Beads bound to a solid support and to nucleic acids

• US RE41,005 E1
• Filed: 10/17/2002
• Issued: 11/24/2009
• Est. Priority Date: 11/06/1996
• Status: Expired due to Term

• Current Assignee: Agena Bioscience Inc. (Mesa Laboratories Inc.)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Lough, David M., Koster, Hubert
• Primary Examiner(s): Maier; Leigh C.
• Application Number:
  US10/277,021
• Time in Patent Office: 2,595 Days
• Field of Search: 536/24.3, 536/25.3, 536/23.1, 536/25.4, 525/332.2, 502/233, 435/6, 436/94
• US Class Current: 435/6.12
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00504 Pins
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2035/1069 : by adjusting the spacing between multiple probes of a single transferring head
• CPC Class Codes: G01N 35/1067 : for transfer to or from containers having different spacing

Abstract

Novel compositions comprised of at least one bead conjugated to a solid support and further conjugated to at least one nucleic acid and preferred methods for making the novel compositions are described. As compared to “flat” surfaces, beads linked to a solid support provide an increased surface area for immobilization of nucleic acids. Furthermore, by selecting a bead with the desired functionality, a practitioner can select a functionalization chemistry for immobilizing nucleic acids, which is different from the chemistry of the solid support.

Claims

1. A composition, comprising a bead conjugated to a solid support and further conjugated to a nucleic acid, wherein the solid support is selected from the group consisting of multiwell plates, arrays of pits and multiwell supports comprising nanoliter wells.

2. A composition of claim 1, wherein the bead is made from a material selected from the group consisting of:

silica gel, glass, magnet, 4—

(hydroxymethyl)phenoxymethylcopoly(styrene—

1% divinylbenzene) resin, chloromethylated copolystyrene—

divinylbenzene resin, metal, plastic, cellulose, dextran cross-linked with epichlorohydrin, and agarose.

3. A composition of claim 1, wherein the bead is swellable.

4. A composition of claim 1, wherein the bead is nonswellable.

5. A composition of claim 1, wherein the bead is in the range of 1 to 100 μ

m in diameter.

6. A composition of claim 1, wherein the nucleic acid is DNA.

7. A composition of claim 1, wherein the nucleic acid is RNA.

19. A composition, comprising a bead conjugated to a solid support and further conjugated to a The composition of claim 1, wherein the nucleic acid molecule comprising protein comprises a peptide nucleic acid.

24. The composition of claim 1, wherein the solid support comprises an array of pits.

25. The composition of claim 1, wherein beads are conjugated to the support in pits on the array.

26. The composition of claim 1, wherein the solid support is a multiwell support comprising nanoliter wells.

27. The composition of claim 1, wherein beads are conjugated to the support in wells on the support.

28. The composition of claim 1, wherein conjugation of the bead to the solid support and/or conjugation of the nucleic acid to the bead is effected through an interaction comprising an ionic, covalent, polar or hydrophobic interaction.

29. The composition of claim 28, wherein interaction is an ionic interaction.

30. The composition of claim 28, wherein the interaction is a covalent interaction.

31. The composition of claim 28, wherein the interaction is a polar interaction.

32. The composition of claim 28, wherein the interaction is a hydrophobic interaction.

43. The composition of claim 1, wherein conjugation of the bead to the solid support and/or conjugation of the nucleic acid to the bead is effected through an acid labile linkage.

44. The composition of claim 1, wherein the nucleic acid is single-stranded.

88. The composition of claim 19, wherein the nucleic acid bound to the beads is RNA.

8. A process of making a bead conjugated to a solid support and further conjugated to a nucleic acid, comprising the steps of conjugating a bead to a nucleic acid;

and conjugating a bead to a solid support, wherein the solid support is selected from the group consisting of multiwell plates, arrays of pits, and multiwell supports comprising nanoliter wells.

9. A process of claim 8, wherein the bead is functionalized.

10. A process of claim 9, wherein the bead is functionalized with carboxy functional groups.

11. A process of claim 9, wherein the bead is functionalized with amino functional groups.

12. A process of claim 9, wherein the bead is conjugated to the nucleic acid prior to conjugation of the bead to the solid support.

