Methods of synthesizing and amplifying polynucleotides by ligation of multiple oligomers

• US 5,998,175 A
• Filed: 07/24/1998
• Issued: 12/07/1999
• Est. Priority Date: 07/24/1998
• Status: Expired due to Term

• Current Assignee: Lumigen, Inc. (Danaher Corporation)
• Original Assignee: Lumigen, Inc. (Danaher Corporation)
• Inventors: Akhavan-Tafti, Hashem
• Primary Examiner(s): Myers, Carla J.
• Assistant Examiner(s): JOHANNSEN, DIANA B
• Application Number:
  US09/121,887
• Time in Patent Office: 501 Days
• Field of Search: 435/91.1, 435/91.2, 435/91.5, 435/91.52, 435/6, 536/25.3, 536/25.32
• US Class Current: 435/91.5
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2563/167 Mass label

Abstract

Methods of synthesizing polynucleotides are disclosed involving the simultaneous ligation of a set of oligomer 5'"'"'-phosphates onto a template-bound primer. The set of these oligomers can be preselected to contain oligomers which are complementary to the template strand or the oligomers can be supplied as a library and allowed to self select. The synthesis by ligation can proceed unidirectionally or bidirectionally from the primer and can be used to synthesize both strands simultaneously by the use of two primers. The ligation is preferably performed with a ligase enzyme. The methods of synthesis are useful in a variety of applications, including cloning, amplification, labeling, diagnostic assays, mutation analysis and screening, gene expression monitoring and sequence analysis.

Claims

1. A method comprising:

a) providing a reaction mixture comprising a single stranded nucleic acid template, a primer having at least 15 bases which is complementary to a portion of the single stranded nucleic acid template, and a plurality of oligonucleotide 5'"'"'-monophosphates, wherein each oligonucleotide 5'"'"'monophoshate consists of not more than 10 bases;

b) hybridizing the primer with the template under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates to form a primer-template hybrid having a single stranded region and a double stranded region; and

c) ligating more than one of the plurality of oligonucleotide 5'"'"'-monophosphates in a contiguous manner onto the primer in one continuous process under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophospates, to extend the double stranded region and synthesize a complementary nucleic acid strand, wherein ligation of oligonucleotide 5'"'"'-monophosphates only occurs in the presence of the hybridized primer.

2. The method of claim 1 wherein the ligation is performed by means of a ligase enzyme.

3. The method of claim 2 wherein the ligase enzyme is T4 DNA ligase.

4. The method of claim 1 wherein each of the oligonucleotide 5'"'"'-monophosphates consists of the same number of bases and the number of bases is from 2 to 10.

5. The method of claim 4 wherein each of the oligonucleotide 5'"'"'-monophosphates consists of the same number of bases and the number of bases is from 2 to 6.

6. The method of claim 4 wherein each of the oligonucleotide 5'"'"'-monophosphates consists of 5 bases.

7. The method of claim 4 wherein the plurality of oligonucleotide 5'"'"'-monophosphates is a library of oligonucleotide 5'"'"'-monophosphates comprising at least 50% of all possible oligonucleotide 5'"'"'-monophosphates of the same length containing bases selected from A, C, G, T and U.

8. The method of claim 1 wherein the synthesis of the strand of nucleic acid is unidirectional and proceeds by ligation to the 3'"'"' end of the primer.

9. The method of claim 1 wherein the primer contains a 5'"'"'-phosphate group and the synthesis of the strand of nucleic acid is unidirectional and proceeds by ligation to the 5'"'"' end of the primer.

10. The method of claim 1 wherein the primer contains a 5'"'"'-phosphate group and the synthesis of the strand of nucleic acid proceeds in a bidirectional manner.

11. The method of claim 1 wherein the primer is immobilized onto a solid phase.

12. The method of claim 1 wherein the primer is in a solution.

13. The method of claim 1 wherein at least some of the oligonucleotide 5'"'"'-monophosphates comprise a detectable label.

14. The method of claim 13 wherein the detectable label is selected from radioisotopes, chemiluminescent labels, fluorescent labels, colorimetric labels, enzymes, binding proteins, antigens, antibodies and haptens.

15. The method of claim 13 wherein said detectable label is cleaved, and wherein the method further comprises a step after step c) in which a label or labels are cleaved from the synthesized complementary nucleic acid strand and subsequently detected.

