Method and apparatus for the automated generation of nucleic acid ligands

• US 20030054360A1
• Filed: 11/21/2001
• Published: 03/20/2003
• Est. Priority Date: 01/19/1999
• Status: Active Application

• Current Assignee: Somalogic Incorporated
• Original Assignee: Somalogic Incorporated
• Inventors: Gold, Larry, Schneider, Daniel J., Smith, Jonathan Drew, Zichi, Dominic A.
• Application Number:
  US09/993,294
• Publication Number:
  US 20030054360A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12N 15/1048 SELEX

Abstract

The present invention includes a method and device for performing the automated SELEX process, including automated photoSELEX process embodiments, and automated affinity SELEX process embodiments. The automated photoSELEX embodiments included an embodiment wherein target protein and nucleic acid ligands are photocrosslinked in solution. The steps of the SELEX process are performed at one or more work stations on a work surface by a robotic manipulator controlled by a computer. Also included in the invention are photocrosslinking nucleic acid ligands to human neutrophil elastase (hNE), HIV-1_MN gp120, human L-selectin, human P-Selectin, human platelet-derived growth factor (PDGF), human alpha-thrombin, human basic fibroblast growth factor (bFGF), HIV-1_MN gp120, Angiogenin, Interleukin-4, β-Nerve Growth Factor (β-NGF), Tansforming Growth Factor β1, Interleukin-7, Kininogen, Plasmin, Serum Amyloid P, Thrombopoietin (Tpo), Coagulation Factor IX, Coagulation Factor XII, Endostatin, Factor II, Collagen, Cytotoxic T lymphocyte-associated protein-4 Fc (CTLA-4 Fc), Hepatocyte Growth Factor (HGF), Insulin-like growth factor binding protein-3 (IGFBP-3), UDP-glucuronosyl transferase (UGT) 1A1, UGT 1A10, and UGT 1A3.

Claims

1. A method for identifying photocrosslinking nucleic acid ligands of a target protein from a candidate mixture of nucleic acids wherein each member of said candidate mixture comprises one or more photoreactive groups, said method comprising:

a) contacting the candidate mixture with said target protein in solution, wherein nucleic acids having an increased affinity to said target protein relative to the candidate mixture form nucleic acid-target protein complexes;

b) irradiating said candidate mixture, wherein said nucleic acid-target protein complexes photocrosslink;

c) immobilizing said target protein on a solid support, whereby said photocrosslinked nucleic acid-target protein complexes are immobilized on said solid support;

d) partitioning said solid support from the remainder of the candidate mixture whereby immobilized photocrosslinked nucleic acid-target protein complexes are partitioned from the remainder of the candidate mixture;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified.

e) amplifying the nucleic acids that photocrosslinked to the target protein to yield a mixture of nucleic acids enriched in sequences that are capable of photocrosslinking the target protein;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified.

2. The method of claim 1 further comprising the step:

f) repeating steps a) through e) using the enriched mixture of each successive repeat as many times as required to yield a desired level of increased enrichment;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified.

3. The method of claim 1 wherein said photocrosslinking nucleic acid ligand is a single-stranded nucleic acid.

4. The method of claim 3 wherein said single-stranded nucleic acid is ribonucleic acid.

5. The method of claim 3 wherein said single-stranded nucleic acid is deoxyribonucleic acid.

6. The method of claim 1 wherein said candidate mixture further comprises fixed sequence regions, and wherein the amplification is performed using the polymerase chain reaction (PCR) with primers complementary to said fixed sequence regions, wherein the 5′

ends of said primers are attached to tail sequences having a lower melting temperature (Tm) than said primers, wherein the polymerase chain reaction comprises a denaturation step, a primer annealing step, and a primer extension step, and wherein said primer annealing step and said primer extension step are performed at a temperature higher than the melting temperature of said tail sequences.

