and

D) The process of making the new mold in process A) the chain | strand which made the 3 'terminal into base pair bonding possible in the process C)

[10] The amplification method according to [9], wherein the oligonucleotide in step C) has a nucleotide sequence complementary to the 3 'end that is the synthetic starting point in step B) at its 5' side.

[11] The amplification method according to [10], further comprising a step in which the complementary chain synthesized using the oligonucleotide in step C) as a synthetic starting point is used as a template in step A).

[12] The amplification method according to [9], wherein the template in step A) is synthesized by the method of [5].

[13] The method of [1] or [9], wherein the chain substitution complementary chain synthesis reaction is performed in the presence of a melting temperature regulator.

[14] The method of [13], wherein the melting temperature modifier is betaine.

[15] The method of [14], wherein 0.2 to 3.0 M of betaine is present in the reaction solution.

[16] A method for detecting a target base sequence in a sample by performing the amplification method according to any one of [9] to [15], and observing whether an amplification reaction product has occurred.

[17] The method of [16], wherein the hybridization is observed by adding a probe containing a nucleotide sequence complementary to the loop to the amplification reaction product.

[18] The method of [17], wherein the probe is labeled with particles and the aggregation reaction caused by hybridization is observed.

[19] The method of [16], wherein the amplification method according to any one of [9] to [15] is carried out in the presence of a nucleic acid detection agent to observe whether an amplification reaction product has been generated based on the signal change of the detection agent. .

[20] A method for detecting a variation in a target base sequence by the detection method according to [16], wherein the variation in the nucleotide sequence to be amplified interferes with the synthesis of any complementary chain constituting the amplification method.

[21] A kit for synthesizing nucleic acids, in which complementary sequences are alternately linked on a single-stranded chain, including the following elements.

i) Oligonucleotide as described in [3], wherein region F2c of the nucleic acid serving as a template is X2c, and F1c located on the 5 'side of F2c is X1c.

ii) an oligonucleotide comprising a base sequence complementary to any region in the complementary chain synthesized using the oligonucleotide of i) as a primer

iii) an oligonucleotide having a nucleotide sequence complementary to region F3c located on the 3 'side of region F2c of the nucleic acid as a template

iv) a DNA polymerase that catalyzes chain substitution type complementary chain synthesis and

v) nucleotides as substrate of element iv)

[22] The method of [21], wherein the oligonucleotide of ii) is an oligonucleotide of i) as a starting point, and any region R2c in the complementary chain synthesized is X2c, and R1c positioned at 5 'of R2c. The kit is an oligonucleotide of [3], which is referred to as X1c.

[23] The kit of [22], further comprising the following elements.

vi) an oligonucleotide having a base sequence complementary to region R3c located on the 3 'side of any region R2c in the complementary chain synthesized using the oligonucleotide of i) as a synthetic starting point.

[24] A kit for detecting a target base sequence, further comprising a detection agent for detecting a product of a nucleic acid synthesis reaction, further comprising the kit of any of [21] to [23].

In the present invention, a nucleic acid in which complementary nucleotide sequences are alternately linked on a single-stranded chain intended for synthesis means a nucleic acid in which complementary nucleotide sequences are linked to each other on a single-stranded chain. Furthermore, in the present invention, a base sequence for forming a loop between complementary base sequences must be included. In the present invention, this sequence is called a loop formation sequence. The nucleic acid synthesized by the present invention is composed of complementary base sequences linked to each other by the loop forming sequences. In general, regardless of whether or not it partially carries base pair bonds, those which do not separate into two or more molecules when dissociating base pair bonds are called single-stranded chains. Complementary base sequences can form base pair bonds on the same chain. The intramolecular base pairing product obtained by base pairing a nucleic acid alternately complementary with a base sequence on a single-stranded chain according to the present invention is not accompanied by the region constituting the double-stranded chain and the base pairing. Gives the loop part

That is, the nucleic acid in which the complementary base sequences are alternately linked on the single-stranded chain in the present invention includes complementary base sequences that can be annealed on the same chain, and the annealing product does not have a base pair bond to the bent hinge portion. It can also be defined as a single-stranded chain nucleic acid constituting a non-loop. In a loop not accompanied by a base pair bond, nucleotides having complementary base sequences can be annealed. The loop formation sequence may be any base sequence. Base pair binding is possible to initiate complementary chain synthesis for substitution, and preferably has a sequence identifiable from base sequences present in other regions to achieve specific annealing. For example, in a preferred embodiment, the base sequence includes substantially the same base sequence as the region F2c (or R2c) located on the 3 'side of the region (ie, F1c or R1c) annealed on the same chain derived from the nucleic acid that is the template. .

In the present invention, substantially identical nucleotide sequences are defined as follows. In other words, when the complementary chain synthesized using any sequence as a template anneals to the target base sequence to give the starting point of the complementary chain, the sequence is substantially identical to the target base sequence. For example, a substantially identical nucleotide sequence to F2 includes a nucleotide sequence that functions as a template that gives an nucleotide sequence that can be an annealing chain of the complementary chain by annealing to F2 in addition to a nucleotide sequence that is exactly the same as F2. The term "annealing" in the present invention means that the nucleic acid forms a double-stranded chain structure by base pair bonds based on Watson-Crick's law. Therefore, even if the nucleic acid chain constituting the base pair bond is a single stranded chain, annealing is performed when the complementary base sequences in the molecule form the base pair bond. In the present invention, annealing and hybridization have the same meaning in that a nucleic acid forms a double-stranded chain structure by base pair bonds.

The number of complementary base sequences constituting the nucleic acid according to the present invention is at least one pair. According to the preferable aspect of this invention, this integer multiple may be sufficient. In this case, theoretically, there is no upper limit to the number of complementary base sequence pairs constituting the nucleic acid in the present invention. When a nucleic acid that is a synthetic product of the present invention is composed of a plurality of pairs of complementary base sequences, the nucleic acids are repeated in the same base sequence.

A nucleic acid in which complementary nucleotide sequences are alternately linked on a single-stranded chain synthesized by the present invention does not necessarily have to have the same structure as a natural nucleic acid. It is known that a nucleic acid derivative can be synthesized by using a nucleotide derivative as a substrate when synthesizing the nucleic acid by the action of the nucleic acid polymerase. As such nucleotide derivatives, nucleotides labeled with radioisotope, nucleotide derivatives labeled with a binding ligand such as biotin or digoxin can be used. By using these nucleotide derivatives, labeling of the nucleic acid derivative as a product is achieved. In addition, by using fluorescent nucleotides as a substrate, a nucleic acid as a product can be used as a fluorescent derivative. Furthermore, this product may be DNA or RNA. Which is produced is determined by the structure of the primer, the type of substrate for the polymerization, and the combination with the polymerization reagent for polymerizing the nucleic acid.

The synthesis of the nucleic acid having the above structure comprises a DNA polymerase having chain substitution activity and a region F1 capable of annealing to some F1c on the same chain at the 3 'end, and this region F1 is annealed to F1c on the same chain. In this way, it is possible to start with a nucleic acid capable of forming a loop including the region F2c capable of base pair binding. Although there are many reports of complementary chain synthesis reactions in which a hairpin loop is formed to form a template, the present invention includes a region for allowing base pair bonding to the hairpin loop portion, and this region is used for the complementary chain synthesis. It is new in that it is. By using this region as a starting point for synthesis, the complementary chain synthesized using itself as a template is first substituted. The region R1c (optional region) present on the 3 'side of the substituted chain is in a state capable of base pair bonding. The region having a base sequence complementary to R1c can be annealed to perform complementary chain synthesis. As a result, the nucleotide sequence from F1 to R1c and its complementary chain are alternately bound to each other via a loop forming sequence. Is generated. In the present invention, for example, a region arbitrarily selected such as R1c can anneal a polynucleotide having a nucleotide sequence complementary to the region, and a complementary chain synthesized using the polynucleotide as a synthetic starting point is seen. As long as it has the function required for invention, it can select from arbitrary areas.

Furthermore, in the present invention, the term nucleic acid is used. In the present invention, a nucleic acid generally includes both DNA and RNA. However, even if constituent nucleotides are substituted with artificial derivatives or natural DNA or RNA is modified, they are included in the nucleic acid of the present invention as long as they function as templates for complementary chain synthesis. The nucleic acid of the present invention is generally included in a biological sample. Biological samples may refer to tissues, cells, cultures, feces or extracts of animals, plants or microorganisms. The biological sample of the present invention includes genomic DNA or RNA of an intracellular parasite such as a virus or mycoplasma. The nucleic acid of the present invention may be derived from a nucleic acid contained in the biological sample. For example, cDNA synthesized on the basis of mRNA and nucleic acid amplified based on a nucleic acid derived from a biological sample are typical of nucleic acids in the present invention.

A loop comprising a region F2c capable of base pair bonding by having a region F1 at the 3 'end capable of annealing to some F1c on the same chain and annealing to F1c on the same chain, characterized by the present invention Nucleic acid that can be formed can be obtained by various methods. In the most preferable aspect, the structure can be provided based on the complementary chain synthesis reaction using the oligonucleotide which has the following structure.

In other words, an oligonucleotide useful in the present invention is an oligonucleotide composed of at least two regions X2 and X1c below and X1c is linked to the 5 'side of X2.

X2: region of nucleic acid having a specific nucleotide sequence region having a nucleotide sequence complementary to X2c

X1c: region having a base sequence substantially the same as region X1c located on the 5 'side of region X2c in a nucleic acid having a specific base sequence

Here, the nucleic acid which has a specific base sequence which determines the structure of the oligonucleotide of this invention means the nucleic acid used as the template when using the oligonucleotide of this invention as a primer. In the case of detecting a nucleic acid based on the synthesis method of the present invention, a nucleic acid having a specific nucleotide sequence is a nucleic acid derived from or to be detected. Nucleic acid having a specific base sequence is at least a part of the base sequence is clear. Or nucleic acid in a state where speculation is possible. The part which should make clear the nucleotide sequence is the said area | region X2c and the area | region X1c located in the 5 'side. These two regions can assume the case where they are continuous and when they exist apart. The relative positional relationship between the two determines the state of the loop portion formed when the product nucleic acid is self-annealed. Moreover, in order that the nucleic acid which is a product preferentially performs magnetic annealing rather than intermolecular annealing, it is preferable that the distance of both does not unnecessarily fall. Therefore, it is preferable that the positional relationship between the two is usually continued with a distance of 0-500 bases therebetween. However, in the formation of a loop by magnetic annealing described later, in a case where both approaches too much, a case which is disadvantageous to form a loop in a preferable state is also expected. In the loop, a structure capable of smoothly initiating a complementary chain synthesis reaction involving annealing of new oligonucleotides and chain substitution using the synthetic oligonucleotide as a starting point thereof is required. Therefore, More preferably, the distance between the area X2c and the area X1c located on the 5 'side is designed to be 0 to 100 bases, and more preferably 10 to 70 bases. In addition, this figure has shown the length which does not contain X1c and X2. The number of bases constituting the loop portion is further the length of the region corresponding to X2.

