Nucleic-acid ink compositions for arraying onto a solid support

• US 20040054160A1
• Filed: 09/16/2002
• Published: 03/18/2004
• Est. Priority Date: 09/16/2002
• Status: Abandoned Application

• Current Assignee: Corning Incorporated
• Original Assignee: Corning Incorporated
• Inventors: Pal, Santona
• Application Number:
  US10/244,898
• Publication Number:
  US 20040054160A1
• Time in Patent Office: Days
• US Class Current: 536/24.3
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• 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 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2527/119 pH
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2527/137 Concentration of a component of medium

Abstract

A medium or ink solution containing nucleic acid is provided for depositing onto a solid support in the manufacture of biological arrays. The medium has a composition that comprises: about 30% to about 80% by volume of an organic solution comprising dimethylsulfoxide (DMSO), ethylene glycol (EG), formamide, or a combination thereof; a buffer with a pH value of about 3.5-9.5; water; and nucleic acid, wherein the nucleic acid denatures to provide for more favorable hybridization. The buffer can be made from a solution that may contain acetate, citrate, citrate-phosphate, maleate, or succinate. The medium permits long-term storage of nucleic acids in solution without excessive degradation, which is a phenomenon associated with many conventional ink solutions.

Claims

1. A medium for suspending a solution of nucleic acid, the medium having a composition comprising:

about 30% to about 80% by volume of an organic solution comprising dimethylsulfoxide (DMSO), ethylene glycol (EG), formamide, or a combination thereof,

a buffer with a pH value of about 3.5-9.5;

water; and

nucleic acid, wherein the nucleic acid denatures to provide for more favorable hybridization.

2. The medium according to claim 1, wherein said buffer is made from a solution that may include acetate, citrate, citrate-phosphate, maleate, or succinate.

3. The medium according to claim 2, wherein when said buffer includes acetate, the pH value is about 6 to about 8.5.

4. The medium according to claim 3, wherein the pH value is about 6.5 to about 7.5.

5. The medium according to claim 2, wherein when said buffer includes citrate, the pH value is about 3.5 to about 7.5.

6. The medium according to claim 5, wherein the pH value is about 4 to about 6.5.

7. The medium according to claim 2, wherein when said buffer includes citrate-phosphate, the pH value is about 6.0 to about 9.

8. The medium according to claim 7, wherein the pH value is about 7 to about 8.5.

9. The medium according to claim 2, wherein when said buffer includes succinate, the pH value is about 3.5 to about 7.

10. The medium according to claim 9, wherein the pH value is about 4 to about 6.5.

11. The medium according to claim 2, wherein when said buffer includes maleate, the pH value is about 5 to about 8.5.

12. The medium according to claim 11, wherein when said composition contains either ethylene glycol or formamide, said maleate buffer is at a pH value of about 5-5.5.

13. The medium according to claim 11, wherein when said composition contains DMSO, said maleate buffer is at a pH value of ˜

8 to 8.5.

14. The medium according to claim 1, wherein said nucleic acid is at a concentration ranging from about 0.01 mg/ml to about 0.5 mg/ml.

15. The medium according to claim 1, wherein the nucleic acid is a double stranded DNA, RNA, or an oligonucleotide.

16. The medium according to claim 1, wherein said composition enables long-term storage and preserves integrity of nucleic acid without instability by precipitation or aggregation of said nucleic acid.

17. The medium according to claim 16, wherein said composition enables prolonged storage and printing over at least 15 days.

18. The medium according to claim 1, wherein said composition comprises about 40% to about 80% DMSO by volume, the buffer contains a final concentration of from about 0.1×

to about 0.8×

of citric acid+sodium citrate.

19. The medium according to claim 18, wherein said composition comprises about 50% DMSO by volume and citrate buffer at a final concentration of about 0.25×

of citric acid+sodium citrate.

20. The medium according to claim 1, wherein said composition comprises about 40% to about 80% DMSO by volume and the buffer contains a final concentration of about 0.1×

to about 0.8×

of acetic acid+sodium acetate.

21. The medium according to claim 20, wherein said composition comprises about 50% DMSO by volume and acetate buffer at a final concentration of about 0.25×

of acetic acid+sodium acetate.

