Method of detecting variation or polymorphism

• US 7,175,985 B1
• Filed: 08/02/2002
• Issued: 02/13/2007
• Est. Priority Date: 11/08/1999
• Status: Expired due to Term

• Current Assignee: Eiken Kagaku Kabushiki Kaisha
• Original Assignee: Eiken Kagaku Kabushiki Kaisha
• Inventors: Notomi, Tsugunori, Kanda, Hidetoshi, Nagamine, Kentaro, Yonekawa, Toshihiro
• Primary Examiner(s): Strzelecka; Teresa E.
• Assistant Examiner(s): CALAMITA, HEATHER
• Application Number:
  US10/129,637
• Time in Patent Office: 1,656 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 536/23.1, 536/24.33
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2531/101 Linear amplification, i.e. non exponential
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2537/1373 Displacement by a nucleic acid
• CPC Class Codes: Y02A 50/30 Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

The method of the present invention is based on a method wherein a nucleic acid is synthesized utilizing the hybridized 3′-end, which is synthesized by complementary strand synthesis, on a specific region of a target nucleotide sequence existing as the nucleotide sequence of the same strand as the origin for the next round of complementary strand synthesis. The hybridization to a specific region, which region is searched for mutations and polymorphisms, is repeatedly carried out according to the present invention. Thus, mutations and polymorphisms in a target nucleotide sequence are exactly copied to the reaction products.

Claims

1. A method for detecting mutations and/or polymorphisms within a specific region of a target nucleotide sequence comprising the steps of:

(1) incubating the following elements (a) to (e) under conditions that allow complementary strand synthesis wherein second and first primers are used as origins;

(a) a nucleic acid sample comprising a target nucleotide sequence;

(b) a DNA polymerase catalyzing complementary strand synthesis which includes strand displacement;

(c) a second primer, wherein the 3′

-end of the second primer anneals to the 3′

-side region of one strand of said target nucleotide sequence and the 5′

-side of the second primer includes a nucleotide sequence complementary to the predicted nucleotide sequence that constitutes a region on the products of the complementary strand synthesis reaction that uses the second primer as the origin;

(d) a first primer, wherein the 3′

-end of the first primer anneals to the 3′

-side region of the other strand of said target nucleotide sequence, and the 5′

-side of the first primer includes a nucleotide sequence complementary to the predicted nucleotide sequence that constitutes a region on the products of the complementary strand synthesis reaction that uses the first primer as the origin; and

(e) nucleotide substrates; and

(2) correlating the amount of product synthesized by a complementary strand synthesis reaction, which uses the target nucleotide sequence as the template, with the presence of a mutation and/or polymorphism in the specific region, wherein a nucleotide sequence arranged on at least one of the 5′

-ends of the second and first primer contains a nucleotide sequence that is complementary to the predicted nucleotide sequence of said specific region or the complementary strand thereof, and wherein the complementary strand, that is synthesized using the nucleotide sequence arranged on the 5′

-end as the template and functions as the origin of complementary strand synthesis by annealing to the specific region or the complementary strand thereof, inhibits the complementary strand synthesis when the nucleotide sequence that contains the specific region is not a predicted one.

2. The method of claim 1, wherein both of the nucleotide sequences arranged on the 5′

-end of the second primer or first primer contain a nucleotide sequence that is complementary to the predicted nucleotide sequence of said specific region or the complementary strand thereof, and wherein the complementary strand, that is synthesized using the nucleotide sequence arranged on the 5′

-end as the template and functions as the origin of complementary strand synthesis by annealing to the specific region or the complementary strand thereof, inhibits the complementary strand synthesis when the nucleotide sequence that contains the specific region is not a predicted one.

3. The method of claim 1, additionally comprising the following elements:

(f) a third primer, wherein the third primer serves as the origin of the complementary strand synthesis reaction, further wherein the 3′

-side of the annealing region of the first primer on the template functions as the origin; and

,

(g) a fourth primer, wherein the fourth primer serves as the origin of the complementary strand synthesis reaction, further wherein the 3′

-side of the annealing region of the second primer on the template functions as the origin.

4. The method of claim 1, wherein a gene comprising a nucleotide sequence similar to the nucleotide sequence of the target nucleotide sequence is present in the same sample.

5. The method of claim 4, wherein the gene is a family gene and/or a pseudogene.

6. The method of claim 5, wherein the family gene and/or the pseudogene is any gene selected from the group consisting of the cytochrome P450 family, human leukocyte histocompatibility antigens, and platelet alloantigens.

7. The method of claim 1, wherein the polymorphism is a single nucleotide polymorphism.

8. The method of claim 1, wherein the target nucleotide sequence is selected from the nucleotide sequences of genes from any pathogenic virus or pathogenic microorganism selected from the group consisting of hepatitis C virus, influenza virus, malaria, and Helicobacter pylori.