In addition, the same or complementary terms used for characterizing the nucleotide sequences constituting the oligonucleotide based on the present invention do not mean to be completely identical or completely complementary. That is, the same as any sequence may include a sequence complementary to the base sequence that can be annealed to any sequence. On the other hand, complementary means a sequence that can be annealed under stringent conditions and can provide a 3 'end that is a synthetic starting point of the complementary chain.

The regions X2 and X1c constituting the oligonucleotide according to the present invention with respect to the nucleic acid having the specific nucleotide sequence are usually arranged continuously so as not to overlap. Alternatively, if there is a common part in the nucleotide sequence of both, it may be arranged partially overlapping. Since X2 needs to function as a primer, it must always be at the 3 'end. On the other hand, X1c is arranged at the 5 'end because it is necessary to impart the function as a primer to the 3' end of the complementary chain synthesized as a template, as described later. The complementary chain obtained by using this oligonucleotide as a synthetic starting point forms a template for synthesis of the complementary chain from the reverse side in the next step, and finally the oligonucleotide portion according to the present invention is also copied into the complementary chain as a template. The 3 'end produced by copying has the base sequence X1, anneals to X1c on the same chain, and forms a loop.

In the present invention, an oligonucleotide means that two conditions are satisfied: one capable of forming complementary base pair bonds and giving -OH groups, which are the synthetic starting point of the complementary chain, at the 3 'end thereof. Therefore, the backbone is not necessarily limited to those by phosphodiester bonds. For example, the phosphothioate body using S as the backbone and the peptide nucleic acid based on peptide bonds may be used instead of O. The base may be any one that enables complementary base pair bonding. In the natural state, there are generally five kinds of ACTG and U, but an analogue such as bromodeoxyuridine may be used. It is preferable that the oligonucleotide used for this invention not only becomes a starting point of a synthesis, but also functions as a template of a complementary chain synthesis. In addition, in this invention, polynucleotide is used as a term containing an oligonucleotide. The term polynucleotide is used when the chain length is not limited, and oligonucleotide is used as a term meaning a nucleotide polymer having a relatively short chain length.

In the various nucleic acid synthesis reactions described below, the oligonucleotides of the present invention have a chain length such that base pair bonds with the complementary chain can be performed while maintaining the required specificity under a given environment. Specifically, it is 5-200 bases, More preferably, it is 10-50 base pairs. Since the chain length of the primer recognized by a known polymerase catalyzing the sequence dependent nucleic acid synthesis reaction is about 5 bases, the chain length of the annealing portion needs to be more than that. In addition, in order to expect specificity as a nucleotide sequence, it is preferable to use the length more than 10 bases. On the other hand, since an excessively long base sequence is difficult to prepare by chemical synthesis, such a chain length is illustrated as a preferable range. In addition, the chain length illustrated here is the chain length of the part which anneals with a complementary chain to the last. As will be described later, oligonucleotides according to the invention can finally anneal individually to at least two regions. Therefore, the chain length exemplified herein should be understood as the chain length of each region constituting the oligonucleotide.

Furthermore, the oligonucleotide of the present invention can be labeled with a known labeling substance. As the label, a binding ligand such as digoxin or biotin, an enzyme, a fluorescent substance or a luminescent substance, a radioisotope, or the like can be represented. In addition, a technique for replacing the base constituting the oligonucleotide with a fluorescent analog (WO 95/05391, Proc. Natl. Acad. Sci. USA, 91, 6644-6648, 1994) is also known.

In addition, the oligonucleotide according to the present invention may be bound to itself in a solid phase. In addition, any part of the oligonucleotide may be labeled with a binding ligand such as biotin, and this may be indirectly solidified by a binding partner such as solidifying avidin. In the case where the solidified oligonucleotide is used as the starting point of the synthesis, since the reaction product of the nucleic acid synthesis reaction is trapped in the solid phase, the separation becomes easy. Detection of the isolated product can be performed by hybridizing a nucleic acid specific indicator or a labeled probe. In addition, by digesting with any restriction enzyme, a fragment of the nucleic acid of interest can also be recovered.

The term template used in the present invention means a nucleic acid on the side of the template for complementary chain synthesis. The complementary chain having a nucleotide sequence complementary to the template has a meaning as a chain corresponding to the template, but the relationship between the two is only relative. That is, the chain synthesize | combined as a complementary chain can function as a template again. That is, the complementary chain can be a template.

Oligonucleotides useful in the present invention may comprise not only these two regions, but also additional regions. While X2 and X1c are arranged at the 3 'end and the 5' end, respectively, it is possible to intervene any sequence between them. It may be, for example, a restriction enzyme recognition sequence, a promoter recognized by an RNA polymerase, or a DNA encoding a ribozyme. By using the restriction enzyme recognition sequence, nucleic acids complementarily linked with complementary nucleotide sequences on a single stranded chain which is a synthetic product of the present invention can be cut into double stranded chain nucleic acids having the same length. By arranging the promoter sequences recognized by the RNA polymerase, transcription to RNA is further performed using the synthetic product of the present invention as a template. At this time, by arranging the DNA encoding the ribozyme, a system for cutting the transcription product by itself is realized. In addition, these subsidiary nucleotide sequences function when they are all double stranded chains. Therefore, when the nucleic acid of the single-stranded chain according to the present invention forms a loop, these sequences do not function. When the nucleic acid is elongated and annealed with a chain having complementary nucleotide sequences in a state that does not include a loop, it functions.

When the promoter is combined with the oligonucleotide based on the present invention in a direction that enables the transcription of the synthesized region, the reaction product based on the present invention repeating the same nucleotide sequence realizes a highly efficient transcription system. By combining this with a suitable expression system, translation into a protein is also possible. That is, it can be used for transcription and translation into proteins in bacteria or animal cells or in vitro.

The oligonucleotide according to the present invention having the above structure can be synthesized chemically. In addition, the natural nucleic acid can be cleaved with a restriction enzyme or the like, and modified or linked to be composed of the above nucleotide sequences.

Using the oligonucleotides useful in the method for synthesizing the nucleic acid according to the present invention, a reaction is performed in combination with a DNA polymerase having a chain substitution activity. Explain. The oligonucleotide (FA in Fig. 5) is first annealed to a nucleic acid on which X2 (corresponding to F2) is a template to form a starting point of the complementary chain. In Fig. 5, the complementary chain synthesized from FA is replaced by the complementary chain synthesis (described later) from the outer primer (F3) to form a single stranded chain (Fig. 5-A). When the complementary chain synthesis is further performed on the obtained complementary chain, the 3 'terminal portion of the nucleic acid synthesized as the complementary chain in Fig. 5-A has a nucleotide sequence complementary to the oligonucleotide of the present invention. That is, since the oligonucleotide of the present invention has the same sequence as the region X1c (corresponding to F1c) at its 5 'end, the 3' end of the nucleic acid synthesized at this time has its complementary sequence X1 (F1). . Fig. 5 shows a state in which the complementary chain synthesized from R1 is replaced by the complementary chain synthesis starting from the outer primer R3. When the 3 'end becomes a state capable of base pair bonding by substitution, X1 (F1) at the 3' end is annealed to X1c (F1c) on the same chain, and an elongation reaction using magnetization proceeds (Fig. 5). -B). And X2c (F2c) located in the 3 'side is left as a loop which does not accompany base pair bond. In this loop, X2 (F2) of the oligonucleotide of the present invention is annealed, and a complementary chain synthesis is performed using this as a starting point for synthesis (Fig. 5-B). At this time, the product of the complementary chain synthesis reaction which uses the synthesize | combined self as a template first is substituted by chain substitution reaction, and it becomes a state which can base-pair bond.

A plurality of oligonucleotides according to the present invention, and a plurality of as shown in Fig. 6 by a basic configuration using any reverse primer capable of performing nucleic acid synthesis using the complementary chain synthesized using the oligonucleotide as a primer as a template. Nucleic acid synthesis products can be obtained. As can be seen from FIG. 6, (D) is a nucleic acid in which complementary nucleotide sequences are alternately linked on a single-stranded chain for synthesis purposes in the present invention. The other product (E) becomes a template for producing (D) again when it becomes single stranded chain by processing, such as heat denaturation. Also, if the product (D), which is a nucleic acid in a double-stranded chain, becomes a single-stranded chain by heat denaturation or the like, the original double-stranded chain does not become the original double-stranded chain, and annealing occurs in the same chain with a high probability. This is because in the complementary sequence having the same melting temperature (Tm), the intramolecular reaction proceeds more preferentially than the intermolecular reaction. Single-stranded chains derived from the product (D) annealed on the same chain are each annealed in the same chain and return to the state of (B), so that each molecule (D) and (E) Grant. By repeating these steps, it is possible to sequentially synthesize nucleic acids in which complementary nucleotide sequences are alternately linked on a single-stranded chain. The exponential increase in the template and product produced in one cycle results in a very efficient reaction.

By the way, in order to implement | achieve the state of FIG. 5- (A), a base pair coupling | bonding must be enabled at least in the part which the reverse primer anneals the complementary chain synthesize | combined initially. This step can be achieved by any method. That is, an outer primer (F3) annealed to the region F3c on the 3 'side is prepared separately from the region F2c to which the oligonucleotide of the present invention anneals to the first template. When the complementary chain is synthesized by a polymerase that catalyzes the chain substitution type complementary chain synthesis using the outer primer as a synthetic starting point, the complementary chain synthesized using the F2c of the present invention as the synthesis starting point is replaced, and then R1 is The region R1c to be annealed is allowed to have a base pair bond (FIG. 5). By using a chain substitution reaction, the reaction so far can be advanced under isothermal conditions.

In the case of using an outer primer, the synthesis from the outer primer (F3) needs to be started after the synthesis from F2c. The simplest method is to make the inner primer concentration higher than the outer primer concentration. Specifically, by using a primer at a concentration difference of 2 to 50 times, preferably 4 to 10 times, the reaction as expected can be performed. The synthesis timing can also be adjusted by setting the melting temperature (Tm) of the outer primer to be lower than the Tm of the X1 (corresponding to F1 or R1) region of the inner primer. That is, (outer primer F3: F3c) ≤ (F2c / F2) ≤ (F1c / F1) or (region on the 3 'side in the outer primer / template) ≤ (X2c: X2) ≤ (X1c: X1) . Note that (F2c / F2) ≤ (F1c / F1) is used to allow annealing between F1c / F1 before F2 anneals to the loop portion. Annealing between F1c / F1 is likely to proceed preferentially because it is an intramolecular reaction. However, it is meaningful to consider Tm to give more desirable reaction conditions. It goes without saying that the same conditions should be considered in the design of the reverse primer. By setting it as such a relationship, it is possible to achieve ideally ideal reaction conditions. The melting temperature (Tm) can be theoretically calculated by the combination of the length of the complementary chain to be annealed and the base constituting the base pair bond, if other conditions are constant. Thus, those skilled in the art can easily lead to the preferred conditions based on the disclosure herein.

