Method for sequencing DNA using biotin-strepavidin conjugates to facilitate the purification of primer extension products

• US 5,484,701 A
• Filed: 01/31/1992
• Issued: 01/16/1996
• Est. Priority Date: 01/26/1990
• Status: Expired due to Fees

• Current Assignee: E. I. du Pont de Nemours and Company (Corteva, Inc.)
• Original Assignee: E. I. du Pont de Nemours and Company (Corteva, Inc.)
• Inventors: Zagursky, Robert J., Straus, Neil A., Cocuzza, Anthony J., Hobbs, Frank W. Jr.
• Primary Examiner(s): Zitomer, Stephanie W.
• Application Number:
  US07/829,857
• Time in Patent Office: 1,446 Days
• Field of Search: 435/6, 435/91, 435/91.1, 435/91.5, 435/91.53, 435/91.2, 436/63, 436/94, 436/501, 436/508, 436/518, 935/76, 935/77, 935/78, 937/77, 937/78
• US Class Current: 435/6.11
• CPC Class Codes: C12N 15/1096 cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: G01N 33/58 involving labelled substances G01N33/53 takes precedence

Abstract

A simplified method for isolating primer extension products and generating them in a form appropriate for electrophoresis is disclosed. The method is compatible with automated DNA sequencing procedures.

Claims

1. In an improved method for sequencing DNA wherein the following steps are conventional:

(a) extending a primer by means of a template-directed primer extension reaction; and

(b) analyzing the primer extension products by means of gel electrophoresis, the improvement comprising;

(i) extending a biotinylated primer by means of a template-directed primer extension reaction to produce biotinylated primer extension products;

(ii) complexing the biotin of said biotinylated primer extension products of step (i) with a biotin-binding protein immobilized on a solid support, said complexing performed either before or after separating the template from the biotinylated primer extension products of step (i);

(iii) separating physically the complexed biotinylated primer extension products of step (ii) from the liquid phase of the primer extension reaction;

(iv) treating the complex of step (iii) with formamide compatible with gel-electrophoresis to dissociate the biotin of said biotinylated primer extension products from the immobilized biotin-binding protein;

(v) analyzing the biotinylated primer extension products of step (iv) by means of gel electrophoresis; and

(vi) sequencing the DNA of the primer extension products obtained.

2. The method of claim 1 wherein the biotinylated primer is extended in step (i) by means of a template, a polymerase, and one or more nucleoside triphosphates.

3. The method of claim 1 wherein the biotin in the biotinylated primer is linked through the 5'"'"'-hydroxyl group of the primer.

4. The method of claim 1 wherein the biotinylated primer extension products of step (i) are treated with a strong base, heat, a single-strand nuclease, or formamide.

5. The method of claim 4 wherein the products of step (i) are treated with a strong base.

6. The method of claim 4 wherein the products of step (i) are treated with heat at a temperature between 25°

and 100°

C.

7. The method of claim 4 wherein the products of step (i) are treated with a single-strand nuclease.

8. The method of claim 1 wherein, in step (ii), the solid support is selected from the group consisting of polymeric beads, and magnetic particles, and paper, plastic and glass surfaces.

9. The method of claim 8 wherein the magnetic particles are chromium dioxide particles.

10. The method of claim 2, wherein, in step (ii), the biotin-binding protein is selected from the group consisting of avidin, streptavidin, and anti-biotin antibodies.

11. The method of claim 1 wherein said electrophoresis-compatible formamide is heated to a temperature about 25°

C. to 100°

C.

28. The method of claim 6, 11, 13, 20, 22, 23,, 24, 25 or 27 wherein the formamide is heated to a temperature of about 95°

C.

