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Publication numberUS20010019835 A1
Publication typeApplication
Application numberUS 09/292,563
Publication dateSep 6, 2001
Filing dateApr 15, 1999
Priority dateNov 9, 1998
Also published asDE69927113D1, DE69927113T2, EP1002877A2, EP1002877A3, EP1002877B1, US6261846
Publication number09292563, 292563, US 2001/0019835 A1, US 2001/019835 A1, US 20010019835 A1, US 20010019835A1, US 2001019835 A1, US 2001019835A1, US-A1-20010019835, US-A1-2001019835, US2001/0019835A1, US2001/019835A1, US20010019835 A1, US20010019835A1, US2001019835 A1, US2001019835A1
InventorsMitsugu Usui
Original AssigneeMitsugu Usui
Export CitationBiBTeX, EndNote, RefMan
External Links: USPTO, USPTO Assignment, Espacenet
Gene amplifying method
US 20010019835 A1
Abstract
A gene amplifying method for efficiently amplifying a gene without using enzyme or branched DNA. A plurality of pairs of probes each composed of three or more portions complementary to such portions in the other probe are used, and hybridized such that they cross in alternation to form a double-stranded polymer.
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Claims(27)
What is claimed is:
1. A gene amplifying method comprising the steps of:
providing a plurality of pairs of probes each composed of three or more portions complementary to such portions of the other probe; and
hybridizing said pairs of probes such that they cross in alternation to form a double-stranded polymer.
2. A gene amplifying method according to
claim 1
, wherein said pair of probes comprise two DNA probes, a DNA probe and an RNA probe, two RNA probes, two PNA probes, a PNA probe and a DNA probe, or a PNA probe and an RNA probe.
3. A gene amplifying method according to
claim 1
, wherein said pair of probes are structured such that complementary portions at three or more sites of the respective probes are each hybridized in a specific manner without fail during one-to-one hybridization.
4. A target gene detecting method comprising the steps of:
providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene;
hybridizing a plurality of said pairs of probes with the target gene by the method according to
claim 1
to form a double-stranded polymer; and
amplifying the probes to detect the target gene.
5. A target gene detecting method comprising the steps of:
providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene;
hybridizing a plurality of said pairs of probes with the target gene by the method according to
claim 2
to form a double-stranded polymer; and
amplifying the probes to detect the target gene.
6. A target gene detecting method comprising the steps of:
providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene;
hybridizing a plurality of said pairs of probes with the target gene by the method according to
claim 3
to form a double-stranded polymer; and
amplifying the probes to detect the target gene.
7. An antigen/antibody detecting method comprising the steps of:
providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene bound to antigen/antibody;
hybridizing a plurality of said pairs of probes with the target gene by the method according to
claim 1
to form a double-stranded polymer; and
detecting antigen/antibody.
8. An antigen/antibody detecting method comprising the steps of:
providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene bound to antigen/antibody;
hybridizing a plurality of said pairs of probes with the target gene by the method according to
claim 2
to form a double-stranded polymer; and
detecting antigen/antibody.
9. An antigen/antibody detecting method comprising the steps of:
providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene bound to antigen/antibody;
hybridizing a plurality of said pairs of probes with the target gene by the method according to
claim 3
to form a double-stranded polymer; and
detecting antigen/antibody.
10. A target gene detecting method comprising the steps of:
providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene;
previously hybridizing said other probe to the target gene;
hybridizing said pairs of probes with the target gene by the method according to
claim 1
to form a double-stranded polymer; and
amplifying the probes to detect the target gene.
11. A target gene detecting method comprising the steps of:
providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene;
previously hybridizing said other probe to the target gene;
hybridizing said pairs of probes with the target gene by the method according to
claim 2
to form a double-stranded polymer; and
amplifying the probes to detect the target gene.
12. A target gene detecting method comprising the steps of:
providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene;
previously hybridizing said other probe to the target gene;
hybridizing said pairs of probes with the target gene by the method according to
claim 3
to form a double-stranded polymer; and
amplifying the probes to detect the target gene.
13. An antigen/antibody detecting method comprising the steps of:
providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene bound to antigen/antibody;
previously hybridizing said other probe to the target gene, and hybridizing said pairs of probes with the target gene by the method according to
claim 1
to form a double-stranded polymer; and
detecting the antigen/antibody.
14. An antigen/antibody detecting method comprising the steps of:
providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene bound to antigen/antibody;
previously hybridizing said other probe to the target gene, and hybridizing said pairs of probes with the target gene by the method according to
claim 2
to form a double-stranded polymer; and
detecting the antigen/antibody.