Furthermore, in order to adjust the annealing timing of the outer primer, a phenomenon called contiguous stacking may be applied. Contiguous stacking is a phenomenon in which annealing is possible by adjoining a double-stranded chain portion of an oligonucleotide that cannot be annealed alone (Chiara Borghesi-Nicoletti et al. Bio Techniques 12, 474-477 (1992)). In other words, the outer primer is adjacent to F2c (X2c) and designed so that it cannot be annealed alone. This makes it possible to anneal the outer primer for the first time when F2c (X2c) is annealed, so that annealing of F2c (X2c) is inevitably given priority. Based on this principle, the example which set the base sequence of the oligonucleotide required as a primer for a series of reaction is described in the Example. This process can also be accomplished by warming denaturation or DNA helicase.

When the template nucleic acid having F2c (X2c) is RNA, the state of Fig. 5- (A) can be realized by another method. For example, when this RNA chain is decomposed, R1 is in a state capable of base pair binding. That is, F2 is annealed to F2c of RNA and complementary chain synthesis | combination is performed as DNA by reverse transcriptase. Subsequently, when RNA that has been templated is degraded by alkali denaturation or enzymatic treatment with a ribonuclease that acts on the RNA of the DNA / RNA double stranded chain, the DNA synthesized from F2 becomes a single stranded chain. As an enzyme that selectively degrades RNA of DNA / RNA double-stranded chains, ribonuclease activity provided with RNaseH and some reverse transcriptases can be used. In this way, the reverse primer can be annealed to R1c which enabled base pair bonding. Therefore, there is no need for an outer primer to make R1c base-bondable.

Alternatively, the chain substitution by the outer primer described above can be performed using the chain substitution activity of the reverse transcriptase. In this case, only the reverse transcriptase can constitute the reaction system. That is, the complementary chain synthesis from F2 annealed to the F2c using RNA as a template, and the complementary chain synthesis and substitution using the outer primer F3 annealed to F3c located on the 3 'side as the starting point, are reverse transcriptases. It becomes possible. If the reverse transcriptase performs the complementary chain synthesis reaction using DNA as a template, the complementary chain synthesis using R1 annealed to the R1c using the substituted complementary chain as a template and the annealing to R3c located on the 3 'side All complementary chain synthesis reactions are carried out by reverse transcriptase, including complementary chain synthesis and substitution reactions based on R3. Alternatively, when the DNA / DNA chain substitution activity cannot be expected from the reverse transcriptase under the obtained reaction conditions, the above-described DNA polymerase having a chain substitution activity may be used in combination. As mentioned above, the aspect which obtains a 1st single-stranded chain nucleic acid using RNA as a template comprises the preferable aspect in this invention. Conversely, even if a DNA polymerase such as Bca DNA polymerase having chain substitution activity and reverse transcriptase activity is used, not only the synthesis of the first single-stranded chain nucleic acid from RNA but also the subsequent DNA The reaction used as a template can also be performed by the same enzyme.

The reaction system described above causes various variations inherent in the present invention by using those having a specific structure as the reverse primer. The most effective variations are described below. In other words, in the most advantageous aspect of the present invention, an oligonucleotide having a structure as described in [5] is used as the reverse primer. The oligonucleotide of [5] is an oligonucleotide in which arbitrary region R2c in the complementary chain synthesized with F2 as a primer is X2c and R1c is X1c. By using such a reverse primer, a series of reactions, such as formation of a loop and complementary chain synthesis and substitution from the loop portion, occur in both the sense chain and the antisense chain (forward side and reverse side). As a result, the synthesis efficiency of the nucleic acid synthesis method in which complementary nucleotide sequences are alternately linked on the single-stranded chain according to the present invention is remarkably improved, and a series of reactions can be performed isothermally. Below, it demonstrates concretely based on FIG. 1-3 which summarized this aspect.

In the following aspect, two types are prepared as an oligonucleotide based on this invention. To illustrate this, we call them FA and RA. The area constituting FA and RA is as follows.

X2X1c

FAF2F1c

RAR2R1c

Here, F2 is a nucleotide sequence complementary to the region F2c of the nucleic acid to be a template. R2 is a base sequence complementary to any region R2c included in the complementary chain synthesized with F2 as a primer. F1c and R1c are any base sequences located downstream of F2c and R2c, respectively. The distance between F2-R2 may be arbitrary here. Although it depends on the synthesis | combining ability of the DNA polymerase which performs a complementary chain synthesis, even if it is about 1 kbp in length, it can fully synthesize | combine. More specifically, when Bst DNA polymerase is used, it is surely synthesized if it is 800 bp, preferably 500 bp or less, between F2 / R2c. In PCR with a temperature cycle, the degradation of enzyme activity due to temperature change stress lowers the synthesis efficiency of long sequences. In a preferred embodiment of the present invention, since the temperature cycle in the nucleic acid amplification step is not necessary, synthesis and amplification can be reliably achieved even with a long base sequence.

First, F2 of FA is annealed to the nucleic acid used as a template, and complementary chain synthesis is performed using this as a synthetic starting point. Hereinafter, up to (4) of FIG. 1, the reaction process is the same as that of the basic aspect (FIG. 5) of this invention demonstrated previously. The sequence annealed as F3 in FIG. 1 (2) is the outer primer demonstrated previously. By carrying out this primer with the DNA polymerase which synthesize | combines a chain substitution type complementary chain synthesis from a synthetic origin, the complementary chain synthesize | combined from FA is substituted and it becomes the state which can base-pair bond.

When R2c is in a state where base pair bond is possible in (4), RA as a reverse primer is annealed by a combination of R2c / R2. Complementary chain synthesis which uses this as a synthetic starting point is performed to the part which reaches F1c which is the 5 'side terminal of FA. Subsequent to this complementary chain synthesis reaction, the replacement outer primer R3 is also annealed, and the complementary chain synthesis is performed with chain substitution, thereby replacing the complementary chain synthesized using RA as a synthetic starting point. The complementary chain substituted at this time has RA at the 5 'side, and the sequence complementary to FA is located at the 3' end.

On the 3 'side of the substituted single-stranded nucleic acid, there is a sequence F1 complementary to F1c on the same chain. F1 anneals rapidly to F1c arranged in the same molecule, and the complementary chain synthesis starts. When the 3 'end (F1) is annealed to F1c on the same chain, a loop including F2c is formed. It is also apparent from Fig. 2- (7) that the loop portion remains in a state capable of base pair bonding. The oligonucleotide FA of the present invention having a base sequence complementary to F2c is annealed to this loop portion to be the starting point of the complementary chain (7). The complementary chain synthesis from the loop portion proceeds while substituting the reaction product of the complementary chain synthesis from F1 described above. As a result, the complementary chain synthesize | combined using itself as a template will be in the state which can base-bond couple at the 3 'end again. This 3 'end has a region R1 that can anneal to R1c on the same chain at the 3' end, and both are preferentially annealed by rapid reaction in the same molecule. In this way, the reaction similar to the reaction from the 3 'terminal synthesize | combined using the FA demonstrated previously as a template advances also in this area | region. As a result, nucleic acids in which complementary nucleotide sequences are alternately linked on the single-stranded chain according to the present invention continue to complement and synthesize complementary chains, and continue to elongate at the 3 'terminal R1. Since the loop formed by annealing to the same chain of the 3 'terminal R1 always includes R2c, annealing to the loop portion of the 3' terminal in subsequent reactions always results in an oligonucleotide with R2 (ie RA).

On the other hand, with respect to a nucleic acid of a single-stranded chain that continues elongation using itself as a template, and focuses on a nucleic acid synthesized from a complementary chain by synthesizing an oligonucleotide that is annealed to the loop portion thereof as a synthetic starting point, the single-stranded according to the present invention Synthesis of nucleic acids in which complementary nucleotide sequences are alternately linked on a chain is progressing. That is, the complementary chain synthesis from the loop portion is completed, for example, in FIG. 2- (7) when the RA reaches. Then, when the nucleic acid substituted by the synthesis of the nucleic acid initiates the complementary chain synthesis (Fig. 3- (8)), the reaction reaches the loop portion that was previously the starting point of synthesis, and the substitution starts again. In this way, the nucleic acid which started synthesis | combination from a loop part is also substituted and, as a result, the 3 'terminal R1 which can be annealed on the same chain is obtained (FIG. 3- (10)). This 3 'terminal R1 anneals to R1c of the same chain to initiate the complementary chain synthesis. Rereading F and R of this reaction is the same as the reaction occurring in Fig. 2- (7). Therefore, the structure shown in FIG. 3- (10) can function as a new nucleic acid which continues its kidney and production | generation of a new nucleic acid.

In addition, the synthesis reaction of the nucleic acid starting from the nucleic acid shown in Fig. 3- (10) always results in elongation having the 3'-terminal F1 as the starting point of synthesis, as opposed to that described above. In other words, in the present invention, the reaction of continuously supplying a new nucleic acid which starts elongation separately with the extension of one nucleic acid proceeds. Moreover, as the chain is stretched, a plurality of loop formation sequences are caused on the same chain as well as the ends. When the loop formation sequence is in a state where base pairs can be formed by a chain substitution synthesis reaction, the oligonucleotides are annealed to become a starting point for a reaction for generating a new nucleic acid. By combining not only the terminal but also the synthetic reaction from the middle of the chain, a more efficient amplification reaction is achieved. As described above, by combining the oligonucleotide RA based on the present invention as a reverse primer, generation of the kidney and a new nucleic acid accompanying it occur. Furthermore, in the present invention, this newly generated nucleic acid itself is elongated, resulting in the production of further new nucleic acid accompanying it. The series of reactions can, in theory, continue permanently to achieve extremely efficient amplification of the nucleic acid. In addition, the reaction of the present invention can be carried out under isothermal conditions.

The reaction product accumulated at this time has a structure in which the base sequence between F1-R1 and its complementary sequence are alternately connected. However, at both ends of the sequence of repeating units, a region consisting of the base sequence of F2-F1 (F2c-F1c) or R2-R1 (R2c-R1c) is contiguous. For example, in FIG. 3- (9), the state is connected from the 5 'side in order of (R2-F2c)-(F1-R2c)-(R1-F1c)-(F2-R2c). This is because the amplification reaction based on the present invention starts from F2 (or R2) with the oligonucleotide as the synthetic starting point, and then the complementary chain synthesis reaction from F1 (or R1) with its 3 'end as the starting point. This is because the process proceeds under the principle of being elongated by.

As the most preferred embodiment, the oligonucleotides FA and RA according to the present invention were used for the oligonucleotides annealed to the loop portion. However, the amplification reaction of nucleic acids according to the present invention can be carried out by using not only oligonucleotides having these limited structures but also oligonucleotides capable of initiating complementary chain synthesis from loops. That is, the 3 'end which continues to stretch is given a loop part again only if it is replaced by the complementary chain synthesis | combination from a loop. Complementary chain synthesis starting from the loop portion always uses a nucleic acid whose complementary nucleotide sequences are alternately linked on a single-stranded chain, and thus, it is obvious that the nucleic acid of the present invention can be synthesized. However, the nucleic acid synthesized here forms a loop after substitution and performs complementary chain synthesis. However, since the nucleic acid does not have a 3 'end for forming a subsequent loop, it cannot function as a new template. Therefore, exponential amplification cannot be expected unlike nucleic acids that have been synthesized by FA or RA. For this reason, oligonucleotides having structures such as FA and RA are useful for the synthesis of highly efficient nucleic acids based on the present invention.