7. The method of claim 1 wherein said photoreactive groups are selected from the group consisting of 5-bromouracil, 5-iodouracil, 5-bromovinyluracil, 5-iodovinyluracil, 5-azidouracil, 4-thiouracil, 5-bromocytosine, 5-iodocytosine, 5-bromovinylcytosine, 5-iodovinylcytosine, 5-azidocytosine, 8-azidoadenine, 8-bromoadenine, 8-iodoadenine, 8-azidoguanine, 8-bromoguanine, 8-iodoguanine, 8-azidohypoxanthine, 8-bromohypoxanthine, 8-iodohypoxanthine, 8-azidoxanthine, 8-bromoxanthine, 8-iodoxanthine, 5-bromodeoxyuracil, 8-bromo-2′

-deoxyadenine, 5-iodo-2′

-deoxyuracil, 5-iodo-2′

-deoxycytosine, 5-[(4-azidophenacyl)thio]cytosine, 5-[(4-azidophenacyl)thio]uracil, 7-deaza-7-iodoadenine, 7-deaza-7-iodoguanine, 7-deaza-7-bromoadenine, and 7-deaza-7-bromoguanine.

8. The method of claim 1 further comprising releasing nucleic acids from the immobilized photocrosslinked nucleic acid-target protein complexes by proteolytic digestion.

9. The method of claim 1 further comprising washing the partitioned solid support under conditions selected from the group consisting of nucleic acid denaturing conditions, protein denaturing conditions, and protein and nucleic acid denaturing conditions.

10. The method of claim 1 wherein said solid support is derivatized with tosyl groups, and wherein said nucleic acid-target protein complexes are immobilized on said solid support through the reaction of the target protein with said tosyl groups.

11. The method of claim 1 wherein said solid support is a bead.

12. The method of claim 11 wherein said bead is a paramagnetic bead.

13. The method of claim 1 wherein said solid support is a multi-well microtiter plate.

14. The method of claim 1 wherein steps a) through e) are carried out by automated machines controlled by a computer.

15. The method of claim 1 wherein steps a) through d) are carried out by automated machines controlled by a computer.

142. The non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is identified by the method of any one of claims 1, 16, or 21.

16. A method for identifying photocrosslinking nucleic acid ligands of a target protein from a candidate mixture of nucleic acids wherein each member of said candidate mixture comprises one or more photoreactive groups, said method comprising:

a) contacting the candidate mixture with said target protein in solution, wherein nucleic acids having an increased affinity to said protein target relative to the candidate mixture form nucleic acid-target protein complexes;

b) irradiating said candidate mixture, wherein said nucleic acid-target protein complexes photocrosslink;

c) contacting said candidate mixture with a tosyl-derivatized solid support whereby nucleic acid-target protein complexes become immobilized on said tosyl-derivatized solid support through the reaction of the tosyl groups with said target protein;

d) partitioning the tosyl-derivatized solid supports from the candidate mixture;

e) releasing nucleic acids from said tosyl-derivatized solid by proteolytic digestion;

f) amplifying the nucleic acids released in e) to yield a mixture of nucleic acids enriched in sequences that are capable of photocrosslinking to the target protein; and

g) repeating steps a) through f) using the enriched mixture of each successive repeat as many times as required to yield a desired level of enrichment for sequence capable of photocrosslinking to the target protein, whereby a photocrosslinking nucleic acid ligand of the target is identified.

17. The method of claim 16 further comprising the step of:

washing the nucleic acid-target protein complexed tosyl-derivatized solid supports under conditions selected from the group consisting of nucleic acid denaturing conditions, protein denaturing conditions, and protein and nucleic acid denaturing conditions.

18. The method of claim 16 wherein said candidate mixture further comprises fixed sequence regions, and wherein the amplification is performed using the polymerase chain reaction (PCR) with primers complementary to said fixed sequence regions, wherein the 5′

ends of said primers are attached to tail sequences having a lower melting temperature (Tm) than said primers, wherein the polymerase chain reaction comprises a denaturation step, a primer annealing step, and a primer extension step, and wherein said primer annealing step and said primer extension step are performed at a temperature higher than the melting temperature of said tail sequences.