9. The method of claim 1, wherein the incubation of step (1) is performed in the presence of a melting temperature regulator.

10. The method of claim 9, wherein the melting temperature regulator is at least one of the compounds selected from the group of betaine, proline, and dimethylsulfoxide.

11. The method of claim 1, wherein the nucleic acid sample is double stranded.

12. The method of claim 1, wherein the method is carried out in the presence of a nucleic acid detector to detect the presence of a mutation and/or polymorphism based on a change in the signal of the detector.

13. The method of claim 1, wherein a nucleotide sequence derived from the same organism as the organism for which a mutation and/or polymorphism is to be detected, and which sequence is confessed to include no mutation and/or polymorphism, is used as an internal standard, and the presence of a mutation and/or polymorphism is detected by comparing the amounts of synthesized products obtained using the nucleotide sequences as templates.

14. The method of claim 1, additionally comprising:

(h) a first loop primer, wherein the first loop primer provides an origin for complementary strand synthesis between a region originating from the first primer in the elongation product of the first primer and said arbitrary region for the first primer; and

/or

(i) a second loop primer, wherein the second loop primer provides an origin for complementary strand synthesis between a region originating from the second primer in the elongation product of the second primer and said arbitrary region for the second primer.

15. The method of claim 1, when the nucleotide sequence that comprises said specific region is not the predicted nucleotide sequence, a mismatch occurs during annealing to the specific region or the complementary strand thereof in the second to the fourth nucleotide from the 3′

-end of the complementary strand which is synthesized using the nucleotide sequence arranged on the 5′

-end of the first primer and/or second primer as the template.

16. A method for detecting mutations and/or polymorphisms in a specific region of a target nucleotide sequence, wherein the nucleotide sequence arranged on at least one of the 5′

-ends of a second and first primer contains a nucleotide sequence that is complementary to the predicted nucleotide sequence of said specific region or the complementary strand thereof, and wherein the complementary strand, that is synthesized using the nucleotide sequence arranged on the 5′

-end as the template and functions as the origin of complementary strand synthesis by annealing to the specific region or the complementary strand thereof, inhibits the complementary strand synthesis when the nucleotide sequence that contains the specific region is not a predicted one, which method comprises the steps of;

a) annealing a first primer to a target nucleotide sequence to carry out a complementary strand synthesis reaction using the primer as the origin, wherein the 3′

-end of the first primer anneals to a 3′

-side region of one of said target nucleotide sequence strands, and the 5′

-side of the first primer includes a nucleotide sequence complementary to the predicted nucleotide sequence that contains a region on the product of the complementary strand synthesis reaction that uses the primer as the origin;

b) putting the region, to be annealed with the second primer, in the elongation product of the first primer synthesized in step a) into a state allowing base pairing of the region to the second primer, annealing them to synthesize the complementary strand using the elongation product of the first primer as a template;

wherein the 3′

-end of the second primer anneals to the 3′

-side region of the other said target nucleotide sequence strand, and the 5′

-side of the second primer includes a nucleotide sequence complementary to the predicted nucleotide sequence that contains a region on the product of the complementary strand synthesis reaction that uses the primer as the origin;

c) carrying out a complementary strand synthesis using the elongation product of the second primer itself as a template by annealing the 3′

-end of the product with said predicted nucleotide sequence to the first primer in said elongation product;

d) carrying out a complementary strand synthesis using the complementary strand synthesized in step c) itself as a template by annealing the 3′

-end of the complementary strand synthesized in step c) with said predicted nucleotide sequence to the second primer in said elongation product; and

e) correlating the amount of synthesized product obtained using the second primer as the origin with the presence of a mutation and/or polymorphism in the specific region.

17. The method of claim 16, wherein step b) comprises a step of converting the elongation product of the first primer to a single strand by displacement, which displacement is conducted by a complementary strand synthesis reaction using the third primer that uses the 3′

-side of the region annealing to the first primer in the template as the origin.

18. The method of claim 16, wherein step c) comprises a step of converting the elongation product of the second primer to a single strand by displacement, which displacement is conducted by a complementary strand synthesis reaction using the fourth primer that uses the 3′

-side of the region annealing to the second primer in the template as the origin.

