Method of sorting a mixture of nucleic acid strands on a binary array

• US 6,103,463 A
• Filed: 05/23/1994
• Issued: 08/15/2000
• Est. Priority Date: 02/19/1992
• Status: Expired due to Term

• Current Assignee: University of Medicine and Dentistry of New Jersey (State of New Jersey)
• Original Assignee: The Public Health Research Institute of the City of New York, Inc.
• Inventors: Chetverin, Alexander B., Kramer, Fred Russell
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Taylor, Janell E.
• Application Number:
  US08/247,530
• Time in Patent Office: 2,276 Days
• Field of Search: 435/6, 435/91, 536/23.1, 536/23.5, 536/24.3, 536/24.33, 536/25.3, 536/27.4, 935/77, 935/78, 935/16-19
• US Class Current: 435/6.12
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00283 Reactor vessels with top opening
• CPC Class Codes: B01J 2219/00313 the reactor vessels being formed by arrays of wells in blocks
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• 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 1/6806 : Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6811 : Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6853 : using modified primers or templates
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/131 : incorporating a restriction site
• CPC Class Codes: C12Q 2525/179 : incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2525/191 : incorporating an adaptor
• CPC Class Codes: C12Q 2531/107 : Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2563/179 : the label being a nucleic acid
• CPC Class Codes: C12Q 2565/519 : characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: Y10S 435/81 : Packaged device or kit
• CPC Class Codes: Y10S 436/808 : Automated or kit

Abstract

A method of sorting mixtures of nucleic acid strands comprising hybridizing the strands to an array of immobilized oligonucleotides, each of which includes a constant segment adjacent to a variable segment. The constant segment of the immobilized oligonucleotides can be made complementary to the ends of strands obtained by digesting a double-stranded nucleic acid with a restriction enzyme and restoring the restriction sites, thereby permitting the sorting of strands according to their variable sequences adjacent to their constant terminal restored restriction sites.

Claims

1. A method of sorting a mixture of nucleic acid strands comprising the steps of:

a) providing a solution containing a mixture of nucleic acid strands in single-stranded form and

b) contacting said solution to a first binary oligonucleotide array of predetermined areas on a surface of a solid support, each area having therein, covalently linked to said surface, copies of a binary oligonucleotide, said binary oligonucleotide consisting of a constant nucleotide sequence adjacent to a variable nucleotide sequence, wherein the constant nucleotide sequence is the same for all oligonucleotides in the array, wherein said step of contacting is carried out under conditions promoting perfect hybridization of said strands to said binary oligonucleotides.

2. A method according to claim 1 wherein said array is comprehensive.

3. A method according to claim 1 wherein said array is a 3'"'"' array.

4. A method according to claim 1 wherein said binary oligonucleotides are complementary to internal sequences that possibly occur in the strands in said mixture.

5. A method according to claim 4 wherein said array is comprehensive.

6. A method according to claim 1 wherein said array is a sectioned array, further comprising the step of amplifying strands hybridized in at least some of said areas to produce copies of said hybridized strands.

7. A method according to claim 1 wherein said step of providing comprises digesting genomic DNA with a restriction endonuclease to create DNA fragments;

(a) modifying said fragments by adding a first constant sequence to their strands'"'"' 3'"'"' termini and a second constant sequence to their strands'"'"' 5'"'"' termini to create priming regions including restored restriction sites; and

(b) denaturing the modified fragments to form a mixture of single nucleic acid strands.

8. A method according to claim 7 wherein said array is a sectioned, comprehensive array, further comprising the step of amplifying strands hybridized in said areas by symmetric PCR.

9. A method according to claim 7 further comprising the step of amplifying said mixture of single nucleic acid strands by asymmetric PCR.

10. A method according to claim 1 wherein said binary oligonucleotides or portions thereof are complementary to terminal sequences that possibly occur in one end of the strands in said mixture and that are non-complementary to internal sequences in the strands in said mixture.

11. A method according to claim 10 wherein said array is a sectioned array, further comprising the step of amplifying strands hybridized in at least some of said areas to produce amplified copies of said single nucleic acid strands.

12. A method according to claim 11 wherein said array is a comprehensive array.

13. A method according to claim 11 wherein said array is a 3'"'"' array.

14. A method according to claim 10 wherein said step of providing comprises digesting genomic DNA with a restriction endonuclease to create DNA fragments, modifying said fragments by adding a first constant sequence to their strands'"'"' 3'"'"' termini to create priming regions including restored restriction sites, and denaturing the modified fragments into a mixture of single nucleic acid strands.