19. The method of claim 16 wherein steps a) through e) are carried out by automated machines controlled by a computer.

20. The method of claim 16 wherein steps a) through f) are carried out by automated machines controlled by a computer.

21. A method for identifying photocrosslinking nucleic acid ligands of a target protein from a candidate mixture of nucleic acids wherein each member of said candidate mixture comprises one or more photoreactive groups, said method comprising:

a) contacting the candidate mixture with the target protein, wherein nucleic acids having an increased affinity to the target relative to the candidate mixture may be partitioned from the remainder of the candidate mixture;

b) partitioning the increased affinity nucleic acids from the remainder of the candidate mixture;

c) amplifying the increased affinity nucleic acids to yield a ligand-enriched mixture of nucleic acids;

d) contacting said ligand-enriched mixture with the target protein in solution, wherein nucleic acid-target complexes form;

e) irradiating said candidate mixture, wherein said nucleic acid-target complexes photocrosslink;

f) immobilizing said target protein on a solid support, whereby said photocrosslinked nucleic acid-target protein complexes are immobilized on said solid support;

g) partitioning said solid support with immobilized photocrosslinked nucleic acid-target complexes from the remainder of the candidate mixture; and

h) amplifying the nucleic acids that photocrosslinked to the target protein to yield a mixture of nucleic acids enriched in sequences that are capable of photocrosslinking the target protein, whereby a photocrosslinking nucleic acid ligand of said target protein is identified.

22. The method of claim 21 further comprising after step c):

I. repeating steps a)-c) using the ligand-enriched mixture of each successive repeat as many times as required to yield a desired level of ligand enrichment.

23. The method of claim 21 further comprising the step:

i) repeating steps d) through h) using the mixture of nucleic acids enriched in sequences that are capable of photocrosslinking the target protein of each successive repeat as many times as required to yield a desired level of increased ligand enrichment;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified.

24. The method of claim 21 wherein in step a) said target protein is associated with a solid support.

25. The method of claim 24 wherein said solid support in step a) is a paramagnetic bead.

26. The method of claim 24 wherein said solid support in step a) is a microtiter plate.

27. The method of claim 21 wherein said partitioning step b) employs filter binding selection.

28. The method of claim 21, wherein said solid support in step f) is a paramagnetic bead.

29. The method of claim 21 wherein said solid support in step f) is derivatized with tosyl groups, whereby said nucleic acid-target complexes become immobilized on said solid support via the reaction between target protein and said tosyl groups.

30. The method of claim 21 further comprising releasing nucleic acids from the immobilized photocrosslinked nucleic acid-target protein complexes by proteolytic digestion.

31. The method of claim 21 further comprising washing the partitioned solid supports with immobilized photocrosslinked nucleic acid-target complexes under conditions selected from the group consisting of nucleic acid denaturing conditions, protein denaturing conditions, and protein and nucleic acid denaturing conditions.

32. The method of claim 21 wherein said candidate mixture further comprises fixed sequence regions, and wherein the amplification is performed using the polymerase chain reaction (PCR) with primers complementary to said fixed sequence regions, wherein the 5′

ends of said primers are attached to tail sequences having a lower melting temperature (Tm) than said primers, wherein the polymerase chain reaction comprises a denaturation step, a primer annealing step, and a primer extension step, and wherein said primer annealing step and said primer extension step are performed at a temperature higher than the melting temperature of said tail sequences.

33. The method of claim 21 wherein steps a)-c) are carried out by automated machines controlled by a computer.

34. The method of claim 21 wherein steps a)-b) are carried out by automated machines controlled by a computer.

35. The method of claim 21 wherein steps d)-h) are carried out by automated machines controlled by a computer.

36. The method of claim 21 wherein steps d)-g) are carried out by automated machines controlled by a computer.

37. A non-naturally occurring photocrosslinking nucleic acid ligand to a protein target selected from the group consisting of human neutrophil elastase (hNE), HIV-1_MN gp120, human L-selectin, human P-Selectin, human platelet-derived growth factor (PDGF), human alpha-thrombin, human basic fibroblast growth factor (bFGF), HIV-1MN gp120, Angiogenin, Interleukin-4 (IL-4), β

-Nerve Growth Factor (β

-NGF), Transforming Growth Factor β

1 (TGF-β

1), Interleukin-7 (IL-7), Kininogen, Plasmin, Serum Amyloid P, Thrombopoietin (Tpo), Coagulation Factor IX, Coagulation Factor XII, Endostatin, Factor H, Collagen, Cytotoxic T lymphocyte-associated protein-4 Fc (CTLA-4 Fe), Hepatocyte Growth Factor (HGF), Insulin-like growth factor binding protein-3 (IGFBP-3), UDP-glucuronosyl transferase (UGT) 1A1, UGT 1A1, and UGT 1A3.

38. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to human neutrophil elastase (hNE).

39. The photocrosslinking nucleic acid ligand of claim 38, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

1-3.

40. The photocrosslinking nucleic acid ligand of claim 38 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

1-3.

41. The photocrosslinking nucleic acid ligand of claim 38 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

1-3.

42. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to thrombin.

43. The photocrosslinking nucleic acid ligand of claim 42, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

9-12.

44. The photocrosslinking nucleic acid ligand of claim 42 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

9-12.

45. The photocrosslinking nucleic acid ligand of claim 42 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

9-12.

46. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to HIV-1_MAN gp120.

47. The photocrosslinking nucleic acid ligand of claim 46, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

4-5 and SEQ ID NOS;

13-16.

48. The photocrosslinking nucleic acid ligand of claim 46 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

4-5 and SEQ ID NOS;

13-16.

49. The photocrosslinking nucleic acid ligand of claim 46 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

4-5 and SEQ ID NOS;

13-16.

50. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to human platelet-derived growth factor (PDGF).

51. The photocrosslinking nucleic acid ligand of claim 50, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

6-8 and SEQ ID. NOS. 17-22

52. The photocrosslinking nucleic acid ligand of claim 50 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

6-8 and SEQ ID NOS;

17-22.

53. The photocrosslinking nucleic acid ligand of claim 50 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

6-8 and SEQ ID NOS;

17-22.

54. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to angiogenin.

55. The photocrosslinking nucleic acid ligand of claim 54, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

23-30.

56. The photocrosslinking nucleic acid ligand of claim 54 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

23-30.

57. The photocrosslinking nucleic acid ligand of claim 54 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

23-30.

58. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Interleukin-4 (IL-4).

59. The photocrosslinking nucleic acid ligand of claim 58, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

31-36.

60. The photocrosslinking nucleic acid ligand of claim 58 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

31-36.

61. The photocrosslinking nucleic acid ligand of claim 58 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

31-36.

62. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to β

-Nerve Growth Factor (β

-NGF).

63. The photocrosslinking nucleic acid ligand of claim 62, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

37-42.

64. The photocrosslinking nucleic acid ligand of claim 62 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

37-42.

65. The photocrosslinking nucleic acid ligand of claim 62 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

37-42.

66. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to human P-Selectin.

67. The photocrosslinking nucleic acid ligand of claim 66, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

43-47.

68. The photocrosslinking nucleic acid ligand of claim 66 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

43-47.

69. The photocrosslinking nucleic acid ligand of claim 66 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

43-47.

70. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Transforming Growth Factor β

1 (TGF-β

1).

71. The photocrosslinking nucleic acid ligand of claim 70, wherein said photocrosslinking nucleic acid ligand is selected from the group consisting of SEQ ID NOS:

48-52.

72. The photocrosslinking nucleic acid ligand of claim 70 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

48-52.

73. The photocrosslinking nucleic acid ligand of claim 70 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand selected from the group consisting of SEQ ID NOS:

48-52.

74. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Interleukin-7.

75. The photocrosslinking nucleic acid ligand of claim 74, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

53.

76. The photocrosslinking nucleic acid ligand of claim 74 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

53.

77. The photocrosslinking nucleic acid ligand of claim 74 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

53.

78. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Kininogen.

79. The photocrosslinking nucleic acid ligand of claim 78, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

54.

80. The photocrosslinking nucleic acid ligand of claim 78 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

54.

81. The photocrosslinking nucleic acid ligand of claim 78 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

54.

82. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to L-Selectin.

83. The photocrosslinking nucleic acid ligand of claim 82, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

55.

84. The photocrosslinking nucleic acid ligand of claim 82 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

55.

85. The photocrosslinking nucleic acid ligand of claim 82 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

55.

86. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Plasmin.

87. The photocrosslinking nucleic acid ligand of claim 86, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

56.

88. The photocrosslinking nucleic acid ligand of claim 86 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

56.

89. The photocrosslinking nucleic acid ligand of claim 86 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

56.

90. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Serum Amyloid P.

91. The photocrosslinking nucleic acid ligand of claim 90, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

57.

