JP2001103999A - Method for detecting nucleic acid - Google Patents

Abstract

PROBLEM TO BE SOLVED: To provide a method for detecting nucleic acid having a simple operation and improved specificity in comparison with a conventional nucleic acid detection technique and general-purpose properties applicable to many kinds of nucleic acids. SOLUTION: This method for detecting or determining a target nucleic acid in a sample having a fixed sequence by using a carrier to which an artificially selected probe group is fixed as a solid phase to detect the nucleic acid and to improve specificity of hybridization.

Description

DETAILED DESCRIPTION OF THE INVENTION

[0001]

[0001] The present invention relates to a method for detecting or quantifying a plurality of target nucleic acid molecules present in a sample.

[0002]

2. Description of the Related Art Techniques for detecting a specific nucleic acid molecule present in a biological sample include analyzing the protein expressed and functioning in a specific organ at the nucleic acid molecule level, and analyzing the protein in the information transmission in the nerve, brain or immune system. It is not only important in the study of expression control and the like, but also extremely important in gene diagnosis such as detection of mutant genes of genetic diseases, diagnosis of cancer, detection of virus-related genes, and the like.

[0003] However, the conventional technology is complicated and involves many steps, and requires skill, so that a considerable amount of time is often required depending on the operation.

[0004] In addition, since genetic diagnosis and the like are used as definitive diagnosis, errors are not allowed, and quickness is also required. Therefore, high accuracy must be maintained while maintaining quickness. Such a request cannot be fully satisfied.

A typical technique for detecting a specific nucleic acid molecule present in a sample is a hybridization method. Hybridization analysis of nucleic acids is a technique for detecting a very small number of target nucleic acids (DNA or RNA) from a wide variety of nucleic acids with a probe, but the hybridization method uses a highly sensitive reporter (enzyme, fluorescent dye, Low copy number (1 to 1000) even when using radioisotopes
Is difficult to detect. Furthermore, since the hybridization method has a major problem of nonspecific reaction, it is difficult to detect only a specific nucleic acid molecule from a plurality of similar nucleic acid molecules.

[0006] As described above, since the nucleic acid hybridization method has sufficient sensitivity and specificity, it is difficult to apply the method to clinical diagnosis requiring highly sensitive detection.

On the other hand, as a DNA detection method completely different from the classical hybridization method, Fodor et al., Science, Vol. 251, 767-
773, 1991, discloses a method for synthesizing oligonucleotides on a matrix using photolithographic techniques. Also, Pilrung et al., US Pat. No. 5,143,8
No. 54, September 1, 1992, teaches a large-scale, photolithographic solid phase synthesis of polypeptides in an array format on a silicon substrate. In addition, Beattie, 1992 San Diego Conference: Gene Recognition (The 1992 San Diego Confe
rence: Genetic Recognition), in November 1992, using a microscopic robotics system, microdroplets containing a specific DNA sequence were dropped onto individual microfabricated sample wells on a glass substrate and placed on the substrate. A method for synthesizing a DNA sequence is disclosed. Hybridization in each sample well is detected by sending a command signal to a miniature electrode test fixture surrounding each individual microwell with an alternating electric field.

[0008] By such a method, various kinds of
The operation of a DNA chip on which DNA has been synthesized is much simpler than that of a hybridization method, so that the speed of diagnosis can be significantly improved.

However, in a conventional DNA chip, only probes having a sequence complementary to the base sequence of the target nucleic acid to be detected are immobilized, so that the optimal hybridization conditions for each probe are constant. Rather, it has the disadvantage that false positive hybridization is likely to occur.

In order to avoid such false-positive hybridization, optimized hybridization conditions may be provided for each probe. Because it is impossible to give, conventional DNA chips have not solved the fundamental problem of hybridization, which is not sufficient in specificity.

[0011] In addition, in the conventional DNA chip, if the type of the target nucleic acid to be detected is changed, its complementary sequence must be re-immobilized again, so that an extremely large variety of nucleic acids are to be detected. It also has the disadvantage that versatility is not sufficient for application to clinical tests.

[0012]

DISCLOSURE OF THE INVENTION The present invention has been made in view of the above circumstances, and has a simpler operation, improved specificity, and a greater variety of properties than conventional nucleic acid detection techniques. The present invention is characterized by providing a nucleic acid detection method having versatility that can be applied to nucleic acids.