15. An antigen/antibody detecting method comprising the steps of:
providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene bound to antigen/antibody;
previously hybridizing said other probe to the target gene, and hybridizing said pairs of probes with the target gene by the method according to
claim 3
to form a double-stranded polymer; and
detecting the antigen/antibody.
16. A target gene detecting method according to
claim 4
, wherein said step of detecting includes binding a fluorescent material to said amplified probes to make the target gene emit light, thereby detecting the target gene.
17. A target gene detecting method according to
claim 10
, wherein said step of detecting includes binding a fluorescent material to said amplified probes to make the target gene emit light, thereby detecting the target gene.
18. An antigen/antibody detecting method according to
claim 7
, wherein said step of detecting includes binding a fluorescent material to said amplified probes to make the target gene bound to the antigen/antibody emit light, thereby detecting the antigen/antibody.
19. An antigen/antibody detecting method according to
claim 13
, wherein said step of detecting includes binding a fluorescent material to said amplified probes to make the target gene bound to the antigen/antibody emit light, thereby detecting the antigen/antibody.
20. A target gene detecting method according to
claim 4
, further comprising the step of previously adding a marker material for detection to said probes to be amplified to detect the target gene.
21. A target gene detecting method according to
claim 10
, further comprising the step of previously adding a marker material for detection to said probes to be amplified to detect the target gene.
22. An antigen/antibody detecting method according to
claim 7
, further comprising the step of previously adding a marker material for detection to said probes to be amplified to detect the antigen/antibody.
23. An antigen/antibody detecting method according to
claim 13
, further comprising the step of previously adding a marker material for detection to said probes to be amplified to detect the antigen/antibody.
24. A pair of probes wherein each of said probes is composed of three or more portions complementary to such portions of the other probe.
25. A pair of probes according to
claim 24
, wherein said pair of probes comprises two DNA probes, a DNA probe and an RNA probe, two RNA probes, two PNA probes, a PNA probe and a DNA probe, or a PNA probe and an RNA probe.
26. A double-stranded polymer formed by using a plurality of the pair of probes according to
claim 24
, and hybridizing them such that they cross in alternation.
27. A double-stranded polymer formed by using a plurality of the pair of probes according to
claim 25
, and hybridizing them such that they cross in alternation.
Description
    BACKGROUND OF THE INVENTION
  • [0001]
    1. Field of the Invention
  • [0002]
    The present invention relates to special and novel probes, a gene amplifying method using cross (alternate) binding of the special probes, and a method of directly detecting a target gene and a method of detecting antigen/antibody using the gene amplifying method.
  • [0003]
    2. Description of the Related Art
  • [0004]
    In recent years, a method of amplifying a gene using a DNA polymerase, represented by a polymerase chain reaction method (hereinafter called the “PCR method”), a method of amplifying a gene by hybridizing polymer DNA having previously branched single-stranded DNA (hereinafter called the “branched DNA probe method”), and so on have been developed for detecting a very small amount of target gene.
  • [0005]
    The amplification of gene by the PCR method involves annealing (hybridize) a primer complementary to a target gene (or a primer), and amplifying the gene through rise and fall of temperature using a thermostable DNA polymerase. Disadvantageously, this method takes a long time from amplification to detection of a gene, and is expensive. In addition, the amplification efficiency and specificity may vary depending on the design of a primer complementary to the target gene.
  • [0006]
    The amplification of gene by the branched DNA probe method, on the other hand, involves previously synthesizing a branched polymer single-stranded DNA probe, and hybridizing the branched polymer single-stranded DNA probe to a target gene to detect the target gene. However, the hybridization of the branched polymer single-stranded DNA probe to the target gene takes a long time because the branched DNA probe is a polymer. In addition, the branched polymer single-stranded DNA is limited in size, so that the detection of the target gene is also limited.
  • OBJECT AND SUMMARY OF THE INVENTION
  • [0007]
    The present invention has been made in view of the problems of the prior art mentioned above, and its object is to provide a method of efficiently amplify a gene without using enzyme or branched DNA.
  • [0008]
    To solve the problem mentioned above, a gene amplifying method according to the present invention comprises the steps of providing a plurality of pairs of probes each composed of three or more portions complementary to such portions of the other probe; and hybridizing said pairs of probes such that they cross in alternation to form a double-stranded polymer.
  • [0009]
    The pair of probes for use in the gene amplifying method, may be two DNA probes, a DNA probe and an RNA probe, two RNA probes, two PNA (Peptide Nucleic Acid or Polyamide Nucleic Acid) probes, a PNA probe and a DNA probe, or a PNA probe and an RNA probe.
