Method for performing amplification of nucleic acid on supports

• US 6,060,288 A
• Filed: 02/14/1997
• Issued: 05/09/2000
• Est. Priority Date: 08/03/1994
• Status: Expired due to Fees

• Current Assignee: Solexa Incorporated (Illumina Incorporated), Mosaid Technologies Incorporated (MOSAID Technologies Inc. (f/k/a Conversant Intellectual Property Management)), MT Technology, Inc.
• Original Assignee: Mosaid Technologies Incorporated (MOSAID Technologies Inc. (f/k/a Conversant Intellectual Property Management))
• Inventors: Boles, Truett C., Kron, Stephen J., Adams, Christopher P., Muir, Andrew R.
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US08/800,840
• Time in Patent Office: 1,180 Days
• Field of Search: 435/5, 435/6, 435/7.1, 435/91.1, 435/91.2, 435/91.21, 536/24.3, 536/24.31, 536/24.32, 536/34.33, 530/387.1, 530/388.1, 436/518, 436/501
• US Class Current: 435/91.2
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer

Abstract

This invention features methods, apparatus and kits for performing nucleic acid hybridization and amplification reactions on a support. Such methods and apparatus are useful in diagnostic and therapeutic processes for synthesizing nucleic acid and detecting target nucleic acids in a sample.

Claims

1. A method of detecting the presence or absence of a target nucleic acid sequence in a test sample comprising the steps of:

a) providing a test sample containing a target nucleic acid sequence;

b) providing an optical fiber having a proximal end and a distal end, said distal end having two or more oligonucleotides immobilized thereon, wherein the nucleotide sequences of the oligonucleotides are complementary to the nucleic acid sequence of the target;

c) contacting the distal end of the fiber with the test sample and maintaining the test sample in contact with the fiber under conditions suitable for the amplification of the target sequence and for time sufficient to obtain a detectable amount of target sequence, thereby producing an amplification product which is immobilized on the optic fiber; and

d) detecting the presence of the target sequence in the test sample by the detection of an optically detectable signal produced by the presence of the amplification product.

2. The method of claim 1 wherein amplification of the test sample is by polymerase chain reaction.

3. The method of claim 1 wherein the amplification of the test sample is by ligase chain reaction.

4. The method of claim 1, wherein optical radiation is transmitted along the optical fiber from the proximal end to the distal end where it directly or indirectly irradiates the immobilized amplification product and causes a detectable signal to be generated.

5. The method of claim 1, wherein a signal from the immobilized amplification product is transmitted through the sample and detected.

6. The method of claim 1, wherein the immobilized product is irradiated by optical radiation transmitted along the optical fiber from the proximal end to the distal end, and an optical signal from the product is transmitted through the sample and detected with a dark field optical configuration being used such that said optical radiation does not directly reach the detection means.

7. The method of claim 1, wherein radiation is transmitted through the sample and directly or indirectly irradiates the immobilized amplification product and causes a detectable signal to be generated.

8. The method of claim 1, wherein an optical signal from the immobilized amplification product is transmitted along the optical fiber from the distal end to the proximal end where the optical signal is detected.

9. The method of claim 1, wherein the immobilized amplification product is irradiated by radiation transmitted through the sample, and an optical signal from the product is transmitted along the optical fiber from the distal end to the proximal end and detected with a dark field optical configuration being used such that said optical radiation does not directly reach the detection means.

10. The method of claim 1, wherein optical radiation is transmitted along the optical fiber from the proximal end to the distal end where it directly or indirectly irradiates the immobilized amplification product and causes a detectable signal to be generated, said signal being transmitted along the optical fiber from the distal end to the proximal end where the optical signal is detected.

11. The method of claim 1, wherein in step b) two or more oligonucleotides are immobilized on the optical fiber distal end, wherein the nucleotide sequence of each oligonucleotide is complementary to two or more target nucleic acid sequences in the test sample and two, or more target nucleic acid sequences are detected.

12. The method of claim 11, for determining the presence of two or more target nucleic acid sequences, wherein at least two oligonucleotides are bound to areas of the distal end of a bundle of optical fibers, with each such area being optically distinguishably accessible by one or more optical fibers in said bundle.

13. The method of claim 11, wherein two or more optical fibers are employed whose distal ends adjacently underlie the immobilized amplification product, whereby optical radiation is transmitted along one or more optical fibers from their proximal ends to their distal ends where said radiation directly or indirectly irradiates the surface bound amplification product and causes a detectable signal to be generated, with said signal being transmitted along one or more optical fibers from the distal end to their proximal ends where the optical signal is detected.

14. The method of claim 13, wherein optical radiation is transmitted along two or more optical fibers from their proximal ends to their distal ends where it directly or indirectly irradiates areas of immobilized amplification product and causes one or more detectable signals to be generated, with said signals being detected though the sample.