16. The method of claim 15 wherein each oligonucleotide 5'"'"'-monophosphate comprises a detectable label which is cleaved before detection and wherein the detection of the cleaved labels is performed by simultaneously determining the molecular mass of each of the cleaved labels.

17. The method of claim 1 further comprising the incorporation of at least one nonextendable oligomer, the ligation of which terminates synthesis of the complementary nucleic acid strand.

24. A method of claim 1 wherein some of the plurality of oligonucleotide 5'"'"'-monophosphates consists of a different number of bases from other of the plurality of oligonucleotide 5'"'"'-monophosphates.

25. The method of claim 1 wherein the synthesis of the complementary nucleic acid strand synthesized in step c) is terminated at a predetermined position by excluding from the plurality of oligonucleotide 5'"'"'-monophosphates at least one oligonucleotide 5'"'"'-monophosphate which is complementary to the single stranded mucleic acid template and has a sequence mecessary to extend the double stranded region.

26. method of claim 1 wherein the single stranded nucleic acid template is produced by separating a double stranded nucleic acid.

27. The method of claim 2 wherein the ligase enzyme is selected from T4 ligase, T7 ligase, Tth ligase, Taq ligase and E. coli DNA ligase.

29. The method of claim 17 wherein each of the nonextendable oligomers is selected from oligomers which have a dideoxy base at the 3'"'"'-end, oligomers which have a blocked 3'"'"'-OH group at the 3'"'"'-end and oligomers which lack a phosphate group at the 5'"'"'-end.

18. A method for synthesizing an immobilized single stranded nucleic acid on a solid support, the nucleic acid having a region with a base sequence which is complementary to a portion of the base sequence of a test single stranded nucleic acid comprising;

a) providing a reaction mixture comprising the test single stranded nucleic acid, a capture probe/primer having at least 15 bases which is complementary to a portion of the test single stranded nucleic acid and which is immobilized on the solid support, and a plurality of oligonucleotide 5'"'"'-monophosphates, wherein each oligonucleotide 5'"'"'-monophosphate consists of not more than 10 bases;

b) hybridizing the capture probe/primer with the test single stranded nucleic acid under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates, to capture the test single stranded nucleic acid and form a captured probe-test nucleic acid hybrid having a single stranded region and a double stranded region;

c) ligating more than one of the plurality of oligonucleotide 5'"'"'-monophosphates to the capture probe/primer under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates, to extend the double stranded region wherein ligation of oligonucleotide 5'"'"'-monophosphates only occurs in the presence of the hybridized primer;

d) removing the oligonucleotide 5'"'"'-monophosphates which are not ligated; and

e) denaturing the captured probe-test nucleic acid hybrid having an extended double stranded region to remove the test nucleic acid and produce the immobilized single stranded nucleic acid.

19. A method for amplifying the amount of a portion of a double stranded nucleic acid having a first strand and a second strand comprising;

a) providing in a reaction mixture the double stranded nucleic acid, a first primer having at least 15 bases which is complementary to a region of the first strand, a second primer having at least 15 bases which is complementary to a region of the second strand wherein the first and second regions define the ends the portion of the double stranded nucleic acid to be amplified, and a plurality of oligonucleotide 5'"'"'-monophosphates, wherein each oligonucleotide 5'"'"'-monophosphate consists of not more than 10 bases;

b) separating the first and second strands of the double stranded nucleic acid;

c) hybridizing the first and second primers with the separated strands under conditions which permit stable hybridization of the primers but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates;

d) ligating onto each of the hybridized first and second primers more than one of the plurality of oligonucleotide 5'"'"'-monophosphates in a contiguous manner in one continuous process under conditions which permit stable hybridization of the primers but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates, to extend the first and second primers, wherein ligation of oligonucleotide 5'"'"'-monophosphates only occurs in the presence of the hybridized primers, thereby producing double stranded nucleic acid; and

e) repeating steps b-d to increase the amount of the portion of the double stranded nucleic acid.

20. The method of claim 19 wherein the ligation is performed by means of a ligase enzyme.

21. The method of claim 20 wherein the ligase enzyme is thermostable.

22. The method of claim 19 wherein at least one of the primers contains a 5'"'"'-phosphate group and wherein libation of oligonucleotide 5'"'"'monophosphates occurs at both ends of primers having 5'"'"'-phosphate groups.