  • [0010]
    The pair of probes are structured such that complementary portions at three or more sites are each hybridized in a specific manner without fail during one-to-one hybridization.
  • [0011]
    A target gene detecting method according to the present invention, in a first aspect, comprises the steps of providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene, hybridizing a plurality of said pairs of probes with the target gene by the gene amplifying method described above to form a double-stranded polymer, and amplifying the probes to detect the target gene.
  • [0012]
    An antigen/antibody detecting method according to the present invention, in a first aspect, comprises the steps of providing a pair of probes, one of which has a gene in one portion thereof complementary to a target gene bound to antigen/antibody, hybridizing a plurality of said pairs of probes with the target gene by the gene amplifying method described above to form a double-stranded polymer, and detecting antigen/antibody.
  • [0013]
    The target gene detecting method according to the present invention, in a second aspect, comprises the steps of providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene, previously hybridizing said other probe to the target gene, hybridizing said pairs of probes with the target gene by the gene amplifying method described above to form a double-stranded polymer, and amplifying the probes to detect the target gene.
  • [0014]
    The antigen/antibody detecting method according to the present invention, in a second aspect, comprises the steps of providing a pair of probes and another probe complementary to a gene in a portion of one of said pair of probes and to a target gene bound to antigen/antibody, previously hybridizing said other probe to the target gene, and hybridizing said pairs of probes with the target gene by the gene amplifying method described above to form a double-stranded polymer, and detecting the antigen/antibody.
  • [0015]
    In the target gene detecting method, an intercalating die such as ethidium bromide, Oligreen, SYBR Green or the like may be bound to the probes amplified by the gene amplifying method to detect an amplified polymer through fluorescence.
  • [0016]
    In the antigen/antibody detecting method according to the present invention, an intercalating die such as ethidium bromide, Oligreen, SYBR Green or the like may be bound to the probes amplified by the gene amplifying method to detect the target gene bound to antigen/antibody or the like through fluorescence.
  • [0017]
    In the target gene detecting method according to the present invention, as a marker material for detection, a donor fluorescent die and an acceptor fluorescent die utilizing fluorescent resonance energy transfer (FRET) such as radioisotope such as 125I, 32P or the like, light emitting and coloring materials such as digoxigenin, acridine ester or the like, alkali phosphatase for utilizing a light emitting material such as dioxyethane or the like, and fluorescent materials such as 4-methyl umbelliferil phosphate or the like, and biotin for utilizing fluorescent, light emitting, coloring materials or the like bound to avidin, may be previously added to the probes to be amplified by the gene amplifying method to detect the target gene.
  • [0018]
    In the antigen/antibody detecting method according to the present invention, as a marker material for detection, a donor fluorescent die and an acceptor fluorescent die utilizing fluorescent resonance energy transfer (FRET) such as radioisotope such as 125I, 32P or the like, light emitting and coloring materials such as digoxigenin, acridine ester or the like, alkali phosphatase for utilizing a light emitting material such as dioxyethane or the like, and fluorescent materials such as 4-methyl umbelliferil phosphate or the like, and biotin for utilizing fluorescent, light emitting and coloring materials or the like bound to avidin, may be previously added to a pair of probes to be amplified by the gene amplifying method to detect the antigen/antibody.
  • [0019]
    Each of said probes according to the present invention is composed of three or more portions complementary to such portions of the other probe.
  • [0020]
    The pair of probes may be two DNA probes, a DNA probe and an RNA probe, two RNA probes, two PNA probes, a PNA probe and a DNA probe, or a PNA probe and an RNA probe.
  • [0021]
    A double-stranded polymer according to the present invention is formed by using a plurality of the pair of probes, and hybridizing them such that they cross in alternation.
  • [0022]
    The DNA probe is composed of single-stranded fragments mainly consisting of phosphoric acid, saccharum and bases (adenine, thymin, guanin and cytosine), while the RNA probe is composed of single-stranded fragments mainly consisting of bases which are adenine, uracil, guanin and cytosine. PNA has a structure in which the skeleton of “phosphoric acid and saccharum” in DNA is replaced by an “N-(2-aminoethyl) glycin derivative” and has the same components of bases as DNA and RNA.
  • [0023]
    The length of the probes for use in the methods mentioned above ranges from 10 bases to 1,000 bases, and most preferably from 10 bases to 100 bases.
  • [0024]
    The pair of probes are not particularly limited in the type of bases in the mutually complementary portions. In addition, the lengths of the complementary portions existing in one probe may be equal or different.
  • [0025]
    The number of probes hybridized to form a double-stranded polymer for use in the methods mentioned above is in a range of 102 to 1015.