15. The method of claim 13, wherein optical radiation is transmitted through the sample to directly or indirectly irradiate one or more areas of immobilized amplification product and causes one or more detectable signals to be generated, with said signals being transmitted along one or more optical fibers from their distal end to their proximal ends where the optical signals are detected.

16. The method of claim 1, wherein an optical signal is detected by optical detection means, including optically sensitive diodes, photo multipliers, television cameras, and both linear and two dimensional photosensitive arrays.

17. The method of claim 1, wherein radiation is applied continuously to the amplification product to produce a detectable signal.

18. The method of claim 1, wherein radiation is applied in a time variant manner to the amplification product to produce a detectable signal.

19. The method of claim 1, wherein radiation is applied discontinuously to the amplification product to produce a detectable signal.

20. The method of claim 1, wherein a detectable signal from the amplification product is detected continuously.

21. The method of claim 1, wherein a detectable signal from the amplification product is detected in a time sensitive manner.

22. The method of claim 1, wherein a detectable signal from the amplification product is detected discontinuously.

23. The method of claim 1, wherein the immobilized amplification product is covered by at least one additional layer that has optical filtration properties.

24. The method of claim 1, wherein the immobilized amplification product is underlaid by at least one additional layer that has optical filtration properties.

25. The method of claim 1, wherein the immobilized amplification product is covered by at least one additional layer that has light scattering properties.

26. The method of claim 1, wherein the immobilized amplification product is underlaid by at least one additional layer that has light scattering properties.

27. The method of claim 1, wherein the immobilized amplification product is covered by at least one additional layer that modifies the access of chemical reagents in solution to the distal surface and/or amplified product.

28. The method of claim 1, wherein the immobilized amplification product is covered by at least one additional layer that modifies the rate of formation of amplified product.

29. The method of claim 1, wherein the immobilized amplification product is covered by at least one additional layer that has light reflecting properties.

30. The method of claim 1, wherein the immobilized amplification product is underlaid by at least one additional layer that has light reflecting properties.

31. The method of claim 1, wherein the immobilized amplification product is covered by at least one additional layer that has optical focusing properties.

32. The method of claim 1, wherein the immobilized amplification product is underlaid by at least one additional layer that has optical focusing properties.

33. The method of claim 1, wherein the distal end of the optical fiber is shaped to enhance the signal detection.

34. The method of claim 1, wherein the distal end of the optical fiber is shaped to enhance the irradiation of the amplified product.

35. The method of claim 1, wherein the oligonucleotide of step b) is between about 5 and 100 nucleotides in length.

36. The method of claim 1, wherein the oligonucleotide of step b) is covalently attached to said optical fiber.

37. A method of detecting the presence or absence of a target nucleic acid sequence in a test sample, comprising the steps of:

a) providing a test sample containing a target nucleic acid sequence;

b) providing an optical fiber having a proximal end and a distal end, said distal end having two or more oligonucleotides immobilized thereon, wherein the nucleotide sequences of the oligonucleotides are complementary to a sequence flanking the target sequence;

c) contacting the distal end of said optical fiber with the test sample in the presence of deoxyribonucleotide triphosphates and one or more appropriate enzymes, under conditions suitable for extension of the primer sequence and amplification of the target sequence thereby producing an amplification product; and

d) detecting the presence of the amplification product, wherein detection of the amplification product is indicative of the presence of the target nucleic acid sequence.

38. The method of claim 37 wherein in step c) the deoxyribonucleotides are detectably labeled and the amplification product is detected by the presence of detectably labeled deoxyribonucleotide in the amplification product.

39. The method of claim 38 wherein the label is an agent selected from the group consisting of chemiluminescent, electrochemiluminescent, luminescent, radioactive, photoabsorbing and fluorescent agents.

40. The method of claim 37 wherein in step c) a detectably labeled moiety which binds to or hybridizes with the amplification product is added optionally either before or during amplification of the target sequence or substantially immediately thereafter completion of amplification and the amplification product is detected by the presence of the detectably labeled moiety bound to or hybridized with the amplification product.

41. The method of claim 40 wherein the label is an agent selected from the group consisting of chemeluminescent, electrochemiluminescent, luminescent, radioactive, photoabsorbing and fluorescent agents.

42. The method of claim 40 wherein the moiety is selected from the group consisting of fluorescent dyes, intercalating agents, nucleic acid probes, nucleic acid analogs, nucleic acid binding proteins, antibodies and chelating agents.