22. The medium according to claim 1, wherein said composition comprises about 40% to about 80% DMSO by volume and the buffer contains a final concentration of about 0.1×

to about 0.8×

of citric acid+sodium phosphate.

23. The medium according to claim 22, wherein said composition comprises about 50% DMSO by volume and citric acid/citrate-phosphate buffer at a final concentration of about 0.25×

of citric acid+sodium phosphate.

24. The medium according to claim 1, wherein said composition comprises about 40% to about 80% DMSO by volume and the buffer contains a final concentration of about 0.1×

to about 0.8×

of succinic acid+sodium hydroxide.

25. The medium according to claim 24, wherein said composition comprises about 50% DMSO by volume and succinic acid/sodium hydroxide buffer at a final concentration of about 0.25×

of succinic acid+sodium hydroxide.

26. The medium according to claim 1, wherein said composition may include EDTA in a final concentration between 0 and about 4 mM.

27. The medium according to claim 26, wherein said composition includes EDTA in a final concentration of about 0.5 mM.

28. The medium according to claim 1, wherein said composition may include agents that can change the viscosity of the ink for enhancing wettability.

29. The method according to claim 28, wherein said composition may include either or both multivalent, cationic, organic and inorganic molecules, and/or neutral polymers.

30. The medium according to claim 29, wherein said cationic molecules include cobalt (III) hexa-amine, spermine, spermidine, poly-lysine, histones.

31. A medium for suspending a solution of nucleic acid, the medium having a composition comprising:

a mixed organic solution of about 1% to about 55% by volume of ethylene glycol (EG) or formamide either individually, together, or with DMSO;

a buffer with a pH value of about 3.5-9.5;

water; and

nucleic acid.

32. The medium according to claim 31, wherein said composition comprises about 40% to about 80% DMSO by volume and citrate buffer at a final concentration from about 0.1×

to about 0.8×

.

33. The medium according to claim 31, wherein said composition comprises about 40% to about 75% DMSO by volume and about 1% to 50% EG by volume and citrate buffer at final concentration from about 0.25×

to about 0.5×

.

34. The medium according to claim 31, wherein said composition comprises about 50% DMSO by volume about 10% to 40% EG by volume and citrate buffer at a final concentration of about 0.25×

.

35. The medium according to claim 31, wherein said composition includes an organic solution comprising about 5% to about 40% EG/formamide by volume.

36. The medium according to claim 31, wherein said composition includes an organic solution comprising about 10% to about 30% EG/formamide by volume.

37. The medium according to claim 31, wherein said composition may include EDTA in a final concentration between 0 and about 4 mM.

38. A method for depositing a nucleic acid on a support, said method comprising:

a) providing a solution of nucleic acid comprising about 30% to about 80% by volume of dimethylsulfoxide (DMSO), ethylene glycol (EG), formamide, or a combination thereof;

a buffer with a pH value of about 3.5-9.5;

water; and

a nucleic acid; and

b) depositing said solution on the support.

39. The method of claim 38, wherein the depositing step comprises immersing a tip of a pin into the solution of nucleic acid;

removing said tip from said solution to provide solution adhered to said tip; and

transferring said solution to the support.

40. The method of claim 38, wherein the depositing step is repeated a plurality of times to provide one or more arrays of nucleic acid.

41. The method according to claim 38, wherein said buffer is made from a solution that may include acetate, citrate, citrate-phosphate, maleate, or succinate.

42. The method according to claim 41, wherein when said buffer is an acetic acid system, the pH value is about 6 to about 8.5.

43. The method according to claim 42, wherein the pH value is about 6.5 to about 7.5.

44. The method according to claim 41, wherein when said buffer is a citric acid system, the pH value is about 3.5 to about 7.5.

45. The method according to claim 44, wherein the pH value is about 4 to about 6.5.

46. The method according to claim 41, wherein when said buffer is a citrate-phosphate system, the pH value is about 6.0 to about 9.

47. The method according to claim 46, wherein the pH value is about 7 to about 8.5.

48. The method according to claim 41, wherein when said buffer is a succinic acid system, the pH value is about 3.5 to about 7.

49. The method according to claim 48, wherein the pH value is about 4 to about 6.5.

50. The method according to claim 41, wherein when said buffer is a maleate system, the pH value is about 5 to about 8.5.