  • BRIEF DESCRIPTION OF THE DRAWINGS
  • [0026]
    [0026]FIG. 1 is a schematic diagram showing an example of a pair of DNA probes;
  • [0027]
    [0027]FIG. 2 is a schematic diagram of an example showing how a pair of DNA probes are bound;
  • [0028]
    [0028]FIG. 3 is a schematic diagram showing the formation of a polymer resulting from hybridization of a pair of DNA probes in alternation;
  • [0029]
    [0029]FIG. 4 is a schematic diagram illustrating an example of a three-dimensional conceptual structure of the polymer shown in FIG. 3;
  • [0030]
    [0030]FIG. 5 is a schematic diagram illustrating DNA probes which are hybridized in binding patterns different from those of FIG. 3;
  • [0031]
    [0031]FIG. 6 illustrates an example of a three-dimensional conceptual structure of the schematic diagram of FIG. 5;
  • [0032]
    [0032]FIG. 7 is a schematic diagram showing an example of a pair of DNA probes in which portions cleaved by a restriction enzyme are inserted;
  • [0033]
    [0033]FIG. 8 is a schematic diagram illustrating an example in which probes are three-dimensionally bound in alternation to form a polymer which is subsequently cleaved using a restriction enzyme;
  • [0034]
    [0034]FIG. 9 is a schematic diagram showing an example of a pair of DNA probes each composed of complementary portions having different lengths from each other;
  • [0035]
    [0035]FIG. 10 is a schematic diagram illustrating the formation of a polymer resulting from alternate hybridization of the pair of DNA probes, shown in FIG. 9.
  • [0036]
    [0036]FIG. 11 is a schematic diagram showing a method of directly detecting a target gene using a pair of DNA probes according to the present invention, wherein a probe having complementary regions to a target gene and the pair of DNA probes according to the present invention (amplifying genes in the figure) is hybridized to the target gene, and then the pair of DNA probes according to the present invention (amplifying gene 1 and amplifying gene 2 in the figure) are added to form a double-stranded polymer while hybridized to the target gene, so that the target gene can be readily detected;
  • [0037]
    [0037]FIG. 12 is a schematic diagram showing a method of detecting a target gene which uses a pair of DNA probes, one of which is a DNA probe (amplifying gene 1 in the figure) structured such that a gene in a portion thereof is complementary to a target gene, and the other of which is a DNA probe (amplifying gene 2 in the figure) making a pair with the one DNA probe, hybridizes a plurality of the pairs of probes with the target probe to form a double-stranded polymer, and detects the target gene;
  • [0038]
    [0038]FIG. 13 is a flow diagram illustrating a first aspect of an antigen/antibody detecting method according to the present invention;
  • [0039]
    [0039]FIG. 14 is a photograph showing the results of Example 1;
  • [0040]
    [0040]FIG. 15 is a photograph showing the results of Example 2; and
  • [0041]
    [0041]FIG. 16 is a photograph showing the results of Example 3.
  • DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
  • [0042]
    Several embodiments of the present invention will hereinafter be described with reference to the accompanying drawings. It goes without saying, however, that these embodiments are merely illustrative, and a variety of modifications may be made without departing from the spirit and scope of the present invention.
  • [0043]
    [0043]FIG. 1 is a schematic diagram showing an example of a pair of DNA probes. Referring specifically to FIG. 1, a DNA probe No. 1 has an X-region, a Y-region and a Z-region, while a DNA probe No. 2 has an X′-region, a Y′-region and a Z′-region.
  • [0044]
    The DNA probe No. 1 and the DNA probe No. 2 are structured such that when they are hybridized, the X-region is bound only with the X′-region; the Y-region is bound only with the Y′-region; and the Z-region is bound only with the Z′-region (see FIG. 2).
  • [0045]
    Stated another way, with a pair of DNA probes each composed of three or more portions complementary to such portions of the other DNA probe, according to the present invention, when they are hybridized such that they cross in alternation, the X-region is bound only with the X′-region; the Y-region is bound only with the Y′-region; and the Z-region is bound only with the Z′-region, as shown in FIG. 2, so that the pair of probes are hybridized in alternation in three binding patterns.
  • [0046]
    Thus, by the use of the probes structured as mentioned above, the two probes are bound in alternation. Specifically, the DNA probe No. 1 and the DNA probe No. 2 are three-dimensionally bound in alternation to produce a polymer, as illustrated in FIG. 3.
  • [0047]
    Consequently, a plurality of pairs of probes, which have been hybridized in alternation in the three binding patterns shown in FIG. 2, can form a double-stranded polymer, one example of which is schematically illustrated in FIG. 3.