23. A method of claim 19 further comprising the incorporation of at least one nonextendable oligomer, the ligation of which terminates synthesis of at least one of the first or second nucleic acid strands.

28. The method of claim 20 wherein the ligase enzyme is selected from T4 ligase, T7 ligase, Tth ligase, Taq ligase and E. coli DNA ligase.

30. The method of claim 23 wherein each of the nonextendable oligomers is selected from oligomers which have a dideoxy base at the 3'"'"'-end, oligomers which have a blocked 3'"'"'-OH group at the 3'"'"'-end and oligomers which lack a phosphate group at the 5'"'"'-end.

31. A method comprising:

a) providing a reaction mixture comprising a single stranded nucleic acid template having a segment of known sequence, a primer having at least 15 bases which is complementary to a portion of the segment of known sequence, and a set of oligonucleotide 5'"'"'-monophosphates, wherein each oligonucleotide 5'"'"'-monophosphate consists of not more than 10 bases, and wherein the oligonucleotide 5'"'"'-monophosphates are selected to be complementary to a part of the segment of known sequence of the template adjacent to the portion of the segment of known sequence to which the primer is complementary;

b) hybridizing the primer with the template under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates to form a primer-template hybrid having a single stranded region and a double stranded region;

c) ligating the set of oligonucleotide 5'"'"'-monophosphates in a contiguous manner onto the primer in one continuous process under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates to extend the double stranded region and synthesize a complementary nucleic acid strand, wherein ligation of oligonucleotide 5'"'"'-monophosphates only occurs in the presence of the hybridized primer.

32. The method of claim 31 wherein the synthesis of the complementary nucleic acid strand synthesized in step c) is terminated at a predetermined position by excluding from the plurality of oligonucleotide 5'"'"'-monophosphates at least one oligonucleotide 5'"'"'-monophosphate which is complementary to a portion of the target single stranded nucleic acid template and has a sequence necessary to extend the double stranded region.

33. The method of claim 31 further comprising the incorporation of at least one nonextendable oligomer, the ligation of which terminates synthesis of the complementary nucleic acid strand.

34. The method of claim 33 wherein each of the nonextendable oligomers is selected from oligomers which have a dideoxy base at the 3'"'"'-end, oligomers which have a blocked 3'"'"'-OH group at the 3'"'"'-end and oligomers which lack a phosphate group at the 5'"'"'-end.

35. The method of claim 31 wherein the ligation is performed by means of a ligase enzyme.

36. The method of claim 35 wherein the ligase enzyme is selected from T4 ligase, T7 ligase, Tth ligase, Taq ligase and E. coli DNA ligase.

37. The method of claim 35 wherein the ligase enzyme is T4 DNA ligase.

38. The method of claim 31 wherein each of the oligonucleotide 5'"'"'-monophosphates consists of the same number of bases and the number of bases is from 2 to 10.

39. The method of claim 38 wherein each of the oligonucleotide 5'"'"'-monophosphates consists of the same number of bases and the number of bases is from 2 to 6.

40. The method of claim 38 wherein each of the oligonucleotide 5'"'"'-monophosphates consists of 5 bases.

41. The method of claim 31 wherein the set of oligonucleotide 5'"'"'-monophosphates contains oligonucleotide 5'"'"'-monophosphates consisting of having different numbers of bases.

42. The method of claim 31 wherein the synthesis of the complementary strand of nucleic acid is unidirectional and proceeds by ligation to the 3'"'"' end of the primer.

43. The method of claim 31 wherein the primer contains a 5'"'"'-phosphate group and the synthesis of the complementary strand of nucleic acid is unidirectional and proceeds by ligation to the 5'"'"' end of the primer.

44. The method of claim 31 wherein the primer contains a 5'"'"'-phosphate group and the synthesis of the complementary strand of nucleic acid proceeds in a bidirectional manner.

45. The method of claim 31 wherein the primer is immobilized onto a solid phase.

46. The method of claim 31 wherein the primer is in a solution.

47. The method of claim 31 wherein at least some of the oligonucleotide 5'"'"'-monophosphates comprise a detectable label.

48. The method of claim 47 wherein the detectable label is selected from radioisotopes, chemiluminescent labels, fluorescent labels, colorimetric labels, enzymes, binding proteins, antigens, antibodies and haptens.