In a series of reactions, the following components are added to a nucleic acid of a single-stranded chain serving as a template to form a base pair bond that is stable to a base sequence complementary to the base sequences constituting FA and RA, and further enhances enzymatic activity. Proceed with incubation at sustainable temperatures.

Four kinds of oligonucleotides:

FA,

RA,

Outer primer F3,

And outer primer R3,

DNA polymerase which performs chain substitution type complementary chain synthesis,

Nucleotide as a substrate of DNA polymerase

Thus, temperature cycles such as PCR are unnecessary. In addition, the stable base pair bond here means the state in which at least one part of the oligonucleotide which exists in a reaction system can give a synthetic origin of a complementary chain. Preferred conditions that result in stable base pair bonding are, for example, set below the melting temperature (Tm). In general, the melting temperature (Tm) is a temperature at which 50% of nucleic acids having base sequences complementary to each other are in base-coupled state. Setting below the melting temperature (Tm) is not an essential condition of the present invention, but is one of the reaction conditions to be considered in order to achieve a high synthesis efficiency. In the case where the nucleic acid to be a template is a double-stranded chain, it is necessary to at least make the base-pairing possible in the region to be annealed by the oligonucleotide. For this purpose, heat modification is generally performed, but this may be done only once as a pretreatment before the start of the reaction.

This reaction is carried out in the presence of a buffer which gives a suitable pH for the enzymatic reaction, salts necessary for maintaining or annealing the catalytic activity of the enzyme, protecting agent of the enzyme, and furthermore, adjusting agent of melting temperature (Tm) as necessary. As the buffer, those having a neutral to weak alkaline to buffering effect such as Tris-HCl are used. pH is adjusted according to the DNA polymerase used. As the salts, KCl, NaCl, or (NH ₄ ) ₂ SO ₄ and the like are appropriately added to maintain the activity of the enzyme and to adjust the melting temperature (Tm) of the nucleic acid. As the protection agent of the enzyme, bovine serum albumin and sugars are used. Moreover, dimethyl sulfoxide (DMSO) and formamide are generally used as a modifier of melting temperature (Tm). By using a melting temperature (Tm) modifier, the annealing of the oligonucleotide can be adjusted under limited temperature conditions. Furthermore, betaine (N, N, N, -trimethylglycine) and tetraalkylammonium salts are effective for improving chain substitution efficiency by the isostabilize action. Betaine can be expected to promote the nucleic acid amplification reaction of the present invention by addition of 0.2 to 3.0 M, preferably about 0.5 to 1.5 M in the reaction solution. These melting temperature regulators act in the direction of lowering the melting temperature, and empirically set conditions for imparting appropriate stringency and reactivity in consideration of other reaction conditions such as salt concentration and reaction temperature.

In the present invention, it is an important feature that a series of reactions do not proceed unless the positional relationship of a plurality of regions is always maintained. This feature can effectively prevent nonspecific synthesis reactions accompanied by nonspecific complementary chain synthesis. In other words, even if any non-specific reaction has occurred, it leads to a low suppression of the possibility that the product will be a starting material for the subsequent amplification process. In addition, the fact that the progress of the reaction is controlled by more regions leads to the possibility of freely configuring a detection system that enables the precise identification of similar sequences.

This feature can be used to detect genetic variation. In the aspect using the outer primer in this invention, 4 primers in total of 2 types of this outer primer and 2 types of primers which consist of the oligonucleotide of this invention are used. That is, if the six regions included in the four oligonucleotides do not function as designed, the synthesis reaction of the present invention does not proceed. In particular, the sequence of the 3 'end of each oligonucleotide which is a synthetic starting point of a complementary chain, and the 5' end of the X1c region whose complementary sequence is a synthetic starting point is important. Therefore, by designing for the mutation to detect this important sequence, by observing the synthesis reaction product according to the present invention, it is possible to comprehensively analyze the presence or absence of mutations such as deletion or insertion of bases or gene polymorphisms such as SNPs. . More specifically, it is designed so that the base to which a mutation and a polymorphism are anticipated corresponds to the 3 'terminal vicinity of the oligonucleotide used as a synthetic starting point of a complementary chain (in a 5' terminal vicinity when a complementary chain becomes a starting point). If there is a mismatch near or near the 3 'end of the complementary chain synthesis, the complementary chain synthesis of the nucleic acid is significantly inhibited. In the present invention, if the terminal structure in the initial product of the reaction is repeated and the reaction is not carried out, it is not linked to a high amplification reaction. Therefore, even if incorrect synthesis is performed, high amplification does not occur with mismatches because the complementary chain synthesis constituting the amplification reaction is always hindered at any one step. As a result, mismatch effectively suppresses the amplification reaction and finally leads to an accurate effect. That is, the nucleic acid amplification reaction based on the present invention can be said to have a more complete base sequence check mechanism. These features are advantages that are difficult to expect in, for example, the PCR method which performs the amplification reaction in two regions simply.

Furthermore, the region X1c, which characterizes the oligonucleotide used in the present invention, is a synthesis starting point after the complementary sequence is synthesized, and the synthesis reaction using the self as a template is achieved by annealing the sequence X1 in the same chain newly synthesized. Proceed. For this reason, the oligonucleotides do not form a loop, even if they produce so-called primer dimers, which are often a significant problem in the prior art. Therefore, nonspecific amplification due to primer dimer cannot occur in principle, contributing to improvement of reaction specificity.

Further, according to the present invention, the above series of reactions can be performed under isothermal conditions by combining the outer primers represented by F3 (Fig. 1- (2)) or R3 (Fig. 2- (5)). In other words, the present invention provides a method for amplifying a nucleic acid in which complementary nucleotide sequences are alternately linked on a single-stranded chain including the step shown in [9] above. In this way, temperature conditions at which stable annealing occurs between F2c / F2, between R2c / R2, between F1c / F1, and between R1c / R1 are selected, and preferably between F3c / F3 and between R3c / R3 , Annealed by a consortium stacking phenomenon promoted by annealing between F2c / F2 and R2c / R2, respectively.

In the present invention, terms such as synthesis and amplification of nucleic acids are used. Synthesis of a nucleic acid in the present invention means extension of a nucleic acid from an oligonucleotide that has become a synthetic starting point. In addition to the synthesis, when the production of another nucleic acid and the extension reaction of the generated nucleic acid occur continuously, a series of reactions are collectively called amplification.

A single-stranded chain nucleic acid having a region F1 capable of annealing to some F1c on the same chain at the 3 'end, whereby the region F1 is annealed to F1c on the same chain, thereby forming a loop comprising a region F2c capable of base pair binding Is an important component of the present invention. Such single-stranded chain nucleic acid can also be supplied based on the following principle. That is, the complementary chain synthesis is performed based on the primer having the following structure in advance.

5 '-[region X1c annealed to region X1c located in the primer]-[loop forming sequence in base pair bonding possible]-[region X1c]-[region having sequence complementary to template] -3'

In the region having a sequence complementary to the template, two kinds of nucleotide sequences complementary to F1 (primer-FA) and nucleotide sequences complementary to R1c (primer RA) are prepared. The nucleotide sequence constituting the nucleic acid to be synthesized at this time includes a nucleotide sequence from the region F1 to the region R1c and a nucleotide sequence from the region R1 to the region F1c having a nucleotide sequence complementary to the nucleotide sequence. In addition, X1c and X1 which can be annealed inside a primer can be made into arbitrary sequences. However, it is preferable that the sequence of the region X1c / X1 be different between the primers FA and RA.

First, the complementary chain synthesis | combination by the said primer FA is performed from region F1 of template nucleic acid. Subsequently, the region R1c of the synthesized complementary chain is in a state capable of base pair binding, and one primer is annealed thereto to be the starting point of the synthesis of the complementary chain. At this time, since the 3 'end of the synthesized complementary chain has a base sequence complementary to the primer FA constituting the 5' end of the first synthesized chain, it has a region X1 at the 3 'end, which is a region on the same chain. Anneal to X1c and form a loop at the same time. In this way, the characteristic 3 'terminal structure according to the present invention is provided, and the subsequent reaction is that of the previous reaction system shown as the most preferred form. In this case, the oligonucleotide annealed to the loop portion is assumed to have a region X2 complementary to the region X2c existing in the loop at the 3 'end and a region X1 on the 5' side. In the previous reaction system, primers FA and RA were used to synthesize a chain complementary to the template nucleic acid, resulting in a loop structure at the 3 'end of the nucleic acid. This method effectively provides terminal structures characteristic of the present invention with short primers. On the other hand, in this aspect, the whole base sequence which comprises a loop from the beginning as a primer is provided, and the synthesis | combination of a longer primer is needed.

If a nucleotide sequence including a restriction enzyme recognition region is used as the reverse primer, another embodiment according to the present invention can be configured. Based on FIG. 6, the case where a reverse primer contains a restriction enzyme recognition sequence is demonstrated concretely. At the time point of Fig. 6- (D), the nick is generated by the restriction enzyme corresponding to the restriction enzyme recognition site in the reverse primer. Using this nick as a starting point, a chain substitution type complementary chain synthesis reaction is started. Since the reverse primer is located at both ends of the double-stranded chain nucleic acid constituting (D), the complementary chain synthesis reaction is also started at both ends. It is basically based on the principle of the SDA method described in the prior art, but since the base sequence serving as the template has a structure in which the base sequences complementary by the present invention are alternately connected, a nucleic acid synthesis system specific to the present invention is constructed. . In addition, the complementary chain portion of the reverse primer containing the nick should not be designed such that the dNTP derivative is inserted so that it is nuclease resistant so that the double strand chain is not cleaved by restriction enzymes.

The promoter of RNA polymerase can be inserted into the reverse primer. Also in this case, transcription is performed by RNA polymerase that recognizes this promoter from both ends of Fig. 6- (D), similarly to the previous embodiment in which the SDA method is applied.

Since the nucleic acid synthesized according to the present invention is composed of nucleotide sequences complementary to each other even as a single stranded chain, most of them form base pair bonds. Using this feature, detection of synthetic products is possible. When the nucleic acid synthesis method according to the present invention is carried out in the presence of a fluorescent dye which is a double-stranded chain-specific intercalater such as ethidiumbromide, SYBR Green I, or Pico Green, An increase in fluorescence intensity is observed. Monitoring this allows tracking of real-time synthesis reactions in closed systems. Although the detection system of this species is also considered to be applied by the PCR method, there are many problems because it is indistinguishable from generation of a signal by a primer dimer or the like. However, when applied to the present invention, it is very unlikely that nonspecific base pair binding will increase, so high sensitivity and low noise can be expected at the same time. Similarly to the double-stranded chain specific intercalator, as a method of realizing a homogeneous detection system, fluorescence energy transfer can be used.

Supporting the nucleic acid synthesis method of the present invention is a DNA polymerase which catalyzes a chain substitution type complementary chain synthesis reaction. The reaction also includes a reaction step that does not necessarily require a chain substituted polymerase. However, it is advantageous to use one kind of DNA polymerase in terms of simplification and economical efficiency of the constituent reagent. As the DNA polymerase of this species, the followings are known. Various variants of these enzymes can also be used in the present invention as long as they have sequence-dependent complementary chain synthesis activity and chain substitution activity. The variant herein may refer to one obtained only by a structure that results in the catalytic activity required by an enzyme, or one that changes catalytic activity, stability, or heat resistance due to amino acid variation or the like.