  • [0048]
    [0048]FIG. 4 illustrates an example of a three-dimensional conceptual structure of the double-stranded polymer of FIG. 3. FIG. 5 is a schematic diagram illustrating a plurality of pairs of the DNA probes which have been hybridized in different binding patterns. FIG. 6 illustrates an example of a three-dimensional conceptual structure of the schematic diagram of FIG. 5.
  • [0049]
    The same principle of hybridization for the two DNA probes illustrated in FIG. 3 applies to hybridization of a DNA probe and an RNA probe, two RNA probes, two PNA probes, a PNA probe and a DNA probe, or a PNA probe and an RNA probe.
  • [0050]
    Illustrating the structure of the present invention using a more specific example, the hybridization of two DNA probes may be performed such that when a probe No. 3 and a probe No. 4 are hybridized, cleaved sites are formed by a restriction enzyme (underlined portions are cleaved by an enzyme called “Hae III”), as shown in FIG. 7.
  • [0051]
    In other words, after the probes have three-dimensionally bound in alternation to form a polymer, a restriction enzyme can be used to prevent the polymer from cross-contamination in a subsequent different experimental operation (see FIG. 8).
  • [0052]
    Illustrating the structure of the present invention using a more specific example, the hybridization of two DNA probes does not require that the lengths of complementary portions in one probe be uniform, as shown in FIG. 9. Specifically, when a probe No. 5 and a probe No. 6 are hybridized, an X-region and an X′-region are hybridized with 24 bases; a Y-region and a Y′-region hybridize with 22 bases; and a Z-region and a Z′-region hybridize with 20 bases (see FIG. 10).
  • [0053]
    Next, the target gene detecting method according to the present invention will be described using more specific examples. In a first aspect as illustrated in FIG. 11, out of a pair of probes, one probe is structured such that a portion of gene in the probe is complementary to a target gene. After the one probe is hybridized with the target gene, a plurality of the pairs of probes are hybridized by the gene amplification method according to the present invention to form a double-stranded polymer which is detected by amplifying the probes.
  • [0054]
    In a second aspect as illustrated in FIG. 12, other than a pair of probes, a probe complementary to a gene in a portion of one of the probes and a target probe is used, and previously hybridized with the target gene. Then, a plurality of the pairs of probes are hybridized by the gene amplifying method mentioned above to form a double-stranded polymer which is detected by amplifying the probes.
  • [0055]
    Next, a first aspect of an antigen/antibody detecting method according to the present invention will be described using a more specific example with reference to FIG. 13. As illustrated, out of a pair of probes, one probe is structured such that a gene in a portion thereof is complementary to a target gene bound to antigen/antibody. Then, a plurality of the pairs of probes are hybridized by the gene amplifying method according to the present invention to form a double-stranded polymer to detect the antigen and the antibody.
  • [0056]
    In the following, the present invention will be described in conjunction with several examples. It goes without saying, however, that the present invention is not limited to these examples.
  • [0057]
    1. Dna Probes used in Example 1 And Example 2:
  • [0058]
    (1) Gene Amplifying Probe 1
  • [0059]
    5-TgA CTT ACT TAA CCg gAA ACA T.AAg CAg gAT CCT CTA AgC CTg A.CgA AgT ATT TAA Cgg Tgg TAT g-3
  • [0060]
    (2) Gene Amplifying Probe 2
  • [0061]
    3-gCT TCA TAA ATT gCC ACC ATA C.TTC gTC CTA ggA gAT TCg gAc T.ACT gAA TgA ATT ggC CTT TgT A-5
  • [0062]
    (3) Gene Amplifying Probe 3
  • [0063]
    [0063]5′- TgC CgA CCg gCg AgC g.TAg CAT ggC CCT CTA g.CTT ATC ggC CTC gAg A-3′
  • [0064]
    (4) Gene Amplifying Probe 4
  • [0065]
    3′- gAA TAg CCg gAg CTC T.ATC gTA CCg ggA gAT C.ACg gCTggC CgC TCgC -5′
  • [0066]
    2. Synthetic HCV-RNA and a variety of DNA probes used in Example 3 and Example 4:
  • [0067]
    (1) HCV-RNA which synthesizes a 5′-noncoding region of hepatitis C virus (hereinafter abbreviated as “synthesized HCV-RNA).
  • [0068]
    (2) HCV-RNA capture Probe A
  • [0069]
    5′(phosphoric acid)-TAg AgC gTg CAg ATA gTC gAT.CCT CAC Agg ggA gTg ATT CAT ggT-3′
  • [0070]
    This is a combination of a meaningless base sequence and a base sequence complementary to HCV-RNA.