15. A method according to claim 10 wherein said step of providing comprises digesting genomic DNA with a restriction endonuclease to create DNA fragments;

(a) modifying said fragments by adding a first constant segment to one of their strands'"'"' 3'"'"' and 5'"'"' termini to create priming regions including restored restriction sites; and

(b) denaturing the modified fragments into a mixture of denatured nucleic acid strands each having a priming region only at one end.

16. A method according to claim 15 wherein said first binary sorting array is a 3'"'"' array.

17. A method according to claim 16 further comprising the steps of

(a) generating an immobilized copy of each strand hybridized to the array by incubation with a DNA polymerase using the immobilized oligonucleotide as a primer and a hybridized strand as a template;

and

(b) washing to remove from the array all materials not covalently bound to the array.

18. A method according to claim 17, wherein said step of modifying comprises adding a first constant sequence to the strands'"'"' 5'"'"' termini and wherein said 3'"'"' array contains binary oligonucleotides to which are hybridized masking oligonucleotides, said masking oligonucleotides covering a part of the constant sequence of said binary oligonucleotides further comprising the steps of

(a) ligating said masking oligonucleotides to denatured nucleic acid strands hybridized to said binary oligonucleotides such that their 3'"'"' termini are immediately adjacent to one of said masking oligonucleotides, and

(b) washing under conditions such that only strands so ligated will remain.

19. A method according to claim 18 wherein said step of adding a first constant sequence includes ligation of a double-stranded oligodeoxyribonucleotide adaptor.

20. A method according to claim 18 wherein said step of adding a first constant sequence includes ligation of a single-stranded oligoribonucleotide.

21. A method according to claim 17 wherein said step of modifying comprises adding a first constant sequence to their strands'"'"' 3'"'"' termini.

22. A method according to claim 21 wherein said first constant sequence is a homopolynucleotide tail added by extension of the strands'"'"' 3'"'"' termini by enzymatic extension.

23. A method according to claim 21 further comprising the step of adding a second constant sequence to the 3'"'"' termini of the immobilized copies.

24. A method according to claim 23 wherein said second constant sequence is a homopolynucleotide tail added by extension of said immobilized copies'"'"' 3'"'"' termini by enzymatic extension.

25. A method according to claim 17 wherein said first binary oligonucleotide array is a sectioned array, further comprising the step of amplifying said washed, immobilized copies to produce amplified copies.

26. A method according to claim 25 wherein said step of amplifying comprises PCR.

27. A method according to claim 25 wherein said first binary oligonucleotide array is a comprehensive array.

28. A method according to claim 25 further comprising contacting said amplified copies from at least one area of said 3'"'"' array to a second binary oligonucleotide array containing immobilized binary oligonucleotides whose constant sequence is identical or complementary to the 3'"'"' terminus of the immobilized copies.

29. A method according to claim 11 further comprising contacting said amplified copies from at least one area of said first binary oligonucleotide array to a second binary oligonucleotide array containing immobilized binary oligonucleotides that are complementary to terminal sequences that possibly occur in either the other ends of said denatured nucleic acid strands or the complements of said other ends, and that are not complementary to internal sequences in the strands in said mixture or their complements.

30. A method according to claim 10 wherein said step of providing comprises digesting genomic DNA with a restriction endonuclease to create DNA fragments, and denaturing said fragments into a mixture of denatured nucleic acid strands.

31. A method according to claim 30 wherein said first binary oligonucleotide array is a 3'"'"' array containing binary oligonucleotides to which are hybridized masking oligonucleotides, further comprising the steps of ligating said masking oligonucleotides to denatured nucleic acid strands hybridized to said binary oligonucleotides such that their 3'"'"' termini are immediately adjacent to one of said masking oligonucleotides, washing under conditions such that only strands so ligated will remain, and generating an immobilized copy of each ligated strand by incubation with a DNA polymerase.

32. A method according to claim 31 further comprising the steps of adding a constant sequence to the 5'"'"' termini of the hybridized strands by ligation of a single-stranded oligoribonucleotide;

incubating with a DNA polymerase to extend the immobilized copies;

washing to remove from the array all materials not covalently bound to the array; and

amplifying said washed, immobilized copies to produce amplified copies.