[0013]

Means for Solving the Problems To solve the above problems, the present invention provides a method for preparing a target nucleic acid N1 in a sample having a predetermined sequence.
A method for detecting or quantifying NNn (n is an integer of 2 or more), comprising: a) a first partial sequence F1〜 in the target nucleic acids N1NNn;
Sequences F1 ′ to Fn ′ complementary to Fn, a first probe group including probes A1 to An with a labeling substance linked to each F1 ′ to Fn ′, and a first probe group in the target nucleic acids N1 to Nn. Two partial arrays S1 ~
A step of preparing a second probe group including probes B1 to Bn having sequences S1 ′ to Sn ′ complementary to Sn and flag sequences FL1 to FLn linked to each of S1 ′ to Sn ′, b) mixing the first probe group, the second probe group, and the sample, the first partial sequence F1 ~ Fn in the target nucleic acid N1 ~ Nn the probe A1 ~ An. While hybridizing, the probe B1 was added to the second partial sequences S1 to Sn.
~ Bn hybridizing, c) the target nucleic acid
The probes A1 to An hybridized to N1 to Nn and the probes B1 to Bn are ligated, and the probes (A1 + B1) to
(An + Bn) to produce, d) the flag array FL1 ~
By hybridizing Fln to the sequences FL1 ′ to FLn ′ complementary to the sequence, the probes (A1 + B1) to (An + B
recovering n) and e) recovering the probe (A1 + B
1) detecting or quantifying the labeling substance in (An + Bn) to detect or quantify the target nucleic acids N1 to Nn in the sample.

[0014]

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS One embodiment of the method of the present invention will be described below with reference to FIG.

The first step of the method comprises:-a sample to be detected or quantified for the presence of target nucleic acid 1, target nucleic acid 2, ..., target nucleic acid n (hereinafter abbreviated as target nucleic acids N1 to Nn); Probe A1 having a sequence complementary to one first partial sequence F1 and a labeling substance bound to the sequence
A probe A2 having a sequence complementary to the first partial sequence F2 of the target nucleic acid 2 and a labeling substance bound to the sequence, ..., complementary to the first partial sequence Fn of the target nucleic acid n A first probe group including a probe An having a sequence and a labeling substance bound to the sequence (hereinafter, abbreviated as probes A1 to An);-a first probe group different from the first partial sequence F1 of the target nucleic acid 1; A probe B1 having a sequence complementary to the two partial sequences S1 and a flag sequence FL1 bound to the sequence,
A probe B2 having a sequence complementary to the second subsequence F2 different from the first subsequence F2 and a flag sequence FL2 bound to the sequence, ..., the first subsequence F of the target nucleic acid n
and a second probe group including a probe Bn having a sequence complementary to the second partial sequence Sn different from n and a flag sequence FLn linked to the sequence (hereinafter abbreviated as probes B1 to Bn) This is the step of performing

The target nucleic acids N1 to N1 to be detected or quantified
Nn can be any nucleic acid having any sequence, but a nucleic acid that can be a marker of a disease, such as a causative gene of a genetic disease, a cancer-related gene, or a nucleic acid derived from a virus, is a particularly preferred target nucleic acid.

Therefore, the samples include body fluids such as blood, urine and saliva, but any sample other than body fluids can be used. If the sample is a solid, it may be dissolved in a liquid by an appropriate method such as enzyme treatment, addition of a surfactant or an organic solvent.

As used herein, the term “nucleic acid” includes cDNA,
All DNAs and RNAs including genomic DNA, synthetic DNA, mRNA, total RNA, hnRNA, and synthetic RNA are meant.

The first partial sequences F1 to F1 in each of the target nucleic acids N1 to Nn
The number of bases of Fn may be 1 or more, but is preferably 20 or more in order to achieve stable hybridization. Each first partial sequence can be arbitrarily selected from the base sequences of the target nucleic acids N1 to Nn.

The second partial sequences S1 to S1 in each of the target nucleic acids N1 to Nn
Although the number of bases of Sn may be one or more, it is preferably 20 or more as in the first partial sequence. Each second subsequence may partially overlap with the corresponding first subsequence as long as it is different from the corresponding first subsequence. It is preferable that the first partial sequence and the second partial sequence in each of the target nucleic acids N1 to Nn are selected so as to be all adjacent to each other in order to facilitate the operation in the subsequent steps.