Bst DNA Polymerase

Bca (exo-) DNA polymerase

Klenow fragment of DNA polymerase I

Vent DNA Polymerase

Vent (Exo-) DNA polymerase (depletion of exo nuclease activity from Vent DNA polymerase)

DeepVent DNA Polymerase

DeepVent (Exo-) DNA polymerase (depletion of exo nuclease activity from DeepVent DNA polymerase)

φ29 phage DNA polymerase

MS-2 Phage DNA Polymerase

Z-Taq DNA polymerase (casting)

KOD DNA Polymerase (Toyo Boseki)

Among these enzymes, Bst DNA polymerase and Bca (exo-) DNA polymerase are particularly preferred enzymes because they have some heat resistance and high catalytic activity. Although the reaction of this invention can be performed at isothermal temperature in a preferable aspect, it cannot necessarily limit that temperature conditions suitable for the stability of an enzyme can always be used for adjustment of melting temperature (Tm). Therefore, it is one of preferable conditions that an enzyme is heat resistant. In addition, even if the isothermal reaction is possible, heat denaturation may also be performed to provide the nucleic acid which is the first template, and in that regard, the use of the heat-resistant enzyme expands the choice of assay protocol. .

Vent (Exo-) DNA polymerase is an enzyme with high heat resistance along with chain substitution activity. However, it is known that the complementary chain synthesis reaction involving chain substitution by DNA polymerase is promoted by the addition of a single strand binding protein (Paul M. Lizardi et al, Nature Genetics 19, 225-232, July, 1998). By applying this action to the present invention, the effect of promoting the complementary chain synthesis can be expected by adding a single-stranded chain binding protein. For example, for Vent (Exo-) DNA polymerase, T4 gene 32 is effective as a single-stranded chain binding protein.

In addition, in the DNA polymerase having no 3'-5 'exonuclease activity, the phenomenon in which the complementary chain synthesis does not stop at the 5' end of the template but proceeds to the state where one base is extruded is known. have. In the present invention, this phenomenon is not preferable because the sequence at the 3 'end when the complementary chain synthesis reaches the end leads to the start of the next complementary chain synthesis. However, addition of the base to the 3 'end by DNA polymerase becomes A with high probability. Therefore, the sequence may be selected so that the synthesis from the 3 'end starts at A so that dATP is not a problem even if one base is added by mistake. In addition, even if the 3 'end protrudes during the synthesis of the complementary chain, the 3' → 5 'exonuclease activity can be used to digest this to make the blunt end. For example, since a natural VentDNA polymerase has this activity, this problem can be avoided by using in combination with Vent (Exo-) DNA polymerase.

Various reagents required for the method for synthesizing or amplifying the nucleic acid according to the present invention can be packaged in advance and supplied as a kit. Specifically, for the present invention, various oligonucleotides required as primers for complementary chain synthesis or as replacement outer primers, dNTPs as substrates for complementary chain synthesis, DNA polymerases for synthesizing chain substituted complementary chains, and enzymes Kits are provided which consist of buffers which impart suitable conditions for the reaction, and furthermore, reagents necessary for the detection of the synthesis reaction products, as required. In particular, in a preferred embodiment of the present invention, since the addition of reagents is not necessary in the reaction solution, the reagents required for one reaction are supplied in a state in which the reagents are dispensed into the reaction vessel, so that the reaction can be started only by the addition of the sample. can do. By using a light emitting signal or a fluorescence signal, a system capable of detecting a reaction product as it is can be completely abolished after the reaction. This is very preferable for the prevention of contamination.

Nucleic acid synthesized by the present invention, the complementary nucleotide sequence alternately linked on a single-stranded chain, for example, has the following usefulness. First, the advantage is accompanied by a special structure with complementary sequences in one molecule. This feature is expected to facilitate detection. That is, a detection system of nucleic acid which increases or decreases a signal in association with base pair binding to a complementary base sequence is known. For example, a combination of a method using a double-stranded chain-specific intercalator as described above as a detection agent and the like can realize a detection system utilizing the characteristics of the synthetic product of the present invention. In such a detection system, once the synthetic reaction product of the present invention is thermally denatured and returned to the original temperature, intramolecular annealing occurs preferentially, thereby rapidly forming base pair bonds between complementary sequences. On the other hand, even if a nonspecific reaction product is present, since it does not have a complementary sequence in the molecule, it is separated into two or more molecules by thermal denaturation and cannot immediately return to the original double-stranded chain. By adding a heat denaturation step before detection in this way, the noise accompanying the non-specific reaction can be reduced. When a DNA polymerase that is not resistant to heat is used, the heat denaturation step also has the meaning of stopping the reaction, which is advantageous in terms of controlling the reaction time.

The second feature is that it always forms a loop that is in a state capable of base pair binding. The structure of the loop in the state which can base-bond is shown in FIG. As can be seen from FIG. 4, the loop is composed of a base sequence F2c (X2c) capable of annealing primers and a base sequence interposed between F2c-F1c (X1c). The sequence between F2c-F1c (generally, between X2c-X1c) is a nucleotide sequence derived from a template. Therefore, template specific detection can be performed by hybridizing a probe having a nucleotide sequence complementary to this region. In addition, since this region is always in a state capable of base pair bonding, it is not necessary to heat-denature before hybridization. In addition, the base sequence which comprises a loop in the amplification reaction product of this invention can be arbitrary length. Therefore, in the case of hybridizing the probe, ideal reaction conditions can be constructed by avoiding contention between the region to be annealed and the region to be hybridized to the probe.

According to a preferred aspect of the present invention, multiple loops capable of base pair binding on a single stranded nucleic acid chain are brought about. This means that a large number of probes can be hybridized to one molecule of nucleic acid, thereby enabling highly sensitive detection. In addition to sensitivity, it is also possible to detect a nucleic acid based on a special reaction principle such as, for example, an aggregation reaction. For example, when a probe fixed to fine particles such as polystyrene latex is added to the reaction product according to the present invention, aggregation of latex particles is observed in conjunction with hybridization with the probe. By measuring the intensity of aggregation optically, high sensitivity and quantitative observation are possible. In addition, since the aggregation reaction can be visually observed, a reaction system without using an optical measuring device can be configured.

Moreover, the reaction product of the present invention, which can bind many labels per molecule of nucleic acid, also enables chromatographic detection. In the field of immunoassay, the analysis method (immunochromatography method) using the chromatographic medium using the label which can be detected visually is put to practical use. This method is based on the principle of washing an unreacted label component by sandwiching analyte from an antibody immobilized on a chromatographic solution and a label antibody. The reaction product of the present invention makes this principle applicable to the analysis of nucleic acids. In other words, analysis in a chromatographic medium is performed by preparing a labeled probe for a loop portion and trapping it with a capture probe immobilized on a chromatographic medium. The complementary sequence for the loop portion can be used for the capture probe. Since the reaction product of the present invention has a plurality of loop portions, it combines a plurality of labeled probes, resulting in a signal that can be visually recognized.

The reaction product according to the present invention, which always provides a region capable of base pair bonding as a loop, enables various detection systems. For example, a detection system using surface plasmon resonance in which a probe with respect to the loop portion is fixed is possible. In addition, if the probe for the loop portion is labeled with a double-stranded chain specific intercalator, more sensitive fluorescence analysis can be performed. Moreover, the nucleic acid synthesize | combined by this invention can also actively use what forms the loop which can couple base pair to both 3 'side and 5' side. For example, it is designed so that one loop is a part consisting of a common sequence in the normal type and the ideal type, and the other loop is an area in which the difference occurs. By identifying the presence of genes in the probe for the common region, a characteristic assay system can be constructed that checks for abnormalities in the other region. Since the synthesis reaction of the nucleic acid according to the present invention can also proceed at isothermal temperature, it is also an advantage that real time analysis can be performed by a general fluorescent photometer. Until now, the structure of a nucleic acid annealed on the same chain is known. However, nucleic acids having alternating complementary nucleotide sequences on a single-stranded chain obtainable by the present invention are novel in that they include a plurality of loop moieties to which other oligonucleotides can bind base pairs.

On the other hand, it is also possible to use a plurality of loop portions themselves provided by the reaction product according to the present invention as a probe. For example, in a DNA chip, it is necessary to integrate a probe with a high density in a limited region. However, with the current technology, the number of oligonucleotides that can be fixed in a certain area is limited. Therefore, by using the reaction product of the present invention, a plurality of probes capable of annealing can be immobilized at a high density. That is, the reaction product according to the present invention may be fixed on a DNA chip using a probe. After amplification, the reaction product may be fixed by a known method, or the immobilized oligonucleotide may be used as an oligonucleotide in the amplification reaction of the present invention, resulting in an immobilized reaction product. By using the immobilized probe in this way, a large number of sample DNAs can be hybridized in a limited region, and as a result, a high signal can be expected.

Brief description of the drawings

FIG. 1: is a schematic diagram which shows a part (1)-(4) of the reaction principle of a preferable aspect of this invention.

Fig. 2 is a schematic diagram showing a part (5)-(7) of the reaction principle of a preferred embodiment of the present invention.

3 is a schematic diagram showing a part (8)-(10) of the reaction principle of a preferred embodiment of the present invention.

4 is a schematic diagram showing the structure of a loop formed by the single-stranded chain nucleic acid according to the present invention.

FIG. 5: is a schematic diagram which shows a part (A)-(B) of the basic aspect by this invention.

FIG. 6: is a schematic diagram which shows the part (C)-(D) of the basic aspect which concerns on this invention.

Fig. 7 is a diagram showing the positional relationship of the respective nucleotide sequences constituting the oligonucleotide in the target nucleotide sequence of M13mp18.

Fig. 8 is a photograph showing the results of agarose electrophoresis of the product obtained by the method for synthesizing a single stranded chain nucleic acid according to the present invention, using M13mp18 as a template.

Lane 1: XIV size marker

Lane 2: 1 fmol M13mp18 dsDNA

Lane 3: no target

9 is a photograph showing the result of agarose electrophoresis by digesting the product of the nucleic acid synthesis reaction according to the present invention obtained in Example 1 with a restriction enzyme.

Lane 1: XIV size marker

Lane 2: BamHI digest of the purified

Lane 3: PvuII digests of the purified

Lane 4: HindIII digest of the purified

Fig. 10 is a photograph showing the results of agarose electrophoresis of the product obtained by the method for synthesizing the single-stranded chain nucleic acid of the present invention by adding betaine using M13mp18 as a template. 0, 0.5, 1, and 2 represent the betaine concentration (M) added to the reaction liquid. N represents a negative control and -21 represents a concentration of template DNA of 10 ^-21 mol.

Fig. 11 is a diagram showing the positional relationship of each base sequence constituting the oligonucleotide in the target base sequence derived from HBV.