13. A process of claim 9, wherein the bead is conjugated to the nucleic acid after the bead is conjugated to the solid support.

18. The method of claim 8, wherein conjugation is effected with a crosslinking agent.

45. The process of claim 8, wherein the nucleic acid is single-stranded.

14. A kit, comprising:

i) beads,

ii) an insoluble support, and

iii) conjugation means for linking nucleic acids to the beads and the beads to the support, wherein the solid support is selected from the group consisting of arrays of pits and multiwell supports comprising nanoliter wells.

15. The kit of claim 14, wherein the solid support is selected from the group consisting of:

beads, capillaries, plates, membranes, wafers, combs, pins, wafers with arrays of pits, and supports with nanoliter wells.

16. The kit of claim 14, wherein the bead is made from material selected from the group consisting of silica gel, glass, magnet, p-benzyloxybenzyl alcohol copolystyrene-divinyl benzene (DVB) resin, chlorotritylchloride copolystyrene-DVB resin, chloromethylated copolystyrene-DVB resin, metal, plastic, cellulose, cross-linked dextran, and agarose gel.

17. A composition, comprising a bead conjugated to a solid support and further conjugated to a nucleic acid, wherein conjugation is effected with a crosslinking agent and the solid support is selected from the group consisting of arrays of pits and multiwell supports comprising nanoliter wells.

20. A composition, comprising a bead conjugated to a solid support and further conjugated to a nucleic acid, wherein conjugation is effected through a photocleavable linkage, and the solid support is selected from the group consisting of arrays of pits and multiwell supports comprising nanoliter wells.

21. The composition of claim 20, wherein the linkage is cleaved by exposure to a laser.

22. The composition of claim 20, wherein the linkage is cleaved by exposure to electromagnetic radiation selected from ultraviolet, visible, infrared radiation or electromagnetic radiation generated by fluorescence or chemiluminescence, or combinations thereof.

23. A composition, comprising a bead conjugated to a solid support and further conjugated to a nucleic acid, wherein conjugation is effected through ionic linkages.

33. A method, comprising:

a) conjugating a bead to a solid support and further conjugating the bead to a nucleic acid, wherein the solid support is selected from the group consisting of arrays of pits and multiwell supports comprising nanoliter wells; and

b) analyzing the nucleic acid by a spectrometric method.

34. The method of claim 33, wherein the solid support comprises an array of pits.

35. The method of claim 34, wherein beads are conjugated to the support in pits on the array.

36. The method of claim 33, wherein the solid support is a multiwell support comprising nanoliter wells.

37. The method of claim 36, wherein beads are conjugated to the support in wells on the support.

46. The method of claim 33, wherein the nucleic acid is single-stranded.

38. A method, comprising:

a) providing a composition comprising a bead conjugated to a solid support and further conjugated to a nucleic acid, wherein the solid support is selected from the group consisting of arrays of pits and multiwell supports comprising nanoliter wells; and

b) analyzing the nucleic acid by a spectrometric method.

39. The method of claim 38, wherein the solid support comprises an array of pits.

40. The method of claim 39, wherein beads are conjugated to the support in pits on the array.

41. The method of claim 38, wherein the solid support is a multiwell support comprising nanoliter wells.

42. The method of claim 41, wherein beads are conjugated to the support in wells on the support.

47. The method of claim 38, wherein the nucleic acid is single-stranded.

48. A method, comprising:

(a) contacting a target nucleic acid with beads conjugated to a solid support and further conjugated to a nucleic acid, wherein target nucleic acid that hybridizes to the nucleic acid conjugated to the beads is captured, and wherein the solid support is selected from the group consisting of arrays of pits and multiwell supports comprising nanoliter wells; and

(b) detecting captured target nucleic acid.

49. The method of claim 48, wherein the nucleic acid conjugated to the beads is single-stranded.

50. The method of claim 48, wherein the solid support comprises an array of pits.

51. The method of claim 50, wherein beads are conjugated to the support in pits on the array.

52. The method of claim 48, wherein the solid support is a multiwell support comprising nanoliter wells.

53. The method of claim 52, wherein beads are conjugated to the support in wells on the support.

54. The method of claim 48, wherein conjugation of the beads to the solid support and/or conjugation of the nucleic acid to the beads is effected through ionic, covalent, polar or hydrophobic interactions.