  • [0071]
    (3) HCV-RNA capture Probe B
  • [0072]
    5′(biotin label)-TAg AgC gTg CAg ATA gTC gAT.CCT CAC Agg ggA gTg ATT CAT ggT-3′
  • [0073]
    This is a combination of a meaningless base sequence and a base sequence complementary to HCV-RNA.
  • [0074]
    (4) Probe C
  • [0075]
    3′-TAC TTA gTg Agg ggA CAC TCC.gAA TAA gTC ATA gCT CAT-5′
  • [0076]
    This is a combination of a base sequence complementary to HCV-RNA and a base sequence complementary to the amplifying probe 5.
  • [0077]
    (5) Probe D
  • [0078]
    3′-gCC CAg gAA AgA ACC TAg TTg gAA TAA gTC ATA gCT CAT-5′
  • [0079]
    This is a combination of a base sequence complementary to HCV-RNA and a base sequence complementary to the amplifying probe 5.
  • [0080]
    (6) Probe E
  • [0081]
    3′-CAT CAC AAC CCA gCg CTT TCC.gAA TAA gTC ATA gCT CAT-5′
  • [0082]
    This is a combination of a base sequence complementary to HCV-RNA and a base sequence complementary to the amplifying probe 5.
  • [0083]
    (7) Gene Amplifying Probe 5
  • [0084]
    5′-CTT ATT CAg TAT CgA gTA TAg CAg gAT CCC TCT AAg.TgC Cgg ACC AgC gAg Cgg-3′
  • [0085]
    This is a base sequence complementary to the capture probes B, C, D.
  • [0086]
    (8) Gene Amplifying Probe 6
  • [0087]
    3′-ACg gCC Tgg TCg CTC gCC.ATC gTC CTA ggg AgA TTC.gAA TAA gTC ATA gCT CAT-5′
  • [0088]
    (9) Gene Amplifying Probe 7
  • [0089]
    3′(biotinized)-ACg gCC Tgg TCg CTC gCC.ATC gTC CTA ggg AgA TTC.gAA TAA gTC ATA gCT CAT-5′
  • EXAMPLE 1
  • [0090]
    1. Object
  • [0091]
    The effect of gene amplification with respect to the temperature of hybridization was proved using gene amplifying probes which are a pair of DNA probes according to the present invention.
  • [0092]
    2. Materials
  • [0093]
    1) The probe 1 for gene amplification and the probe 2 for gene amplification were used for gene amplification.
  • [0094]
    2) 20×SSC (333 mM-NaCl, 333 mM-C6H5O7Na3.2H2O, pH 7.0) was used as a buffering solution.
  • [0095]
    3. Method
  • [0096]
    5 μL of the gene amplifying probe 1 and the gene amplifying probe 2 each prepared to be 1013 copies/μL were added in a sterilized microtube of 0.2 mL, respectively. 40 μL of 20×SSC was further added, and the microtube was covered with a lid. Then, the microtube was boiled at 94° C. for 30 seconds, and warmed at 50° C., 52° C., 54° C., 56° C., 58° C., 60° C., 62° C., 64° C., 66° C., 68° C. and 70° C. for 30 minutes, respectively.
  • [0097]
    After the warming, electrophoresis was performed using 0.5% agarose gel to confirm the effect of the gene amplification through ethidium bromide coloring.
  • [0098]
    4. Results
  • [0099]
    [0099]FIG. 14 is a photograph showing the results of Example 1 with electrophoresis at 100 volts for 30 minutes using 0.5% agarose gel.
  • [0100]
    The agarose gel is a gel which can divide DNA molecules according to the size, and 0.5% agarose gel is generally used to separate DNA molecules of 30,000-40,000 base pairs.
  • [0101]
    The photograph of FIG. 14 shows a polymer which has grown so much with increasing temperatures that it can no longer migrate with 0.5% agarose gel as a result of an exactly alternate double-stranded polymer formed by the pair of DNA probes depending on the temperature of hybridization.
  • EXAMPLE 2
  • [0102]
    1. Object
  • [0103]
    It was proved that a polymer amplfied by probes for gene amplification, which are a pair of DNA probes according to the present invention, can be cleaved by a restriction enzyme.
  • [0104]
    2. Materials
  • [0105]
    1) The gene amplifying probe 3 and the gene amplifying probe 4 were used for gene amplification.
  • [0106]
    2) Hae III (made by Takara Shuzo (brewer) Co., Ltd.) was used as a restriction enzyme.
  • [0107]
    3) M-Buffer (made by Takara Shuzo (brewer) Co., Ltd.) was used as a buffering solution for restriction enzyme.