The probes A1 to An comprise a sequence F1 'complementary to the first partial sequences F1 to Fn arbitrarily selected from the target nucleic acids N1 to Nn.
~ Fn ', the target nucleic acids N1 to Nn and the probe A1
When ~ A is mixed, the probes A1 ~ An
It can hybridize with F1 'to Fn' in N1 to Nn.

Here, the term "complementary sequence" means a sequence capable of specifically hybridizing only to a predetermined target nucleic acid under appropriate conditions.

A target substance 11 is linked to each of the probes A1 to An in order to enable detection or quantification of the target nucleic acids N1 to Nn. Preferred labeling substances are fluorescent substances such as FITC,
A light emitting substance, a radioactive substance such as ³² P, a highly absorbent substance, a high light reflective substance, a high potential substance, a magnetic substance, and a dye, but are not limited thereto. In particular, fluorescent substances, radioactive substances, and dyes are preferred target substances. Note that different target substances can be bound to the probes A1 to An, respectively.

Since the probes B1 to Bn have a sequence complementary to the second partial sequence arbitrarily selected from the target nucleic acids N1 to Nn, when the target nucleic acids N1 to Nn and the probes B1 to Bn are mixed, Probes B1 to Bn correspond to S1 ′ in corresponding target nucleic acids N1 to Nn.
~ Sn 'can be hybridized. here,
The “complementary sequence” is as described above.

Flag sequences FL1 to FLn are connected to the probes B1 to Bn, respectively, in order to specifically recover the probes B1 to Bn and the sequences to which the probes B1 to Bn are connected in a later step. Although the number of bases and the sequence of the flag sequence may be arbitrary, it is preferable to select a combination having the same optimal hybridization conditions.

The flag sequences FL1 to FLn correspond to the target nucleic acids N1 to Nn.
At least in part, to facilitate detection or quantification of
Preferably, they are all different. However, when a plurality of types of labeling substances are bound to the probes A1 to An, specific detection or quantification by the labeling substance becomes possible, so that a part or all of each flag sequence can be the same sequence. .

As described above, since the first partial sequence F1 to Fn and the second partial sequence S1 to Sn in each of the target nucleic acids N1 to Nn are preferably selected to be adjacent to each other, F1 to Fn and S1 ~ Sn is selected in this way, the probe B1 ~ Bn and the probe A1 ~ An
Will hybridize to the corresponding target nucleic acids N1-Nn adjacent to each other. Therefore, as shown in FIG. 1, each flag sequence in the probes B1 to Bn is preferably linked to an end that does not face each labeling substance in the probes A1 to An.

In the second step of the present method, the probes A1 to An and the probes B1 to Bn are hybridized to the corresponding target nucleic acids N1 to Nn, and the probes A1 to An and the probes B1 to Bn are ligated.

In order to hybridize each probe to the corresponding target nucleic acid, if the target nucleic acid is single-stranded, a sample containing the target nucleic acid and both probe groups may be mixed without performing any additional treatment. When the target nucleic acids N1 to Nn are double-stranded, for example, the mixture is allowed to stand at a high temperature of about 90 ° C. for several minutes to dissociate complementary bonds, and then both probe groups are added.
The hybridization may be performed by leaving the mixture at a temperature of about 50 ° C. for 2 to 3 hours. Of course, hybridization conditions, that is, the type of buffer used, temperature conditions, time, etc. can be appropriately selected according to the type of target nucleic acid.
Those skilled in the art will be self-evident.

When hybridization is performed, the probes A1 to An and the probes B1 to Bn bind to the corresponding target nucleic acids N1 to Nn. Therefore, if a ligase or the like is applied, the probes A1 to An By connecting probes B1 to Bn, probe A1 + B1, probe A2 + B2, ... probe
A1 + Bn (hereinafter abbreviated as probe (A1 + B1) to (An + Bn))
Can be created.

Suitable ligases which can be used to ligate both probe groups include Thermus Aquaticus (Therm
us aquaticus), but not limited thereto, and any DNA ligase or RNA ligase may be used depending on the type of target nucleic acid.

Alternatively, both probe groups may be linked by a chemical method instead of the enzymatic method.