12. A method for ioslating primer extension products from template-directed extension reactions comprising the following steps:

(a) complexing the biotin of a biotinylated primer to a biotin-binding protein immobilized on a solid support;

(b) extending the complexed biotinylated primer of step (a) by means of a template-directed primer extension reaction;

(c) separating the template from the complexed biotinylated primer extension products of step (b);

(d) separating physically the complexed biotinylated primer extension products of step (c) from the liquid phase of the primer extension reaction;

(e) treating the complex of step (d) with formamide to dissociate the biotin of said biotinylated primer extension products from the biotin-binding protein immobilized on a solid support; and

(f) sequencing the DNA of the primer extension products obtained.

13. The method of claim 12 wherein the biotin is linked through the 5'"'"'-hydroxyl group of the primer.

14. The method of claim 12 wherein, in step a, the solid support is selected from the group consisting of polymeric beads, magnetic particles, and paper, plastic and glass surfaces.

15. The method of claim 14 wherein the magnetic particles are chromium dioxide particles.

16. The method of claim 12 wherein, in step a, the biotin-binding protein is selected from the group consisting of avidin, streptavidin, and anti-biotin antibodies.

17. The method of claim 12 wherein the biotinylated primer is extended in step b by means of a template, a polymerase, and one or more nucleoside triphosphates.

18. The method of claim 12 wherein step c is accomplished by treating the products of step b with a strong base, heat, or a single-strand nuclease.

19. The method of claim 12 wherein the products of step b are treated with a strong base.

20. The method of claim 12 wherein the products of step b are treated with heat at a temperature of about 25°

C. to 100°

C.

21. The method of claim 12 wherein the products of step b are treated with a single-strand nuclease.

22. The method of claim 12 wherein the electrophoresis-compatible formamide is heated to a temperature about 25°

C. to 100°

C.

29. The method of claim 7 or 21 wherein the single-strand nuclease is mung bean nuclease.

23. A method for isolating primer extension products from template-directed polymerase extension reactions comprising the following steps;

(a) extending a 5'"'"'-biotinylated primer by means of a template-directed polymerase extension reaction;

(b) separating the template from the 5'"'"'-biotinylated extension products of step (a) by the use of mung bean nuclease;

(c) complexing the biotin of the 5'"'"'-biotinylated extension products of step (a) with streptavidin on streptavidin-coated chromium dioxide particles;

(d) separating physically the complex of step (c) from the liquid phase of the primer extension reaction by means of a magnet;

(e) treating the complex of step (d) with formamide heated to a temperature between about 25°

C. to 100°

C. to dissociate the biotin of the 5'"'"'-biotinylated primer extension products from the streptavidin-coated chromium dioxide particles; and

(f) resolving the size the 5'"'"'-biotinylated primer extension products of step (e) by means of DNA sequencing of the primer extension products.

24. A method for isolating primer extension products from template-directed polymerase reactions comprising the following steps:

(a) extending a 5'"'"'-biotinylated oligonucleotide primer by means of a template-directed polymerase extension reaction;

(b) separating the template from the 5'"'"'-biotinylated extension products of step (a) by heating at a temperature of about 25°

C. to 100°

C.;

(c) complexing the biotin of the 5'"'"'-biotinylated extension products of step (a) with streptavidin on streptavidin-coated chromium dioxide particles;

(d) separating physically the complex of step (c) from the liquid phase of the primer extension reaction by means of a magnet;

(e) treating the complex of step (d) with formamide heated to a temperature between about 25°

C. to 100°

C.;

(f) analyzing the 5'"'"'-biotinylated primer extension products of step (d) by means of DNA sequencing; and

(g) sequencing the DNA of the primer extension products obtained.

25. A method for dissociating a complex, said complex consisting essentially of biotinylated primer extension products and solid-supported biotin-binding protein immobilized on a solid support, comprising treating said complex with formamide.

26. The method of claim 25 wherein the formamide is heated to a temperature between about 25°

C. to 100°

C.

27. A method for dissociating a complex, said complex consisting essentially of a biotinylated nucleic acid and a biotin-binding protein, comprising treating said complex with formamide heated to a temperature between about 25°

C. to 100°

C.