51. The method according to claim 50, wherein when said composition contains either ethylene glycol or formamide, said maleate buffer is at a pH value of about 5-5.5.

52. The method according to claim 50, wherein when said composition contains DMSO, said maleate buffer is at a pH value of ˜

8 to 8.5.

53. The method according to claim 38, wherein said nucleic acid is at a concentration ranging from about 0.01 mg/ml to about 0.5 mg/ml.

54. The method according to claim 38, wherein the nucleic acid is a double stranded DNA, RNA, or an oligonucleotide.

55. The method according to claim 38, wherein said composition enables long-term storage and preserves integrity of nucleic acid without instability by precipitation or aggregation of said nucleic acid.

56. The method according to claim 38, wherein said composition enables prolonged storage and printing over at least 15 days.

57. The method according to claim 38, wherein said solution comprises about 40% to about 60% DMSO by volume and a buffer at a final concentration of from about 0.1×

to about 0.4×

of citric acid+sodium citrate.

58. The method according to claim 57, wherein the solution comprises about 50% DMSO by volume and the buffer at a final concentration of about 0.25×

of citric acid+sodium citrate.

59. The method according to claim 38, wherein said solution comprises about 40% to about 60% DMSO by volume and a buffer at a final concentration of from about 0.1×

to about 0.4×

of acetic acid+sodium acetate.

60. The method according to claim 38, wherein said solution comprises about 40% to about 60% DMSO by volume and a buffer at a final concentration of from about 0.1×

to about 0.4×

citric acid+sodium phosphate.

61. The method according to claim 38, wherein said solution comprises about 40% to about 60% DMSO by volume and a buffer at a final concentration of from about 0.1×

to about 0.4×

succinic acid+sodium hydroxide.

62. The method according to claim 38, wherein the support has a planar surface capable of retaining the nucleic acid.

63. The method according to claim 62, wherein the support is either a membrane or a glass substrate.

64. The method according to claim 63, wherein said glass substrate is either a two-dimensional, solid glass surface or a three-dimensional, porous glass surface.

65. The method according to claim 62, wherein said glass substrate comprises a surface that is functionalized to facilitate adhesion of the nucleic acid.

66. The method according to claim 65, wherein said glass substrate is coated with anhydride functional groups.

67. The method according to claim 68, wherein said glass substrate is coated with a styrene-co-maleic anhydride (SMA) copolymer.

68. The method according to claim 65, wherein said glass substrate comprises an aminated surface.

69. The method according to claim 68, wherein said aminated surface is coated with an aminoalkylsilane.

70. The method according to claim 68, wherein said aminated surface is coated with an aminating agent comprising either y-aminopropylsilane or polylysine.

71. A method for depositing a nucleic acid on a solid support, said method comprising:

depositing on the solid support a solution of nucleic acid comprising a mixed organic solution of about 1% to about 55% by volume of ethylene glycol (EG) or formamide either individually, together, or with DMSO;

a buffer with a pH value of about 3.5-9.5;

water; and

nucleic acid.

72. The method according to claim 71, wherein said composition comprises about 40% to about 80% DMSO by volume and citrate buffer at a final concentration from about 0.1×

to about 0.8×

.

73. The medium according to claim 71, wherein said composition comprises about 40% to about 75% DMSO by volume and about 1% to 50% EG by volume and citrate buffer at final concentration from about 0.25×

to about 0.5×

.

74. The method according to claim 71, wherein said composition comprises about 50% DMSO by volume about 10% to 40% EG by volume and citrate buffer at a final concentration of about 0.25×

.

75. The method according to claim 71, wherein said composition includes an organic solution comprising about 5% to about 40% EG/formamide by volume.

76. The method according to claim 71, wherein said composition includes an organic solution comprising about 10% to about 30% EG/formamide by volume.

77. The method according to claim 71, wherein the nucleic acid is at a concentration ranging from about 0.01 mg/ml to about 0.5 mg/ml.

78. The method according to claim 71, wherein the nucleic acid is DNA

79. The method according to claim 71, wherein the nucleic acid is an oligonucleotide.

80. The method according to claim 71, further comprising subjecting the nucleic acid on said solid support to thermal denaturation.