43. The method of claim 37, wherein the primer of step b) is between about 5 and 100 nucleotides in length.

44. The method of claim 37, wherein the primer of step b) is covalently attached to the optical fiber.

45. A method of detecting a target nucleic acid sequence in a test sample, comprising the steps of:

a) providing a test sample containing a target nucleic acid sequence;

b) providing an optical fiber having a proximal end and a distal end, said distal end having a first oligonucleotide immobilized thereon, said nucleotide sequence of the oligonucleotide being complementary to a sequence within the target sequence;

c) contacting the distal end of the optical fiber with the test sample in the presence of a second oligonucleotide being complementary to a sequence within the target sequence that is immediately contiguous with the sequence complementary to the first oligonucleotide sequence and at least one ligase enzyme under conditions suitable for annealing of the first and second oligonucleotides to the target sequence, ligation of the annealed oligonucleotides and amplification of the target sequence, thereby producing an amplification product; and

d) detecting the presence of the amplification product, wherein detection of the amplification product is indicative of the presence of the target sequence.

46. The method of claim 45 wherein the second oligonucleotide of step c) is detectably labeled and the amplification product is detected by the presence of the detectably labeled second oligonucleotide in the product.

47. The method of claim 46 wherein the label is an agent selected from the group consisting of chemeluminescent, electrochemiluminescent, luminescent, radioactive, photoabsorbing and fluorescent agents.

48. The method of claim 45 wherein in step c) a detectably labeled moiety which binds to or hybridizes with the amplification product is added optionally either during amplification of the target sequence or substantially immediately thereafter completion of amplification and the amplification product is detected by the presence of the detectably labeled moiety bound to or hybridized with the amplification product.

49. The method of claim 48 wherein the label is an agent selected from the group consisting of chemeluminescent, electrochemiluminescent, luminescent, radioactive, photoabsorbing and fluorescent agents.

50. The method of claim 48 wherein the moiety is selected from the group consisting of fluorescent dyes, intercalating agents, nucleic acids probes, nucleic acid analogs, nucleic acid binding proteins, antibodies and chelating agents.

51. A method for determining polynucleotide damage and repair ex vivo in a double stranded oligonucleotide having about 30-500 base pairs and including a lesion, said method comprising:

a) providing an optical fiber having a proximal end and a distal end, said distal end having a double stranded oligonucleotide immobilized on an optical fiber;

b) treating said optical fiber having said oligonucleotide immobilized thereto with a composition comprising,

i. a lysate from a candidate cell population and

ii. a polynucleotide repair reagent, for a time sufficient for said lysate to act upon said lesion and effect incorporation of said polynucleotide repair reagent into said lesion; and

c) measuring a property of the oligonucleotide treated as in step b) while coupled to said optical fiber, the resulting measurement being determinative of the extent of repair of said oligonucleotide.

52. A method according to claim 51, wherein said measurement is performed using an antibody specific for polynucleotide lesions, said polynucleotide repair reagent consisting of unlabeled deoxyribonucleotide triphosphates and polynucleotide repair is measured by a loss of antibody binding to said oligonucleotide.

53. A method according to claim 51, wherein said measurement is assessed by determining the amount of signal producing polynucleotide repair reagent incorporated into said polynucleotide, said signal producing polynucleotide repair reagent being selected from the group consisting of radiolabeled deoxyribonucleotide triphosphates, fluoresceinated deoxyribonucleotide triphosphates, and biotinylated deoxyribonucleotide triphosphates.

54. A method for determining the ability of neoplastic cells to repair lesions formed by therapeutic agents in double stranded oligomeric polynucleotide having about 30-500 base pairs, said method comprising:

a) providing said double stranded oligonucleotide covalently coupled to an optical fiber;

b) treating said optical fiber having said oligonucleotide covalently coupled thereto with a composition comprising,

i. a lysate from said neoplastic cells and

ii a polynucleotide repair reagent, for a time sufficient for said lysate to act upon said lesion and effect incorporation of said polynucleotide repair reagent into said lesion; and

c) measuring a property of the oligonucleotide treated as in step b) while coupled to said optical fiber, the resulting measurement being determinative of the extent of repair of said oligonucleotide.

55. A method according to claim 54, wherein said measurement is performed using an antibody specific for polynucleotide lesions, said polynucleotide repair reagent consists of unlabeled deoxyribonucleotide triphosphates and polynucleotide repair is measured by a loss of antibody binding to said oligonucleotide.

56. A method according to claim 54, wherein said measurement is assessed by determining the amount of signal producing polynucleotide repair reagent incorporated into said polynucleotide, said signal producing polynucleotide repair reagent being selected from the group consisting of radiolabeled deoxyribonucleotide triphosphates, fluoresceinated deoxyribonucleotide triphosphates, and biotinylated deoxyribonucleotide triphosphates.

57. A method according to claim 54, wherein said lesions are the result of radiation.

58. A method according to claim 54, wherein said lesions are the result of exposure to chemotherapeutic agents.