19. The method of claim 16, wherein the nucleotide sequence arranged on at least one of the 5′

-ends of a second and first primer contains a nucleotide sequence that is complementary to the predicted nucleotide sequence of said specific region or to the complementary strand thereof, and wherein the complementary strand, that is synthesized using the nucleotide sequence arranged on the 5′

-end as the template and functions as the origin of complementary strand synthesis by annealing to a specific region or the complementary strand thereof, inhibits the complementary strand synthesis when the nucleotide sequence that contains the specific region is not a predicted one, which method additionally comprises the steps of;

1) carrying out the complementary strand synthesis reaction of step (c) in the method of claim 16 by forming a loop forming region, that forms a base pair with a nucleotide sequence complementary to the 3′

-end of the first primer, by annealing the 3′

-end and the predicted nucleotide sequence within the elongation product of the second primer, and using the 3′

-end of itself as the origin for the complementary strand synthesis;

2) annealing the first primer to the loop forming region, and carrying out complementary strand synthesis using the first primer as the origin with DNA polymerase catalyzing complementary strand synthesis which includes a strand displacement;

3) displacing the product elongated from its own 3′

-end by a complementary strand synthesis reaction using a primer, that anneals to the loop forming region as the origin, to enable base pairing of the 3′

-end and said predicted nucleotide sequence again;

4) forming a single stranded nucleic acid by displacing the complementary strand synthesized using the loop forming region as the origin by annealing the 3′

-end, that was put in a state to form a base pair in step

     3), to said predicted nucleotide sequence as the origin of the complementary strand synthesis to carry out a complementary strand synthesis reaction which uses itself as the template;

5) forming a loop forming region, that forms a base pair with a nucleotide sequence complementary to the 3′

-end of the second primer, by annealing the 3′

-end and said predicted nucleotide sequence for the second primer, and by complementary strand synthesis;

6) annealing the second primer to the loop forming region, and carrying out a complementary strand synthesis using the second primer as the origin by DNA polymerase catalyzing complementary strand synthesis including a strand displacement;

7) repeating steps

     3) to

     6); and

8) following step

     7) and/or in parallel with step

     7), detecting the formation of a single stranded nucleic acid, in which the target nucleotide sequence and the complementary strand thereof are repeatedly linked, and correlating the amount of formation with a mutation and/or polymorphism.

20. The method of claim 19, additionally comprising the steps of:

9) carrying out the complementary strand synthesis reaction using the single stranded nucleic acid formed in step

     4) as the template by annealing the 3′

-end thereof to said predicted nucleotide sequence for the second primer, forming a loop forming region, that forms a base pair with a nucleotide sequence complementary to the 3′

-end of the second primer, and using the 3′

-end of itself as the origin for the complementary strand synthesis;

10) annealing the second primer to the loop forming region, which region was formed by annealing the 3′

-end with its own said specific region, and carrying out complementary strand synthesis using the second primer as the origin by DNA polymerase catalyzing complementary strand synthesis which includes a strand displacement;

11) displacing the product elongated from its own 3′

-end by a complementary strand synthesis reaction using a primer, that anneals to the loop forming region as the origin, to enable base pairing of the 3′

-end and said predicted nucleotide sequence again;

12) forming a single stranded nucleic acid by displacing the complementary strand synthesized using the loop forming region as the origin by annealing the 3′

-end, that was put in a state to form a base pair in step

     11), to said predicted nucleotide sequence as the origin of complementary strand synthesis to carry out a complementary strand synthesis reaction which uses itself as the template;

13) forming a loop forming region, that forms a base pair with a nucleotide sequence complementary to the 3′

-end of the first primer, by annealing of the 3′

-end and said predicted nucleotide sequence and carrying out complementary strand synthesis;

14) annealing the first primer to the loop forming region, and carrying out a complementary strand synthesis using the first primer as the origin by DNA polymerase catalyzing complementary strand synthesis which includes strand displacement;

15) repeating steps

     11) to

     14); and

16) following step

     15) and/or in parallel with step

     15), detecting the formation of a single stranded nucleic acid, in which the target nucleotide sequence and the complementary strand thereof are repeatedly linked, and correlating the amount of formation with a mutation and/or polymorphism.

21. The method of claim 20, additionally comprising the step of:

17) forming a loop forming region, that forms a base pair with a nucleotide sequence complementary to the 3′

-end of the first primer, by annealing the 3′

-end of the single stranded nucleic acid formed in step

     12) with said predicted nucleic acid sequence on itself, and carrying out a complementary strand synthesis reaction using the 3′

-end of itself as the origin and itself as the template.

22. The method of claim 16, wherein the nucleotide sequence arranged on the 5′

-end of both of the second primer and first primer contains a nucleotide sequence complementary to the predicted nucleotide sequence of said specific region or the complementary strand thereof, and wherein the complementary strand, that is synthesized using the nucleotide sequence arranged on the 5′

-end as the template and functions as the origin of complementary strand synthesis by annealing to the specific region or the complementary strand thereof, inhibits the complementary strand synthesis when the nucleotide sequence that contains the specific region is not a predicted one.