33. A method according to claim 32 wherein said step of amplifying comprises PCR.

34. A method according to claim 32 wherein said first sorting array is a comprehensive array.

35. A method according to claim 32 further comprising contacting said amplified copies from at least one area of said 3'"'"' array to a second binary array containing immobilized binary oligonucleotides whose constant sequence is identical or complementary to the 3'"'"' terminus of said immobilized copies.

36. A method according to claim 16 further comprising the steps of adding a constant sequence to the 3'"'"' termini of the immobilized copies by enzymatic extension thereof;

washing to remove from the array all materials not covalently bound to the array; and

amplifying said washed, immobilized copies to produce amplified copies.

37. A method according to claim 36 wherein said step of amplifying comprises PCR.

38. A method according to claim 36 wherein said first sorting array is a comprehensive array.

39. A method according to claim 36 further comprising contacting said amplified copies from at least one area of said 3'"'"' array to a second terminal binary array containing immobilized binary oligonucleotides whose constant sequence is identical or complementary to the 3'"'"' terminus of said immobilized copies.

40. A method according to claim 10 wherein said step of providing comprises digesting genomic DNA with a site-specific cleaving agent to create DNA fragments.

41. A method according to claim 40 wherein said agent is an endonuclease.

42. A method according to claim 40 wherein said agent is a chemical agent.

43. A method according to claim 10 wherein said nucleic acid strands are cDNA strands.

44. A method according to claim 10 wherein said nucleic acid strands are RNA strands.

45. A method according to claim 44 wherein said RNA strands are eukaryotic mRNA strands, and wherein said step of providing comprises removing 5'"'"'-cap structures.

46. A method according to claim 44 wherein said RNA strands lack a poly(A) tail.

47. A method according to claim 10 wherein said step of providing comprises digesting genomic DNA with a restriction endonuclease to create DNA fragments;

(a) modifying said fragments by adding a first constant sequence to their strands'"'"' 3'"'"' termini and a second constant sequence to their strands'"'"' 5'"'"' termini to create priming regions including restored restriction sites; and

(b) denaturing the modified fragments into a mixture of single nucleic acid strands.

48. A method according to claim 47 wherein the 3'"'"' priming regions are complementary to the 5'"'"' priming regions.

49. A method according to claim 48 wherein said array is a 3'"'"' array, further comprising the steps of

(a) generating an immobilized copy of each strand hybridized to the array by incubation with a DNA polymerase;

and

(b) washing to remove from the array all materials not covalently bound to the array.

50. A method according to claim 49 wherein said array is a sectioned array, further comprising the step of amplifying strands hybridized in at least some areas by PCR to produce amplified copies of each said immobilized copy.

51. A method according to claim 50 wherein said array is a comprehensive array.

52. A method according to claim 48 wherein addition of said first constant sequence and said second constant sequence includes ligation of a double-stranded oligodeoxyribonucleotide adaptor to the strands'"'"' 5'"'"' termini.

53. A method according to claim 48 wherein addition of said first constant sequence and said second constant sequence includes ligation of a single-stranded oligonucleotide to the strands'"'"' 5'"'"' termini.

54. A method according to claim 48 wherein addition of said first constant sequence and said second constant sequence includes enzymatic extension of the strands'"'"' 3'"'"' termini by the synthesis of a homopolynucleotide tail.

55. A method according to claim 50 further comprising contacting said amplified copies from at least one areas of said 3'"'"' array to a second binary array under conditions promoting hybridization of said amplified copies to the binary oligonucleotides in said second array.

56. A method according to claim 55 wherein said amplified copies are produced by symmetric PCR and wherein said second array is a 3'"'"' array.

57. A method according to claim 55 wherein said first array and said second array are comprehensive.

59. A method according to claim 17 further comprising

(a) contacting at least one area of said array containing the immobilized copies with at least one oligonucleotide probe having a predetermined sequence, under conditions promoting hybridization of said at least one probe;

and

(b) determining whether or not said at least one probe has hybridized to said at least one area.

60. A method according to claim 1 further comprising removing strands that have not perfectly hybridized.

61. A method according to claim 60 further comprising adding a terminal extension to at least one terminus of the strands, said terminal extension having a sequence which substantially does not occur in the strands.

62. A method according to claim 61 wherein a terminal extension is added to the strands by ligation of hybridized strands to masking oligonucleotides, said masking oligonucleotides being also hybridized to said binary oligonucleotides.

63. A method according to claim 62 wherein a second terminal extension is added to the strands prior to said step of contacting, said second terminal extension being added to termini not hybridized to said binary oligonucleotides during said step of contacting.