When the probes A1 to An and the probes B1 to Bn are not adjacent to each other, a DNA polymerase or an RNA polymerase, preferably a thermostable DNA such as Taq polymerase is used.
After introducing a nucleobase into the gap between both probe groups by polymerase chain reaction (PCR) using a polymerase, both probe groups may be connected by an enzymatic technique or a chemical technique.

In the third step, each probe (A1 + B1) to (An + Bn) is dissociated from the corresponding target nucleic acid. Probe dissociation is achieved by denaturation treatments, including thermal denaturation and chemical denaturation. When dissociating the probe by thermal denaturation, under physiological conditions, 85 ° C. or more, preferably 90 ° C.
The above temperature may be used, but it will be obvious to those skilled in the art that an appropriate temperature can be selected according to the GC content in the probe.

The denaturation step can be omitted if the end of the probe hybridized to the target nucleic acid further extends from the end of the target nucleic acid to form a single-stranded region. It would be desirable to add a denaturation step.

In the fourth step, probes (A1 + B1) to (An
+ Bn) is specifically recovered, and an operation of detecting or quantifying the target nucleic acid is performed.

To specifically recover the probes (A1 + B1) to (An + Bn), a sequence complementary to the flag sequences FL1 to FLn
A method using a solid support on which FL1 'to FLn' are immobilized is extremely preferable. The solid phase carrier to which the sequence complementary to the flag sequence should be immobilized includes substrates such as silicon and glass, particles, containers such as test tubes and vials, tubes including capillaries such as fibers and capillaries, affinity columns, and filters. , Electrodes, etc., but are not limited thereto. Preferred solid supports are silicon substrates, particles, and capillaries.

As described above, since the flag sequences FL1 to FLn are artificial sequences contained in the probe B, the flag sequences FL1 to FLn are designed to improve the specificity of hybridization with the probes (A1 + B1) to (An + Bn). FL1 to FLn can be selected.

More specifically, the probes (A1 + B1) to (An
The optimal hybridization conditions (eg, temperature, salt concentration, etc.) for each probe can be uniformly adjusted by appropriately selecting the GC content of + Bn), the composition of the nucleic acid base, and the like. Will be significantly reduced or lost, and the specificity will be greatly improved.

On the other hand, in the conventional nucleic acid detection method in which the complementary sequence of the target nucleic acid is immobilized, the optimal hybridization conditions for each immobilized probe are completely different, so that it is suitable for all probes. It is impossible to set the conditions that have been set, and the specificity is reduced.

If only the first partial sequence and the second partial sequence are changed without changing the flag sequence, it is possible to detect and quantify a desired target nucleic acid with one kind of solid phase carrier. Therefore, the method is highly versatile.

Since the labeling substance is linked to the probes (A1 + B1) to (An + Bn) specifically recovered by the above operation, the probe is prepared by an appropriate method according to the labeling substance.
(A1 + B1) to (An + Bn) can be detected or quantified. Since ligation must occur after hybridization with the target nucleic acid, detection or quantification of the probes (A1 + B1) to (An + Bn) enables indirect detection or quantification of each target nucleic acid.

Next, another embodiment of the method of the present invention will be described with reference to FIG.

The first step of the present method is basically the same as the first step of the method shown in FIG. 1, and the target nucleic acids N1 to Nn
The sample to be detected or quantified, the first probe group including the probes A1 to An, the operation of mixing the second probe group including the probes B1 to Bn is performed, the probe A1 to An is the tag sequence Tg1 The only difference is that Tgn.

The tag sequence may be any substance that can specifically bind to a specific substance such as a small molecule such as biotin, a protein such as an antibody, etc., in addition to the base sequence.

In the second step of hybridization and ligation, a probe (A1
The third step of recovering (+ B1) to (An + Bn) is basically the same as the corresponding step of the method described in FIG. In FIG. 2, the denaturation process is omitted, but the denaturation process may be performed, and it is usually preferable to perform the denaturation process.

In the fourth step, probes (A1 + B1) to (An + B
n) using the complementary sequence Tg1 ′ to Tgn ′ of Tg1 to Tgn that is not present in the free probe B1 to Bn collected secondarily together with the probe (A1 + B1) to (An + Bn), This is the step of detecting or quantifying.