  • [0108]
    4) 20×SSC (333 mM-NaCl, 333 mM-C6H5O7Na3.2H2O, pH 7.0) was used as a buffering solution.
  • [0109]
    3. Method
  • [0110]
    5 μL of the gene amplifying probe 3 and the gene amplifying probe 4 each prepared to be 1013 copies/μL were added in a sterilized microtube of 0.2 mL, respectively. 5 μL of 20×SSC and 35 μL of sterilized distilled water were further added to produce a reaction solution A, and the microtube was covered with a lid. Similarly to the reaction solution A, 2.5 μL of the gene amplifying probe 3 and the gene amplifying probe 4 each prepared to be 1013 copies/μL were added in a sterilized microtube of 0.2 mL, respectively. 5 μL of 20×SSC and 40 μL of sterilized distilled water were further added to produce a reaction solution B, and the microtube was covered with a lid. The reaction solutions A, B were boiled at 94° C. for 30 seconds, and warmed at 62° C. for 30 minutes, respectively.
  • [0111]
    After the warming, 5 μL of M-Buffer and 5 μL of Hae III were added to each of the reaction solutions A, B for reaction at 37° C. for 24 hours, and electrophoresis was performed using 2% agarose gel to confirm an amplified polymer cleaved by the restriction enzyme through ethidium bromide coloring.
  • [0112]
    4. Results
  • [0113]
    [0113]FIG. 15 is a photograph showing the results of Example 2 with electrophoresis at 100 volts for 30 minutes using 2% agarose gel. The photograph shows that a pair of DNA probes forming a exactly alternate double-stranded polymer is was cleaved to minimum units by the restriction enzyme.
  • EXAMPLE 3
  • [0114]
    1. Materials
  • [0115]
    1) The gene amplifying probe 5 and the gene amplifying probe 6 were used for gene amplification.
  • [0116]
    2) Magnetic beads bound with streptavidin (product name: Streptavidin MagneSphere made by Promega) was used for a solid phase for B/F separation.
  • [0117]
    3) 20×SSC and 0.5×SSC (40-times diluent of 20×SSC) were used as buffering solutions.
  • [0118]
    2. Method
  • [0119]
    10 μL each of synthetic HCV-RNA prepared to be 101 copy/10 μL, 102 copy/10 μL, 103 copy/10 μL, 104 copy/10 μL, 105 copy/10 μL, 106 copy/10 μL, 107 copy/10 μL, 108 copy/10 μL, 109 copy/10 μL, and 1010 copy/10 μL were each added in a sterilized microtube of 0.2 mL. Next, 1 μL each of the HCV-RNA capture probe B, probe C, probe D and probe E prepared to be 1013 copies/μL, 10 μL of the gene amplifying probe 5 prepared to be 1013 copies/μL, and 25 μL of 20×SSC were added. The respective microtubes were covered with a lid, the ingredients were mixed by a mixer, and warmed at 62° C. for 60 minutes.
  • [0120]
    Once the temperature lowered to a room temperature, 5 μL of the gene amplifying probe 6 prepared to be 1013 copies/μL was added to each of the microtubes. Then, each of the microtubes was covered with a lid, and the ingredients were mixed by a mixer and warmed at 62° C. for 60 minutes.
  • [0121]
    Once the temperature lowered to a room temperature, 10 μL of Streptavidin MagneSphere (hereinafter called the “magnetic beads”) was added to each of the microtubes for reaction at 37° C. for 30 minutes. After the reaction, the magnetic beads were trapped using a magnet, and supernatant was removed. Then, 50 μL of 0.5×SSC and 10 μL of ethidium bromide (made by Wako Junyaku Co., Ltd.) prepared to be 100 μg/mL were added for reaction at a room temperature for 20 minutes.
  • [0122]
    After the reaction, the magnetic beads were trapped using a magnet, and supernatant was removed. Then, 50 μL of 0.5×SSC was added. Immediately, the magnetic beads were trapped using a magnet, and supernatant was removed. Then, 50 μL of 0.5×SSC was added, and all ingredients were transferred to a flat-bottom 96 well plate. Ultraviolet rays were irradiated from the bottom of the 96 well plate, and an amplified gene, which ended up to emit fluorescence by intercalation of ethidium bromide, was photographed.
  • [0123]
    3. Results
  • [0124]
    [0124]FIG. 16 is a photograph showing the fluorescence by the ethidium bromide produced by irradiating ultraviolet rays from the bottom of the 96 well plate. As can be seen in FIG. 16, the strongest fluorescence was found at 1010 copies/10 μL, and the fluorescence became gradually weaker in accordance with the amount of synthetic HCV-RNA.
