P
USRE41005EExpiredUtilityPatentIndex 82

Beads bound to a solid support and to nucleic acids

Assignee: SEQUENOM INCPriority: Nov 6, 1996Filed: Oct 17, 2002Granted: Nov 24, 2009
Est. expiryNov 6, 2016(expired)· nominal 20-yr term from priority
Inventors:KOSTER HUBERTLOUGH DAVID M
C07H 21/00B01J 2219/00511B01J 2219/00315B01J 2219/00317B01J 2219/0052B01J 2219/00722B01J 2219/005B01J 2219/00497B01J 2219/00648B01J 2219/0072B01J 2219/00585B01J 2219/00659B01J 2219/00468G01N 35/1067C40B 40/10C40B 60/14B01J 2219/00725C12Q 1/6837B01J 2219/00387C40B 40/06G01N 2035/1069B01J 2219/00596B01J 2219/00527B01J 2219/00504C12Q 1/6872
82
PatentIndex Score
10
Cited by
382
References
88
Claims

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

exact text as granted — not AI-modified
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 μm 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. 
     
     
       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. 
     
     
       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. 
     
     
       18. The method of  claim 8 , wherein conjugation is effected with a crosslinking agent. 
     
     
       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. 
     
     
       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. 
     
     
       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. 
     
     
       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. 
     
     
       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. 
     
     
       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.   
     
     
       45. The process of  claim 8 , wherein the nucleic acid is single- stranded.   
     
     
       46. The method of  claim 33 , wherein the nucleic acid is single- stranded.   
     
     
       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. 
     
     
       88. The composition of  claim 19 , wherein the nucleic acid bound to the beads is RNA.

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