Since the free probes B1 to Bn hybridized to FL1 ′ to FLn ′, the absolute amount of the probe (A1 + B1) to (An + Bn) hybridized to FL1 to FLn was reduced. Unlike the process, in the fourth process, the probe
Since only (A1 + B1) to (An + Bn) are hybridized, the absolute amount of the labeling substance that hybridizes to the immobilized probe (Tg1 ′ to Tgn ′ in the figure) increases, and the target nucleic acid can be detected with high sensitivity. It can be detected or quantified.

In FIG. 2, after the third step, the probe (A
1 + B1) to (An + Bn) are dissociated as they are, but the probes (A1 + B1) to (An + B
It will be obvious that n) may be truncated.

[0050]

As described above, the present invention provides a method for detecting or quantifying a nucleic acid which is excellent in specificity and simplicity and has improved versatility.

[Brief description of the drawings]

FIG. 1 is a diagram showing one embodiment of the present invention.

FIG. 2 is a diagram showing another embodiment of the present invention.

──────────────────────────────────────────────────続 き Continued on the front page (51) Int.Cl. ⁷ Identification symbol FI Theme coat ゛ (Reference) G01N 33/566 C12M 1/00 A // C12M 1/00 1/40 B 1/40 C12N 15/00 A F-term (Reference) 4B024 AA11 AA19 CA01 CA09 CA11 HA08 HA12 HA13 4B029 AA23 BB20 CC03 4B063 QA01 QA19 QQ03 QQ42 QQ52 QR01 QR31 QR32 QR56 QR66 QR82 QS34 QX02 QX07

Claims (9)

[Claims] 1. A target nucleic acid N1 in a sample having a predetermined sequence
To Nn (n is an integer of 2 or more), comprising: a) sequences F1 ′ to Fn ′ that are complementary to the first partial sequences F1 to Fn in the target nucleic acids N1 to Nn; A first probe group including probes A1 to An having a labeling substance linked to each of F1 'to Fn', and a sequence S1 complementary to second partial sequences S1 to Sn in the target nucleic acids N1 to Nn. Preparing a second probe group including probes B1 to Bn having '~ Sn' and a flag sequence FL1 to FLn connected to each of S1 'to Sn', b) the first probe Group, the second probe group,
By mixing the sample, the probes A1 to An are hybridized to the first partial sequences F1 to Fn in the target nucleic acids N1 to Nn, and the probe B1 is hybridized to the second partial sequences S1 to Sn. And Bn hybridizing, c) ligating the probes A1 to An and the probes B1 to Bn hybridized to the target nucleic acids N1 to Nn, the probes (A1 + B1) to (An + Bn) And d) a sequence complementary to said flag sequence FL1-Fln.
Recovering the probes (A1 + B1) to (An + Bn) by hybridizing to FL1 ′ to FLn ′, and e) removing the labeled substance in the collected probes (A1 + B1) to (An + Bn). Detecting or quantifying the target nucleic acids N1 to Nn in the sample by detection or quantification. 2. After step c) of the method according to claim 1,
The method further comprises a step of denaturing a hybrid consisting of probes (A1 + B1) to (An + Bn) and the target nucleic acid molecule. 3. The method according to claim 1, wherein at least one of the probes A1 to An has a tag sequence, and after step d), complements the tag sequence with the sequence. By hybridizing to the specific sequence, the probe (A1 + B
1) A method comprising a step of recovering (An + Bn). 4. The method according to claim 1, wherein a sequence complementary to the flag sequence is immobilized on a solid support, and the probe ( A1 +
A method characterized by recovering (An) to (An + Bn). 5. The method according to claim 1, wherein the solid support is selected from the group consisting of a substrate, a particle, a tube, and a fiber. 6. The method according to claim 1, wherein the first partial sequences F1 to Fn and the second partial sequences S1 to Sn corresponding to each of the F1 to Fn. Are adjacent. 7. The method according to any one of claims 1 to 6, wherein the probes A1 to An and the probes B1 to Bn corresponding to A1 to An are ligated by ligase. A method characterized by the following. 8. The method of claim 7, wherein the probe A is ligated by ligase prior to ligating the probe A by PCR.
A method comprising performing an operation to extend 1 to An and the probes B1 to Bn. 9. The method according to any one of claims 1 to 8, wherein the target substance is a fluorescent substance, a luminescent substance, a dye,
And radioactive isotopes.