55. The method of claim 54, wherein conjugation of the beads to the solid support and/or conjugation of the nucleic acid to the beads is effected through ionic interactions.

56. The method of claim 54, wherein conjugation of the beads to the solid support and/or conjugation of the nucleic acid to the bead is effected through covalent interactions.

57. The method of claim 54, wherein conjugation of the beads to the solid support and/or conjugation of the nucleic acid to the bead is effected through polar interactions.

58. The method of claim 54, wherein conjugation of the beads to the solid support and/or conjugation of the nucleic acid to the beads is effected through hydrophobic interactions.

59. The method of claim 48, wherein the nucleic acid is detected by a spectrometric method.

60. The method of claim 59, wherein the spectrometric method comprises fluorescence detection.

61. The method of claim 48, wherein the captured target nucleic acid is from a biological sample.

62. The method of claim 48, wherein the nucleic acid conjugated to the beads is DNA.

63. The method of claim 48, wherein the nucleic acid conjugated to the beads is RNA.

64. A method, comprising:

(a) contacting a target nucleic acid with beads bound to a solid support and further bound to a nucleic acid, wherein target nucleic acid that hybridizes to the nucleic acid bound to the beads is captured, and wherein the solid support is selected from the group consisting of arrays of pits and multiwell supports comprising nanoliter wells; and

(b) detecting captured target nucleic acid.

65. The method of claim 64, wherein the nucleic acid bound to the beads is single-stranded.

66. The method of claim 64, wherein the nucleic acid bound to the beads is DNA.

67. The method of claim 64, wherein the nucleic acid is detected by a spectrometric method.

68. The method of claim 67, wherein the spectrometric method comprises fluorescence detection.

69. A method for capturing a target polynucleotide, which comprises:

contacting a target polynucleotide of a biological sample with a complex comprising a bead conjugated to a solid support and further conjugated to a capture nucleic acid that can hybridize to the target polynucleotide, wherein;

the bead is conjugated to the solid support by an interaction selected from the group consisting of an ionic interaction, polar interaction and hydrophobic interaction; and

the solid support is selected from the group consisting of glass supports, silicon wafers, supports with arrays of pits and supports with nanoliter wells;

whereby the target polynucleotide is captured by the complex.

70. The method of claim 69, wherein the interaction is an ionic interaction.

71. The method of claim 69, wherein the interaction is a polar interaction.

72. The method of claim 69, wherein the interaction is a hydrophobic interaction.

73. The method of claim 69, wherein the solid support is a glass surface.

74. The method of claim 69, wherein the solid support is a support with an array of pits.

75. The method of claim 69, wherein the solid support is a support with nanoliter wells.

76. The method of claim 69, wherein the solid support is a silicon wafer.

77. The method of claim 69, wherein the capture nucleic acid is DNA.

78. The method of claim 69, wherein the capture nucleic acid is RNA.

79. A composition for capturing a target polynucleotide of a biological sample, which comprises a bead of conjugated to a solid suppoer and further conjugated to a capture nucleic acid that can hybridize to the target polynucleotide, wherein:

the bead is conjugated to the solid support by an interaction selected from the group consisting of an ionic interaction, polar interaction and hydrophobic interaction; and

the solid support is selected from the group consisting of glass supports, silicon wafers, supports with arrays of pits and supports with nanoliter wells.

80. The composition of claim 79, wherein the interaction is an ionic interaction.

81. The composition of claim 79, wherein the interaction is a polar interaction.

82. The composition of claim 79, wherein the interaction is a hydrophobic interaction.

83. The composition of claim 79, wherein the solid support is a glass surface.

84. The composition of claim 79, wherein the solid support is a support with an array of pits.

85. The composition of claim 79, wherein the solid support is a support with nanoliter wells.

86. The composition of claim 79, wherein the solid support is a silicon wafer.

87. The composition of claim 79, wherein the nucleic acid bound to the beads is DNA.