Fig. 12 is a photograph showing the results of agarose electrophoresis of a product obtained by the method for synthesizing a single stranded chain nucleic acid according to the present invention, using HBV-M13mp18 inserted in M13mp18 as a template.

Lane 1: XIV size marker

Lane 2: 1 fmol HBV-M13mp18 dsDNA

Lane 3: no target

Fig. 13 is a photograph showing the result of alkali-modified gel electrophoresis of the product obtained by the method for synthesizing a single stranded chain nucleic acid according to the present invention.

Lane 1: HindIII digestion fragment of lambda phage

Lane 2: the reaction product of Example 1

Lane 3: reaction product of Example 3

Fig. 14 is a photograph showing the results of agarose electrophoresis of the product obtained by the method for synthesizing a single stranded nucleic acid according to the present invention when the concentration of the target M13mp18 is changed. Above is the result of 1 hour of reaction time and below is 3 hours of reaction time.

Lane 1: M13mp18 dsDNA 1 × 10 ^-15 mol / tube

Lane 2: M13mp18 dsDNA 1 × 10 ^-16 mol / tube

Lane 3: M13mp18 dsDNA 1 × 10 ^-17 mol / tube

Lane 4: M13mp18 dsDNA 1 × 10 ^-18 mol / tube

Lane 5: M13mp18 dsDNA 1 × 10 ^-19 mol / tube

Lane 6: M13mp18 dsDNA 1 × 10 ^-20 mol / tube

Lane 7: M13mp18 dsDNA 1 × 10 ^-21 mol / tube

Lane 8: M13mp18 dsDNA 1 × 10 ^-22 mol / tube

Lane 9: no target

Lane 10: XIV size marker

Fig. 15 is a diagram showing the positional relationship of each region with respect to the position of the mutation and the target base sequence. Underlined guanine is substituted with adenine in the variant.

Figure 16 is a photograph showing the result of agarose electrophoresis of the product by the amplification reaction of the present invention.

M: 100 bp ladder (New England Biolabs)

N: No mold (purified water)

WT: Wild mold M13mp18 1 fmol

MT: variant mold M13mp18FM 1 fmol

Fig. 17 is a diagram showing the positional relationship of each base sequence constituting the oligonucleotide in the base sequence encoding the target mRNA.

Fig. 18 is a photograph showing the result of agarose electrophoresis of a product obtained by the method for synthesizing a single stranded chain nucleic acid according to the present invention targeting mRNA.

Best Mode for Carrying Out the Invention

Example 1 Amplification of the Region in M13mp18

Using M13mp18 as a template, a method for synthesizing nucleic acids in which complementary nucleotide sequences are alternately linked on a single-stranded chain according to the present invention was attempted. The primers used for the experiment are four types of M13FA, M13RA, M13F3, and M13R3. M13F3 and M13R3 are outer primers for substituting the first nucleic acid obtained using M13FA and M13RA as a synthetic starting point, respectively. Since the outer primer is a primer which will be the starting point of the complementary chain after M13FA (or M13RA), the outer primer is designed to anneal using the constipation stacking phenomenon in the region adjacent to M13FA (or M13RA). In addition, annealing of M13FA (or M13RA) occurs preferentially, and these primer concentrations were set high.

The base sequences constituting each primer are as shown in the sequence table. The structural features of the primers are summarized below. Moreover, the positional relationship of each area | region with respect to the target base sequence is shown in FIG.

Area on primer 5 'side / 3' area

Same as region F1c of the synthetic complementary chain by M13FAM13FA

Complement to the area F2c / M13mp18

Same as the region R1c of the synthetic complementary chain by M13RAM13RA

Complementary to region R2c of the synthetic complementary chain by C / M13FA

Complementary to F3c adjacent to 3 'side of region F2c of M13F3M13mp18

Complementary to R3c adjacent to 3 'side of region R2c of the synthetic complementary chain by M13R3M13FA

Such primers synthesize a nucleic acid in which the region from M1mp18 region F1c to R1c and its complementary nucleotide sequence are alternately linked on a single stranded chain through a loop forming sequence including F2c. The reaction solution composition for the synthesis method of the nucleic acid according to the present invention by these primers is shown below.

Composition of reaction solution (in 25 μL)

20 mM Tris-HCl pH8.8

10 mM KCl

10 mM (NH ₄ ) ₂ SO ₄

6 mM MgSO ₄

0.1% Triton X-100

5% Dimethylsulfoxide (DMSO)

0.4 mM dNTP

primer :

800 nM M13FA / SEQ ID NO: 1

800 nM M13RA / SEQ ID NO: 2

200 nM M13F3 / SEQ ID NO: 3

200 nM M13R3 / SEQ ID NO: 4

Target: M13mp18 dsDNA / SEQ ID NO: 5

Reaction: The said reaction liquid was heated at 95 degreeC for 5 minutes, the target was denatured and it was set as single stranded chain. The reaction solution was transferred to ice-water, 4U of Bst DNA polymerase (NEW ENGLAND BioLabs) was added, and it was made to react at 65 degreeC for 1 hour. After the reaction, the reaction was stopped at 80 ° C. for 10 minutes and transferred to ice water again.

Confirmation of reaction: 1 μL of loading buffer was added to 5 μL of the reaction solution, and electrophoresis was performed at 80 mV for 1 hour using 2% agarose gel (0.5% TBE). As the molecular size marker, XIV (100 bp ladder, manufactured by Boehringer Mannheim) was used. After gelation, the gel was stained with SYBR Green I (Molecular Probes, Inc.) to confirm the nucleic acid. The results are as shown in FIG. Each lane corresponds to the following sample.

1.XIV size marker

2. 1 fmol M13mp18 dsDNA

3. No target

In lane 3, no band was identified except that the unreacted primers were stained. Lane 2 identified the product as a band of little or no smeared staining at high size and ladder of low size bands when the target was present. Among the low-sized bands, the bands around 290 bp and 450 bp each consisted of double-stranded chains of SEQ ID NO: 11 and SEQ ID NO: 12, which are products expected by the synthesis reaction of the present invention (Fig. 2- ( 7) and FIG. 2- (10) correspond to double stranded chains) and SEQ ID NO: 13 (corresponds to the long single stranded chain in FIG. 3- (9)), so the reaction is expected. It was confirmed that it is progressing as mentioned. High-sized smeared patterns and non-phoretic bands are those in which the reaction product does not have a constant size, and the partial single-stranded chain, or double, because the present reaction is basically a continuous reaction. Since it is accompanied by a complex structure that forms a complex of strand chains, it was thought to give such a result of electrophoresis as a result.

Example 2 Confirmation of Restriction Enzyme Digestion of Reaction Products

Digestion by restriction enzymes was carried out for the purpose of clarifying the structure of nucleic acids in which complementary nucleotide sequences were alternately linked on the single-stranded chain according to the present invention obtained in Example 1. Digestion with restriction enzymes resulted in the fragments of theory, while the high size smear pattern or non-phoretic bands observed in Example 1 disappeared, all of them on the single-stranded chain synthesized by the present invention. It can be assumed that the nucleic acid is alternately linked to the complementary base sequence.

The reaction solution of Example 1 was pooled from 8 tubes (200 µL), and purified after phenol treatment by ethanol precipitation. The precipitate was recovered and redissolved in 200 μL of TE buffer, and the 10 μL was digested with restriction enzymes BamHI, PvuII and HindIII at 37 ° C. for 2 hours. The digest was electrophoresed at 80 mV for 1 hour using 2% agarose gel (0.5% TBE). As the molecular size marker, SUPER LADDER-LOW (100 bp ladder) (manufactured by Gensura Laboratories, Inc.) was used. After gelation, the gel was stained with SYBR Green I (Molecular Probes, Inc.) to confirm the nucleic acid. The results are as shown in FIG. Each lane corresponds to the following sample.

1.XIV size marker

2. BamHI Digest of Purified

3. PvuII Digestion of Purified

4. HindIII Dihydrate of Purified

Here, the nucleotide sequences constituting the amplification product having a relatively short chain length are estimated to be SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, and the like. From these base sequences, the size of each restriction enzyme digestion fragment to be estimated is shown in Table 1. L in the table indicates that the phoretic position is undetermined because it is a fragment including a loop (single strand chain).

Since most of the bands in the micronization changed to the bands of the estimated size after digestion, it was confirmed that the target reaction product was amplified. It has also been shown that there are few nonspecific products.

Example 3 Promotion of Amplification by Addition of Betaine

An experiment was conducted to investigate the effect of nucleic acid amplification by addition of betaine (N, N, N, -trimethylglycine, SIGMA) into the amplification reaction solution. In the same manner as in Example 1, using M13mp18 as a template, a method for synthesizing nucleic acids in which relative base sequences were alternately linked on a single-stranded chain according to the present invention was performed in the presence of various concentrations of betaine. The primer used for the experiment is the same as that used in Example 1. The template DNA amount was ^10-21 mol (M13mp18), and water was used as a negative control. Betaine to be added was added to the reaction solution so as to have a concentration of 0, 0.5, 1, and 2 M. The reaction liquid composition is shown below.

Composition of reaction solution (in 25 μL)

20 mM Tris-HCl pH8.8

4 mM MgSO ₄

0.4 mM dNTPs

10 mM KCl

10 mM (NH ₄ ) ₂ SO ₄

0.1% Triton X-100

primer :

800 nM M13FA / SEQ ID NO: 1

800 nM M13RA / SEQ ID NO: 2

200 nM M13F3 / SEQ ID NO: 3

200 nM M13R3 / SEQ ID NO: 4

Target: M13mp18 dsDNA / SEQ ID NO: 5

The polymerase used, reaction conditions, and electrophoresis conditions after the reaction were the same as those described in Example 1.

The results are shown in FIG. In the reaction in the presence of betaine concentration 0.5 and 1.0 M, the amount of amplification products increased. In addition, the amplification product was not confirmed when increasing to 2.0 M. As a result, it has been shown that the amplification reaction is promoted in the presence of appropriate betaine. In the case of betaine concentration 2M, it was thought that the reason why the amplification product fell was because Tm fell too much.

Example 4 Amplification of HBV Gene Sequence

Using the M13mp18 dsDNA in which the partial sequence of the HBV gene was inserted as a template, the nucleic acid synthesis method according to the present invention was tried. The primers used for the experiment are four types of HB65FA (SEQ ID NO: 6), HB65RA (SEQ ID NO: 7), HBF3 (SEQ ID NO: 8), and HBR3 (SEQ ID NO: 9). HBF3 and HBR3 are outer primers for substituting the first nucleic acid obtained using HB65FA and HB65RA as a synthetic starting point, respectively. Since the outer primer is a primer which will be the starting point of the complementary chain from the back of the HB65FA (or HB65RA), the outer primer is designed to anneal using the contiguous stacking phenomenon in the region adjacent to the HB65FA (or HB65RA). In addition, these primer concentrations were set high so that annealing of HB65FA (or HB65RA) would occur preferentially. The target sequence (430 bp) of the present Example derived from HBV inserted into M13mp18 is shown in SEQ ID NO: 10.

The base sequences constituting each primer are as shown in the sequence table. The structural features of the primers are summarized below. Moreover, the positional relationship of each area | region with respect to the target base sequence is shown in FIG.