92. The photocrosslinking nucleic acid ligand of claim 90 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

57.

93. The photocrosslinking nucleic acid ligand of claim 90 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

57.

94. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Thrombopoietin (Tpo).

95. The photocrosslinking nucleic acid ligand of claim 94, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

58.

96. The photocrosslinking nucleic acid ligand of claim 94 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

58.

97. The photocrosslinking nucleic acid ligand of claim 94 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

58.

98. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Coagulation Factor IX.

99. The photocrosslinking nucleic acid ligand of claim 98, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

59.

100. The photocrosslinking nucleic acid ligand of claim 98 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

59.

101. The photocrosslinking nucleic acid ligand of claim 98 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

59.

102. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Coagulation Factor XII.

103. The photocrosslinking nucleic acid ligand of claim 102, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

60.

104. The photocrosslinking nucleic acid ligand of claim 102 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

60.

105. The photocrosslinking nucleic acid ligand of claim 102 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

60.

106. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Endostatin.

107. The photocrosslinking nucleic acid ligand of claim 106, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

61.

108. The photocrosslinking nucleic acid ligand of claim 106 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

61.

109. The photocrosslinking nucleic acid ligand of claim 106 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

61.

110. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Factor H.

111. The photocrosslinking nucleic acid ligand of claim 110, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

62.

112. The photocrosslinking nucleic acid ligand of claim 110 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

62.

113. The photocrosslinking nucleic acid ligand of claim 110 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

62.

114. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Collagen.

115. The photocrosslinking nucleic acid ligand of claim 114, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

63.

116. The photocrosslinking nucleic acid ligand of claim 114 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

63.

117. The photocrosslinking nucleic acid ligand of claim 114 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

63.

118. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Cytotoxic T lymphocyte-associated protein-4 Fc (CTLA-4 Fc).

119. The photocrosslinking nucleic acid ligand of claim 118, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

64.

120. The photocrosslinking nucleic acid ligand of claim 118 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

64.

121. The photocrosslinking nucleic acid ligand of claim 118 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

64.

122. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Hepatocyte Growth Factor (HGF).

123. The photocrosslinking nucleic acid ligand of claim 122, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

65.

124. The photocrosslinking nucleic acid ligand of claim 122 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

65.

125. The photocrosslinking nucleic acid ligand of claim 122 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

65.

126. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to Insulin-like growth factor binding protein-3 (IGFBP-3).

127. The photocrosslinking nucleic acid ligand of claim 126, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

66.

128. The photocrosslinking nucleic acid ligand of claim 126 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

66.

129. The photocrosslinking nucleic acid ligand of claim 126 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

66.

130. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to UDP-glucuronosyl transferase (UGT) 1A1.

131. The photocrosslinking nucleic acid ligand of claim 130, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

67.

132. The photocrosslinking nucleic acid ligand of claim 130 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photo crosslinkidng nucleic acid ligand comprising the sequence shown in SEQ ID NO:

67.

133. The photocrosslinking nucleic acid ligand of claim 130 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

67.

134. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to UDP-glucuronosyl transferase (UGT) 1A10.

135. The photocrosslinking nucleic acid ligand of claim 134, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

68.

136. The photocrosslinking nucleic acid ligand of claim 134 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

68.

137. The photocrosslinking nucleic acid ligand of claim 134 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

68.

138. The purified and isolated non-naturally occurring photocrosslinking nucleic acid ligand of claim 37 wherein said photocrosslinking nucleic acid ligand is a photocrosslinking nucleic acid ligand to UDP-glucuronosyl transferase (UGT) 1A3.

139. The photocrosslinking nucleic acid ligand of claim 138, wherein said photocrosslinking nucleic acid ligand comprises the sequence shown in SEQ ID NO:

69.

140. The photocrosslinking nucleic acid ligand of claim 138 wherein said photocrosslinking nucleic acid ligand is substantially homologous to a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

69.

141. The photocrosslinking nucleic acid ligand of claim 138 wherein said photocrosslinking nucleic acid ligand has substantially the same structure as a photocrosslinking nucleic acid ligand comprising the sequence shown in SEQ ID NO:

69.