  • EXAMPLE 4
  • [0125]
    1. Materials
  • [0126]
    1) The gene amplifying probe 5 and the gene amplifying probe 7 were used for gene amplification.
  • [0127]
    2) A 96 well plate (product name: NucleoLink™ made by Nunc) was used for a solid phase for B/F separation.
  • [0128]
    3) “HPR-Streptavidin” made by ZYMED Laboratories, Inc. was used as Peroxidase Conjugated Streptavidin.
  • [0129]
    4) A coloring kit T for peroxidase made by Sumitomo Bakelite Co., Ltd. was used as a coloring reagent.
  • [0130]
    5) 2N-H2SO4 was used for an enzyme reaction stop solution.
  • [0131]
    6) 20×SSC and 0.5×SSC were used as buffering solutions.
  • [0132]
    2. Method
  • [0133]
    10 μL each of synthetic HCV-RNA prepared to be 0 copy/10 μL, 103 copies/10 μL, 104 copies/10 μL, 105 copies/10 μL, 106 copies/10 μL, and 107 copies/10 μL were added to each of wells in a 96 well plate (NucleoLink™ made by Nunc) previously bound with the HCV-RNA capture probe A (special blocking was not applied). Then, 10 μL each of the probe C, probe D, probe E prepared to be 1011 copies/μL, 10 μL of the gene amplifying probe 5 prepared to be 1011 copies/μL, and 60 μL of 20×SSC were added.
  • [0134]
    After mixing the ingredients by a pipette, they were heated at 94° C. for 30 seconds, and warmed at 62° C. for 60 minutes.
  • [0135]
    Once the temperature lowered to a room temperature, 10 μL of the gene amplifying probe 5 prepared to be 1011 copies/μL, and 20 μL of the gene amplifying probe 7 were added to each of the microtubes. They were mixed by a pipette, and then heated at 94° C. for 30 seconds, and warmed at 62° C. for 60 minutes.
  • [0136]
    After the temperature lowered to a room temperature, 0.5×SSC including 0.1%-Tween20 was used to wash four times. 100 μL of “HRP-Streptavidin” was added in each well, and warmed at 37° C. for 20 minutes. After removing the solution in each well by means of suction, 0.5×SSC including 0.1%-Tween20 was used to wash four times.
  • [0137]
    100 μL of the coloring kit T for peroxidase was added to each well for reaction in a dark room (at a room temperature) for 10 minutes. After the reaction, 100 μL of the enzyme reaction stop solution was added, and the light absorption was measured at wavelength of 450 nm.
  • [0138]
    3. Results
  • [0139]
    The results of Example 4 are shown in Table 1 below. Coloring was confirmed in accordance with the amount of added synthesized HCV-RNA in a range of 103 to 107 copies from the fact that coloring was observed in Peroxidase Conjugated Streptavidin labelled at one of a pair of DNA probes which were hybridized in alternation to form a double-stranded polymer.
    TABLE 1
    Number of Copies Absorbance
    0 1.497
    103 1.843
    104 1.897
    105 1.955
    106 2.064
    107 2.343
  • [0140]
    As described above, the gene amplifying method according to the present invention can efficiently amplify a gene without using a DNA polymerase or branched DNA.
  • [0141]
    Also, the antigen/antibody detecting method according to the present invention can efficiently detect antigen/antibody by making use of the gene amplifying method.
  • [0142]
    Obviously various minor changes and modifications of the present invention are possible in the light of the above teaching. It is therefore to be understood that within the scope of the appended claims the invention may be practiced otherwise than as specifically described.
Referenced by
Citing PatentFiling datePublication dateApplicantTitle
US7393636Oct 30, 2002Jul 1, 2008Sanko Junyaku Co., Ltd.Method for forming self-assembly substance using oligonucleotide synthesized by gene amplification reaction, self-assembly substance and method for detecting gene
US7927804Mar 14, 2007Apr 19, 2011Eisai & Managment Co., Ltd.Method of forming signal probe-polymer
US20030175689 *Aug 14, 2001Sep 18, 2003Mitsugu UsuiGene detecting method
US20060286553 *Oct 30, 2002Dec 21, 2006Mitsugu UsuiMethod for forming self-assembly substance using oligonucleotide synthesized by gene amplification reaction, self-assembly substance and method for detecting gene
US20080318226 *Feb 28, 2006Dec 25, 2008Eisair & Dmanagement Co., Ltd.Signal Amplification Method
Classifications
U.S. Classification435/91.1, 435/91.2, 435/6.13
International ClassificationC12N15/09, C12Q1/68, G01N33/50, G01N33/566
Cooperative ClassificationC12Q1/6804, C12N15/10, Y10T436/143333, C12Q1/682
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