Area on primer 5 'side / 3' area

Same as the region F1c of the synthetic complementary chain by HB65FAHB65FA

/ Complementary to area F2c of HBV-M13mp18

Same as the region R1c of the synthetic complementary chain by HB65RAHB65RA

Complementary to region R2c of the synthetic complementary chain by HB65FA

Complementary to F3c adjacent to 3 'side of region F2c of HBF3HBV-M13mp18

Complementary to R3c adjacent to 3 'side of region R2c of the synthetic complementary chain by HBR3HB65FA

By such primers, regions F1c to R1c and their complementary sequences of M13mp18 (HBV-M13mp18) in which partial sequences of the HBV gene were inserted are alternately connected on a single stranded chain through a loop formation sequence including F2c. Nucleic acid is synthesized. The reaction solution was reacted under the same conditions as in Example 1 except for using the primers, and the reaction solution was analyzed by agarose electrophoresis. The results are as shown in FIG. Each lane corresponds to the following sample.

1.XIV size marker

2. 1 fmol HBV-M13mp18 dsDNA

3. No target

Similarly to Example 1, only when the target was present, the product was identified as a ladder of low-sized bands and smeared stains at high sizes and bands that were hardly run in the gel (lane 2). Among the low-sized bands, bands near 310 bp and 480 bp, respectively, match the size of the double-stranded chains of SEQ ID NO: 17 and SEQ ID NO: 18, which are expected products of the present reaction, so that a reaction is expected. It was confirmed that it is going as it is. The large sized smeared pattern and the unmoved band were presumed to be caused by the structure of the synthetic product characteristic of the present invention, as described in the results of Example 1. This experiment confirmed that the present invention can be carried out even if the targets to be amplified are different.

Example 5 Identification of Synthesis Reaction Product Size

In order to confirm the structure of the synthesized nucleic acid based on the present invention, the length was analyzed by electrophoresis under alkaline denaturation conditions. To 5 μL of the reaction solution in the presence of the targets of Examples 1 and 4, 1 μL of alkaline loading buffer was added, respectively, using a 0.7% agarose gel (50 mM NaOH, 1 mM EDTA) for 14 hours. , Electrophoresis at 50 mA. As molecular size markers, lambda phage HindIII digestive fragments were used. After gelation, the gel was neutralized with 1 M Tris pH 8 and stained with SYBR Green I (Molecular Probes, Inc.) to confirm the nucleic acid. The results are shown in FIG. Each lane corresponds to the following sample.

1. HindIII digestive fragment of lambda phage

2. Reaction product of Example 1

3. Reaction product of Example 4

When the reaction product is run under alkaline denaturation conditions, it is possible to check the size in a single-stranded chain state. In Example 1 (lane 2) and Example 4 (lane 3), it was confirmed that the main product is in 2 kbase. In addition, the product according to the present invention was found to extend to at least 6 kbase or more in the range that can be confirmed by this analysis. In addition, it was newly confirmed that the bands which were not run under the undenatured conditions of Example 1 and Example 4 were separated into individual single-stranded chains in a denatured state, and were reduced in size.

Example 6 Confirmation of Target Concentration-dependent Amplification in Amplification of the Region in M-13mp13

The effect of the concentration change of the target on the method for synthesizing the nucleic acid according to the present invention was observed. The nucleic acid synthesis method according to the present invention was carried out under the same conditions as in Example 1 except that the target M13mp18 dsDNA was 0 to 1 fmol and the reaction time was 1 hour and 3 hours. In the same manner as in Example 1, by electrophoresis on 2% agarose gel (0.5% TBE), the nucleic acid was confirmed by SYBR Green I (Molecular Probes, Inc.) staining. As the molecular size marker, XIV (100 bp ladder, Boehringer Mannheim) was used. The results are shown in FIG. 14 (top: reaction time 1 hour, bottom: reaction time 3 hours). Each lane corresponds to the following sample.

1: M13mp18 dsDNA 1 × 10 ^-15 mol / tube

2: M13mp18 dsDNA 1 × 10 ^-16 mol / tube

3: M13mp18 dsDNA 1 × 10 ^-17 mol / tube

4: M13mp18 dsDNA 1 × 10 ^-18 mol / tube

5: M13mp18 dsDNA 1 × 10 ^-19 mol / tube

6: M13mp18 dsDNA 1 × 10 ^-20 mol / tube

7: M13mp18 dsDNA 1 × 10 ^-21 mol / tube

8: M13mp18 dsDNA 1 × 10 ^-22 mol / tube

9: no target

10: XIV size marker

The bands common to each lane seen after the run were stained with unreacted primers. Regardless of the reaction time, no amplification products were observed at all when no target was present. Only in the presence of the target, a staining pattern of the amplified product was obtained, depending on the concentration of the target. In addition, by lengthening the reaction time, it was possible to confirm the amplified product to a lower concentration.

Example 7 Detection of Point Mutations

(1) Preparation of M13mp18FM (variant type)

As target DNA, M13mp18 (wild type) and M13mp18FM (variant type) were used. The production of the mutant M13mp18FM introduced monobasic substitution using LA PCR ™ in vitro Mutagenesis Kit. Then, the sequence was confirmed by sequencing. The sequence in the F1 region is shown below.

Wild type: CCGGGGATCCTCTAGAGTCG (SEQ ID NO .: 19)

Variant: CCGGGGATCCTCTAGAGTCA (SEQ ID NO: 20)

(2) design of primer

The primer to be used was made to have a base different in sequence from the wild type and the mutant type at the 5 'end of the F1c region of the FA primer. The positional relationship of each region with respect to the position of the variation and the target base sequence is shown in FIG. 15.

(3) amplification reaction

Using M13mp18 (wild type) and M13mp18FM (variant) as templates, experiments were conducted to determine whether a template-specific amplification reaction occurred with a combination of primers specific for each of the following.

Primer set for wild type amplification: FAd4, RAd4, F3, R3

Primer set for variant amplification: FAMd4, RAd4, F3, R3

The base sequence of each primer is as follows.

FAd4: CGACTCTAGAGGATCCCCGGTTTTTGTTGTGTGGAATTGTGAGCGGAT (SEQ ID NO: 21)

FAMd4: TGACTCTAGAGGATCCCCGGTTTTTGTTGTGTGGAATTGTGAGCGGAT (SEQ ID NO: 22)

RAd4: CGTCGTGACTGGGAAAACCCTTTTTGTGCGGGCCTCTTCGCTATTAC (SEQ ID NO: 23)

F3: ACTTTATGCTTCCGGCTCGTA (SEQ ID NO .: 24)

R3: GTTGGGAAGGGCGATCG (SEQ ID NO: 25)

(4) Detection of point mutations in M13mp18

The composition of the reaction solution is as follows.

1 fmol (2 µl) of target M13mp18 or M13mp18FM was added to the reaction solution, and heated at 95 ° C for 5 minutes to denature the target to form a single stranded chain. The reaction solution was transferred to ice water, and 1 µL (8 U) of Bst DNA polymerase (NEW ENGLAND BioLabs) was added, followed by reaction at 68 ° C or 68.5 ° C for 1 hour. After the reaction, the reaction was stopped at 80 ° C. for 10 minutes and transferred again to ice water.

As shown in Fig. 16, when wild type FAd4 was used as the FA primer, amplification was effectively observed only in the presence of the wild type template. On the other hand, when mutant FAMd4 was used as the FA primer, amplification was effectively observed only in the presence of the wild type template.

From the above results, it was shown that the point mutation can be efficiently detected by using the amplification reaction of the present invention.

Example 8 Amplification Reaction Targeting mRNA

A nucleic acid synthesis method according to the present invention was attempted as a target nucleic acid as mRNA. The target mRNA is a prostate cancer cell line LNCaP cell (ATCC No. CRL-1740), a cell expressing prostate specific antigen (PSA), and a chronic myeloid leukemia cell line K562 cell (ATCC No. CCL-243) was mixed at 1:10 ⁶ to 100: 10 ⁶ , and total RNA was extracted using RNeasy Mini kit from Qiagen (Germany). The primers used for the experiment are four types, PSAFA, PSARA, PSAF3, and PSAR3. PSAF3 and PSAR3 are outer primers for substituting the first nucleic acid obtained using PSAFA and PSARA as a synthetic starting point, respectively. In addition, these primer concentrations were set high so that annealing of PSAFA (or PSARA) would occur preferentially. The base sequences constituting each primer are as follows.

primer :

PSAFA: TGTTCCTGATGCAGTGGGCAGCTTTAGTCTGCGGCGGTGTTCTG (SEQ ID NO .: 26)

PSARA: TGCTGGGTCGGCACAGCCTGAAGCTGACCTGAAATACCTGGCCTG (SEQ ID NO: 27)

PSAF3: TGCTTGTGGCCTCTCGTG (SEQ ID NO: 28)

PSAR3: GGGTGTGGGAAGCTGTG (SEQ ID NO .: 29)

The structural features of the primers are summarized below. In addition, the positional relationship of each primer with respect to the DNA sequence encoding the target mRNA and the recognition site of restriction enzyme Sau3AI are shown in FIG. 17.

Area on primer 5 'side / 3' area

Same as region F1c of the synthetic complementary chain by PSAFAPSAFA

/ Complementary to region F2c of the target base sequence

Same as the region R1c of the synthetic complementary chain by PSARAPSARA

/ Complementary to region R2c of the synthetic complementary chain by PSAFA

Complementary to F3c adjacent to 3 'side of region F2c of PSAF3 target nucleotide sequence

Complementary to R3c adjacent to 3 'side of region R2c of the synthetic complementary chain by PSAR3PSAFA

The reaction solution composition for the method for synthesizing the nucleic acid according to the present invention is shown below.

Composition of reaction solution (in 25 μL)

20 mM Tris-HCl pH8.8

4 mM MgSO ₄

0.4mM dNTPs

10 mM KCl

10 mM (NH ₄ ) ₂ SO ₄

0.1% Triton X-100

0.8 M betaine

5 mM DTT

1600 nM PSAFA & PSARA Primer

200 nM PSAF3 & PSAR3 Primer

8U Bst DNA Polymerase

100U ReverTra Ace (TOYOBO, Japan)

5 μg pre RNA

All ingredients were mixed on ice. In this experiment, since a target is mRNA (single stranded chain), the process of forming a single stranded chain by heat denaturation is unnecessary. Reaction was performed at 65 degreeC for 45 minutes, and reaction was stopped at 85 degreeC for 5 minutes. After completion of the reaction, 5 μL of the reaction solution was electrophoresed using 2% agarose and detected by SYBR Green I.

The results are shown in FIG. Each lane corresponds to the following sample.

Lane BstRTLNCaP cell count / 10 ⁶ K562

1- + 0

2- + 10

3 + -0

4 + -10

5 ++ 0

6 ++ 1

7 ++ 10

Digested 1 μL of the reaction solution of 8 lane 6 into Sau3AI.