64. A method according to claim 60 further comprising releasing hybridized strands on a sectioned array into solution without mixing of material in said areas and rebinding them to said binary oligonucleotides followed by removing unhybridized strands.

65. A method according to claim 60 further comprising releasing hybridized strands in solution and rebinding to a replica array followed by removing unhybridized strands.

66. A method according to claim 60 wherein the mixture of nucleic acid strands comprises RNA.

67. A method according to claim 60 wherein the mixture of nucleic acid strands is comprised of DNA fragments obtained by site specific degradation.

68. A method according to claim 61 wherein the mixture is comprised of DNA fragments obtained by digestion with a restriction endonuclease and wherein the constant region of the binary oligonucleotide contains the complement of the restriction endonuclease recognition site, and wherein addition of the terminal extension restores the recognition site.

69. A method according to claim 60 further comprising generating complementary copies of hybridized strands.

70. A method according to claim 69 wherein the array is a 3'"'"' array wherein each binary oligonucleotide has its variable sequence adjacent to the 5'"'"' end of its constant sequence, and the copies are generated using a DNA polymerase and using the binary oligonucleotide as a primer.

71. A method according to claim 69 wherein the array is a 5'"'"' array wherein each binary oligonucleotide has its variable sequence adjacent to the 3'"'"' end of its constant sequence, and the copies are generated using a DNA polymerase using a primer hybridized to a 3'"'"' terminal extension of the hybridized strands, and the copies are then ligated to the 5'"'"' end of the binary oligonucleotide.

72. A method according to claim 62 further comprising amplifying the hybridized strands.

73. A method according to claim 69 further comprising removing the hybridized strands and amplifying the complementary copies of the hybridized strands.

74. A method according to claim 73 wherein the hybridized strands have 3'"'"' and 5'"'"' terminal extensions, and the amplification is a polymerase chain reaction.

75. A method according to claim 73 wherein the hybridized strands have a terminal extension and the amplification is linear.

76. A method according to claim 1 further comprising sorting the hybridized nucleic acid strands or their copies in an area of the first binary array by contacting them to a second oligonucleotide array.

77. A method according to claim 76 wherein the strands or their copies are contacted to all areas of the array.

78. A method according to claim 1 wherein the nucleic acid strands are contacted to all areas of a second binary array.

79. A method according to claim 76 wherein cleavable primers are used following said step of contacting for amplification of hybridized strands.

80. A method according to claim 79 further comprising cleaving the cleavable primers from the strands and adding new terminal extensions.

81. A method according to claim 76 wherein the contents of an area of the first binary array are contacted with only predetermined areas of a second binary array.

82. A method according to claim 1 further wherein contents in an area of the binary array are contacted with the corresponding area of a replica array.

83. A method according to claim 76 wherein the second oligonucleotide array is a second binary array.

84. A method according to claim 1 wherein the solid support includes additional areas having additional oligonucleotides covalently linked thereto that do not contain said constant nucleotide sequence.

85. A method according to claim 1 wherein the solid support comprises additional regions containing additional oligonucleotides having a constant sequence different from the constant sequence of the binary oligonucleotide.

86. A method according to claim 85 wherein the additional region comprises an additional array.

87. A method according to claim 1 wherein immobilized oligonucleotides of said array further comprise additional sequences to the constant and variable sequences of the binary oligonucleotides.

88. A method according to claim 87 wherein the additional sequence is an additional constant sequence.

89. A method according to claim 87 wherein the additional sequence is an additional variable sequence.

58. A method for sorting partials by their variable termini on a binary oligonucleotide array, which partials have been prepared by random chemical or enzymatic degration of one or more nucleic acid strands, said binary array comprising an array of predetermined areas on a surface of a solid support, each area having therein copies of a binary oligonucleotide of a predetermined sequence, said binary oligonucleotide consisting of a constant nucleotide sequence adjacent to a variable nucleotide sequence, said variable nucleotide sequence being at the free end of the binary oligonucleotides, said binary oligonucleotide also having a complementary masking oligonucleotide hybridized to all or a part of the constant nucleotide sequence, including the portion of the constant nucleotide sequence adjacent the variable nucleotide sequence, comprising the steps of:

(a) hybridizing the partials to the array by their termini under conditions that promote the formation of perfect hybrids; and

(b) ligating the termini of the partials to the masking oligonucleotide.