49. The method of claim 47 wherein said detectable label is cleaved, and wherein the method further comprises a step after step c) in which a label or labels are cleaved from the synthesized complementary nucleic acid strand and subsequently detected.

50. The method of claim 49 wherein each oligonucleotide 5'"'"'-monophosphate comprises a detectable label which is cleaved before detection and wherein the detection of the cleaved labels is performed by simultaneously determining the molecular mass of each of the cleaved labels.

59. The method of claim 31 wherein the single stranded nucleic acid template is produced by separating a double stranded nucleic acid.

51. A method for synthesizing an immobilized single stranded nucleic acid on a solid support comprising:

a) providing a reaction mixture comprising a test single stranded nucleic acid having a segment of known sequence, a capture probe/primer having at least 15 bases which is complementary to a portion of the segment of known sequence and which is immobilized on the solid support, and a set of oligonucleotide 5'"'"'-monophosphates, wherein each oligonucleotide 5'"'"'-monophoshate consists of not more than 10 bases, and wherein the oligonucleotide 5'"'"'-monophospates are selected to be complementary to a part of the segment of known sequence of the test single stranded nucleic acid adjacent to the portion of the segment of known sequence to which the primer is complementary;

b) hybridizing the capture probe/primer with the test single stranded nucleic acid under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates to form a captured probe-test nucleic acid hybrid;

c) ligating the set of oligonucleotide 5'"'"'-monophosphates onto the capture probe/primer under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates to extend the capture probe/primer wherein ligation of oligonucleotide 5'"'"'-monophosphates;

d) removing the oligonucleotide 5-monophosphates which are not ligated; and

e) denaturing the captured probe-test nucleic acid hybrid to remove the test nucleic acid and produce the immobilized single stranded nucleic acid.

52. A method for amplifying the amount of a segment of a double stranded nucleic acid of known sequence, the segment having a first strand and a second strand comprising:

a) providing a reaction mixture comprising the double stranded nucleic acid, a first primer having at least 15 bases which is complementary to a first portion of the first strand, a second primer having at least 15 bases which is complementary to a first portion of the second strand, wherein the first portion of the first strand and the first portion of the second strand define the ends of the segment of the double stranded nucleic acid to be amplified, a first set of oligonucleotide 5'"'"'-monophosphates selected to be complementary to a second portion of the first strand, wherein each oligonucleotide 5'"'"'-monophosphate consists of not more than 10 bases, and a second set of oligonucleotide 5'"'"'-monophosphates selected to be complementary to a second portion of the second strand, wherein each oligonucleotide 5'"'"'-monophosphate consists of not more than 10 bases;

b) separating the first and second strands of the double stranded nucleic acid;

c) hybridizing the first and second primers with the separated strands under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates;

d) ligating the first set of oligonucleotide 5'"'"'-monophosphates in a contiguous manner onto the hybridized first primer and ligating the second set of oligonucleotide 5'"'"'-monophosphates in a contiguous manner onto the hybridized second primer in one continuous process to extend the first and second primers thereby producing the segment of the double stranded nucleic acid, wherein ligation of oligonucleotide 5'"'"'-phosphates is performed under conditions which permit stable hybridization of the primer but not stable hybridization of the oligonucleotide 5'"'"'-monophosphates and only wherein ligation occurs in the presence of the hybridized primers; and

e) repeating steps b-d to increase the amount of the segment of the double stranded nucleic acid of known sequence.

53. The method of claim 52 wherein the ligation is performed by means of a ligase enzyme.

54. The method of claim 53 wherein the ligase enzyme is selected from T4 ligase, T7 ligase, Tth ligase, Taq ligase and E. coli DNA ligase.

55. The method of claim 53 wherein the ligase enzyme is thermostable.

56. The method of claim 53 wherein at least one of the primers contains a 5'"'"'-phosphate group and the ligating onto the at least one primer containing the 5'"'"'-phosphate group of the plurality of oligonucleotide 5'"'"'-monophosphates is bidirectional.

57. The method of claim 52 further comprising the incorporation of at least one nonextendable oligomer.

58. The method of claim 57 wherein each of the nonextendable oligomers is selected from oligomers which have a dideoxy base at the 3'"'"'-end, oligomers which have a blocked 3'"'"'-OH group at the 3'"'"'-end and oligomers which lack a phosphate group at the 5'"'"'-end.