Digested 1 μL of the reaction solution of 9 lane 7 into Sau3AI

10 size marker 100 bp ladder (New England Biolabs)

Without either Bst DNA polymerase or ReverTra Ace, amplification products were not obtained (lanes 1-4). In the presence of both enzymes, amplification products were detected in the presence of LNCaP-derived RNA (lanes 5 to 7). One million K562 cells were also detectable with extracted RNA from one LNCaP (lane 6). The amplified product was digested into fragments of expected size when digested with the restriction enzyme site Sau3AI in the sequence inside the target (lanes 8 and 9).

From the above results, it was confirmed that the target reaction product was obtained even when RNA was used as a target in the method for synthesizing the nucleic acid according to the present invention.

Industrial availability

A novel oligonucleotide and a method for synthesizing a nucleic acid using the same according to the present invention are provided for a method for synthesizing nucleic acids in which complementary base sequences are alternately connected on a single-stranded chain without complicated temperature control. Complementary chains synthesized using oligonucleotides based on the present invention as primers are always the starting point for synthesizing new complementary chains whose 3 'end is used as a template. At this time, the formation of a loop that causes annealing of a new primer, and the product of the complementary chain synthesis reaction, which is first synthesized by the complementary chain synthesis from this part, is replaced again, thus making it possible to bond base pairs. do. The nucleic acid synthesized using the self as a template thus obtained contributes to the improvement of their nucleic acid synthesis efficiency in combination with, for example, a known nucleic acid synthesis method such as SDA.

Furthermore, according to the preferred aspect of the present invention, not only can achieve the efficiency improvement of the known nucleic acid synthesis method, but also does not require complicated temperature control, and can also expect a high amplification efficiency, furthermore, high specificity A novel method for synthesizing nucleic acids is provided. In other words, by applying the oligonucleotide based on the present invention to the template chain and its complementary chain, nucleic acids in which complementary nucleotide sequences are alternately linked on a single-stranded chain are continuously synthesized. This reaction, in principle, continues until the starting material required for synthesis is depleted, in the meantime continuing to produce new nucleic acid that has begun synthesis from the loop portion. In this way, the elongation from the oligonucleotides annealed in the loop performs chain substitution to supply 3'-OH for elongation of long single-stranded chain nucleic acids (i.e., plural pairs of complementary sequences linked). On the other hand, 3'-OH of a long single-stranded chain achieves elongation by performing a complementary chain synthesis reaction using itself as a template, and replaces a new complementary chain synthesized from the loop. This amplification reaction proceeds under isothermal conditions while maintaining high specificity.

The oligonucleotide in the present invention functions as a primer for the nucleic acid synthesis reaction according to the present invention when two contiguous regions are arranged as designed. This greatly contributes to maintaining specificity. For example, in PCR, high specificity can be expected in the present invention as compared with the initiation of a nonspecific amplification reaction by nonspecific missannealing regardless of the intended positional relationship of the two primers. It can be easily explained. This feature can be used to accurately detect SNPs with high sensitivity.

A feature of the present invention is that such a reaction can be easily achieved with an extremely simple reagent configuration. For example, although the oligonucleotide according to the present invention has a special structure, it is a matter of selection of a nucleotide sequence, and is a simple oligonucleotide as a substance. Moreover, in a preferable aspect, reaction can be advanced only with DNA polymerase which catalyzes a chain substitution type complementary chain synthesis reaction. Furthermore, in carrying out the present invention using RNA as a template, all enzymatic reactions can be carried out by using a DNA polymerase having a reverse transcriptase activity such as Bca DNA polymerase and a chain substituted DNA polymerase activity. It can be performed by an enzyme. The reaction principle of realizing amplification reaction of high nucleic acid by such a simple enzyme reaction is not known until now. Moreover, even if it is applied to well-known nucleic acid synthesis reactions, such as SDA, it does not need a new enzyme by the combination with this invention, and can adapt to various reaction systems only by combining oligonucleotide based on this invention. Do. Therefore, the nucleic acid synthesis method according to the present invention can be said to be advantageous also in terms of cost.

As described above, the method for synthesizing the nucleic acid of the present invention and the oligonucleotide therefor are a new principle that simultaneously solves a plurality of difficult problems such as operability (no temperature control), improvement of synthesis efficiency, economical efficiency, and high specificity. To provide.

Claims (24)

A method for synthesizing a nucleic acid in which complementary nucleotide sequences are alternately linked on a single-stranded chain comprising the following steps. a) a step of providing a nucleic acid capable of forming a loop comprising a region F2c capable of base pair binding by having a region F1 that can anneal to some F1c on the same chain at the 3 'end and the region F1 annealed to F1c b) A step of performing complementary chain synthesis using the 3 'end of F1 annealed to F1c as a synthetic starting point. c) annealing the oligonucleotide comprising the F2 having the sequence complementary to the region F2c at the 3 'end, and synthesizing the complementary chain by a polymerase which catalyzes the chain substitution complementary chain synthesis reaction using the synthesis starting point; Substituting the complementary chain synthesized in b) d) annealing polynucleotides comprising a sequence complementary to any region in the complementary chain substituted in step c) to enable base pair bonding at the 3 'end, and the chain substitution complement using the 3' end as a synthetic starting point. A step of substituting the complementary chain synthesized in step c) by performing a complementary chain synthesis by a polymerase catalyzing the chain synthesis reaction The loop according to claim 1, wherein in step d), the synthetic starting point is a region R1 at the 3 'end of the same chain that can be annealed to region R1c, and R1 comprises a region R2c capable of base pair bonding by annealing to R1c. How it is formed. An oligonucleotide consisting of at least two regions X2 and X1c below, wherein X1c is linked to the 5 'side of X2. X2: region having a nucleotide sequence complementary to any region X2c of a nucleic acid having a specific nucleotide sequence X1c: region having a base sequence substantially the same as region X1c located on the 5 'side of region X2c in a nucleic acid having a specific base sequence The method according to claim 1, wherein the nucleic acid in step a) is a second nucleic acid provided by the following step. i) annealing the region F2c of the nucleic acid having the region F2 of the oligonucleotide of claim 3 in which the region X2 is the region F2 and the region X1c is the region F1c, ii) a step of synthesizing a first nucleic acid having a nucleotide sequence complementary to a template using F2 of the oligonucleotide as a synthetic starting point; iii) allowing any pair of the first nucleic acid synthesized in step ii) to be capable of base pair binding, iv) An oligonucleotide having a nucleotide sequence complementary to the region that enables base pair binding of the first nucleic acid in step iii) is annealed, and a second nucleic acid is synthesized using the synthesis starting point and F1 at the 3 'end. To make base-pair binding possible The oligonucleotide of claim 4, wherein the region allowing base pair bonding in step iii) is R2c, and the oligonucleotide in step iv) is region X2c is region R2c, and region X1c is region R1c. Way to be. The outer primer and the first nucleic acid according to claim 4 or 5, wherein the step of bringing the base pair bonds in the steps iii) and iv) into an enabling state is performed at the 3 'side of F2c in the template. The process by the chain substitution complementary chain synthesis | combination by the polymerase which catalyzes the chain substitution complementary chain synthesis reaction which uses the outer primer annealed at the 3 'side of the area | region as the starting point of a synthesis | combination in the step (iv) of the synthesis starting point. The method according to claim 6, wherein the melting temperature of each oligonucleotide to be used for the reaction and its complementary region in the template has the following relationship under the same stringency. (Region on the 3 'side in the outer primer / template) ≤ (F2c / F2 and R2c / R2) ≤ (F1c / F1 and R1c / R1) The method according to any one of claims 4 to 7, wherein the nucleic acid serving as a template is RNA, and the complementary chain synthesis in step ii) is performed with an enzyme having reverse transcriptase activity. Amplification of nucleic acids in which complementary nucleotide sequences are alternately linked on a single-stranded chain by repeating the following steps. A) At the 3 'end and the 5' end, a loop having a base sequence complementary to the terminal region on the same chain and allowing base pair bonding between both when the complementary base sequences are annealed Process of providing the mold to be formed B) a step of performing complementary chain synthesis using the 3 'end of the template annealed in the same chain as a synthetic starting point, C) A polymer which anneals an oligonucleotide comprising a complementary nucleotide sequence at the 3 'end in the loop located at the 3' end side of the loop at the loop portion, and catalyzes the chain substitution complementary chain synthesis reaction using this as a synthetic starting point. Synthesizing the complementary chain by laase, replacing the complementary chain synthesized in step B), and leaving the 3 'end in a state capable of base pair bonding; and D) The process of making the new mold in process A) the chain | strand which made the 3 'terminal into base pair bonding possible in the process C) The amplification method according to claim 9, wherein the oligonucleotide in step C) has a base sequence complementary to the 3 'end which is the starting point of synthesis in step B) at its 5' side end. The amplification method according to claim 10, further comprising a step in which the complementary chain synthesized using the oligonucleotide in step C) as a synthetic starting point is used as a template in step A). The amplification method according to claim 9, wherein the template in step A) is synthesized by the method of claim 5. The method according to claim 1 or 9, wherein the chain substitution complementary chain synthesis reaction is carried out in the presence of a melting temperature regulator. The method of claim 13, wherein the melting temperature modifier is betaine. The method according to claim 14, wherein 0.2 to 3.0 M of betaine is present in the reaction solution. The method of detecting the target base sequence in a sample by performing the amplification method in any one of Claims 9-15, and observing whether the amplification reaction product was produced. 17. The method of claim 16, wherein the hybridization is observed by adding a probe comprising a nucleotide sequence complementary to the loop to the amplification product. 18. The method of claim 17, wherein the probe is particle labeled to observe agglomeration reactions caused by hybridization. 17. The method according to claim 16, wherein the amplification method according to any one of claims 9 to 15 is carried out in the presence of a detection agent of a nucleic acid to observe whether or not an amplification reaction product has been generated based on a signal change of the detection agent. A method for detecting a variation in a target base sequence by the detection method according to claim 16, wherein the variation in the base sequence to be amplified interferes with any one of the complementary chain synthesis constituting the amplification method. A kit for synthesizing nucleic acids comprising alternating nucleotide sequences complementary on a single-stranded chain, including the following elements. i) The oligonucleotide according to claim 3, wherein region F2c of the nucleic acid to be a template is X2c, and F1c located on the 5 'side of F2c is X1c. ii) an oligonucleotide comprising a base sequence complementary to any region in the complementary chain synthesized using the oligonucleotide of i) as a primer iii) an oligonucleotide having a nucleotide sequence complementary to region F3c located on the 3 'side of region F2c of the nucleic acid as a template iv) a DNA polymerase that catalyzes chain substitution type complementary chain synthesis and v) nucleotides as substrate of element iv) The oligonucleotide of ii) according to claim 21, wherein any region R2c in the complementary chain synthesized using the oligonucleotide of i) as a synthetic starting point is X2c, and R1c located at 5 'of R2c is X1c. The kit is an oligonucleotide of claim 3. The kit of claim 22, further comprising the following elements. vi) an oligonucleotide having a base sequence complementary to region R3c located on the 3 'side of any region R2c in the complementary chain synthesized using the oligonucleotide of i) as a synthetic starting point. The kit according to any one of claims 21 to 23, further comprising a detection agent for detecting a product of a nucleic acid synthesis reaction, the kit for detecting the target base sequence.