143. An automated machine for identifying photocrosslinking nucleic acid ligands of a target protein from a candidate mixture of nucleic acids wherein each member of said candidate mixture comprises photoreactive groups, wherein said automated machine performs the steps of:

a) contacting the candidate mixture with said target protein in solution, wherein nucleic acids having an increased affinity to said target protein relative to the candidate mixture form nucleic acid-target protein complexes;

b) irradiating said candidate mixture, wherein said nucleic acid-target protein complexes photocrosslink;

c) immobilizing said target protein on a solid support, whereby said photocrosslinked nucleic acid-target protein complexes are immobilized on said solid support;

d) partitioning said solid support from the remainder of the candidate mixture whereby immobilized photocrosslinked nucleic acid-target protein complexes are partitioned from the remainder of the candidate mixture;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified following amplification of the nucleic acids that photocrosslinked to the target protein to yield a mixture of nucleic acids enriched in sequences that are capable of photocrosslinking the target protein;

and wherein steps a)-d) are performed at one or more work stations on a work surface by a robotic manipulator controlled by a computer.

144. An automated machine for identifying photocrosslinking nucleic acid ligands of a target protein from a candidate mixture of nucleic acids wherein each member of said candidate mixture comprises photoreactive groups, wherein said automated machine performs the steps of:

a) contacting the candidate mixture with said target protein in solution, wherein nucleic acids having an increased affinity to said target protein relative to the candidate mixture form nucleic acid-target protein complexes;

b) irradiating said candidate mixture, wherein said nucleic acid-target protein complexes photocrosslink;

c) immobilizing said target protein on a solid support, whereby said photocrosslinked nucleic acid-target protein complexes are immobilized on said solid support;

d) partitioning said solid support from the remainder of the candidate mixture whereby immobilized photocrosslinked nucleic acid-target protein complexes are partitioned from the remainder of the candidate mixture;

e) amplifying the nucleic acids that photocrosslinked to the target protein to yield a mixture of nucleic acids enriched in sequences that are capable of photocrosslinking the target protein;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified;

wherein steps a)-e) are performed at one or more work stations on a work surface by a robotic manipulator controlled by a computer.

145. An automated machine for identifying photocrosslinking nucleic acid ligands of a target protein from a candidate mixture of nucleic acids wherein each member of said candidate mixture comprises photoreactive groups, said automated machine comprising:

a) means for contacting the candidate mixture with said target protein in solution, wherein nucleic acids having an increased affinity to said target protein relative to the candidate mixture form nucleic acid-target protein complexes;

b) means for irradiating said candidate mixture, wherein said nucleic acid-target protein complexes photocrosslink;

c) means for immobilizing said target protein on a solid support, whereby said photocrosslinked nucleic acid-target protein complexes are immobilized on said solid support;

d) means for partitioning said solid support from the remainder of the candidate mixture whereby immobilized photocrosslinked nucleic acid-target protein complexes are partitioned from the remainder of the candidate mixture;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified following amplification of the nucleic acids that photocrosslinked to the target protein to yield a mixture of nucleic acids enriched in sequences that are capable of photocrosslinking the target protein;

wherein steps a)-d) are performed at one or more work stations on a work surface by a robotic manipulator controlled by a computer.

146. An automated machine for identifying photocrosslinking nucleic acid ligands of a target protein from a candidate mixture of nucleic acids wherein each member of said candidate mixture comprises photoreactive groups, said automated machine comprising:

a) means for contacting the candidate mixture with said target protein in solution, wherein nucleic acids having an increased affinity to said target protein relative to the candidate mixture form nucleic acid-target protein complexes;

b) means for irradiating said candidate mixture, wherein said nucleic acid-target protein complexes photocrosslink;

c) means for immobilizing said target protein on a solid support, whereby said photocrosslinked nucleic acid-target protein complexes are immobilized on said solid support;

d) means for partitioning said solid support from the remainder of the candidate mixture whereby immobilized photocrosslinked nucleic acid-target protein complexes are partitioned from the remainder of the candidate mixture

e) means for amplifying the nucleic acids that photocrosslinked to the target protein to yield a mixture of nucleic acids enriched in sequences that are capable of photocrosslinking the target protein;

whereby a photocrosslinking nucleic acid ligand of said target protein is identified;

wherein steps a)-e) are performed at one or more work stations on work surface by a robotic manipulator controlled by a computer.