Templated molecules and methods for using such molecules

1. A library comprising a plurality of different small non-peptide molecules,

each small non-peptide molecule linked to a double stranded identifier oligonucleotide comprising sequences identifying the small non-peptide molecule, wherein

at least one strand of the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived on its nucleobase or on its ribose or deoxyribose unit.

2. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the C8 position of an adenine nucleobase.

3. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the C8 position of a guanine nucleobase.

4. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the C7 position of a adenine nucleobase.

5. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the C7 position of a guanine nucleobase.

6. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the C5 or C6 position of a cytidine nucleobase.

7. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the C5 position of a thymidine nucleobase.

8. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the C5 position of a uridine nucleobase.

9. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one derivatized nucleotide or derivatized nucleotide analog selected from the group consisting of

10. The library according to claim 9 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is located at the 5′ or 3′ end of the identifier oligonucleotide.

11. The library according to claim 9 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is located internally in the identifier oligonucleotide.

12. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the 2′-, 4′- or 5′-position of a ribose or deoxyribose.

13. The library according to claim 1 , wherein the identifier oligonucleotide comprises at least one nucleotide or nucleotide analog derivatived at the 2′ position of a ribose or deoxyribose.

14. The library according to claim 1 , wherein the identifier oligonucleotide comprises more than one nucleotide or nucleotide analog derivatived on its nucleobase or on its ribose or deoxyribose unit.

15. The library according to claim 14 , wherein at least one derivatized

nucleotide or derivatized nucleotide analog is selected from the group consisting of

nucleotides comprising an adenine nucleobase derivatized at the C8 position,

nucleotides comprising a guanine nucleobase derivatized at the C8 position,

nucleotides comprising a deaza-adenine nucleobase derivatized at the C7 position,

nucleotides comprising a deaza-guanine nucleobase derivatized at the C7 position,

nucleotides comprising a cytosine nucleobase derivatized at the C5 position or at the C6 position,

nucleotides comprising a thymidine nucleobase derivatized at the C5 position, and

nucleotides comprising a uridine nucleobase derivatized at the C5 position.

16. The library according to claim 15 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is selected from the group consisting of

17. The library according to claim 16 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is located at the 5′ or 3′ end of the identifier oligonucleotide.

18. The library according to claim 16 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is located internally in the identifier oligonucleotide.

19. The library according to claim 15 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is derivatived at the 2′-, 4′- or 5′-position of a ribose or deoxyribose.

20. The library according to claim 15 , at least one derivatized nucleotide or derivatized nucleotide analog is derivatived at the 2′ position of a ribose or deoxyribose.

21. The library according to claim 1 , wherein the small non-peptide molecule is linked to the double stranded identifier through a linker comprising an aliphatic chain.

22. The library according to claim 1 , wherein the small non-peptide molecule is linked to the double stranded identifier through a linker comprising a polyether.

23. The library according to claim 22 , wherein the polyether is polyethyleneglycol.

24. The library according to claim 1 , wherein the small non-peptide molecule is linked to the double stranded identifier through a linker comprising a double stranded, a partially double stranded, or a single stranded natural or unnatural oligonucleotide.

25. The library according to claim 24 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is selected from the group consisting of nucleotides comprising a cytosine nucleobase derivatized at the C5 position or at the C6 position, nucleotides comprising a thymidine nucleobase derivatized at the C5 position, or nucleotides comprising a uridine nucleobase derivatized at the C5 position.

26. The library according to claim 25 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is selected from the group consisting of

27. The library according to claim 15 , wherein the small non-peptide molecule is linked to the double stranded identifier through a linker comprising an aliphatic chain.

28. The library according to claim 15 , wherein the small non-peptide molecule is linked to the double stranded identifier through a linker comprising a polyether.

29. The library according to claim 28 , wherein the polyether is polyethyleneglycol.

30. The library according to claim 15 , wherein the small non-peptide molecule is linked to the double stranded identifier through a linker comprising a double stranded, a partially double stranded, or a single stranded natural or unnatural oligonucleotide.

31. The library according to claim 30 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is selected from the group consisting of nucleotides comprising a cytosine nucleobase derivatized at the C5 position or at the C6 position, nucleotides comprising a thymidine nucleobase derivatized at the C5 position, or nucleotides comprising a uridine nucleobase derivatized at the C5 position.

32. The library according to claim 31 , wherein at least one derivatized nucleotide or derivatized nucleotide analog is selected from the group consisting of

33. The library of claim 1 , wherein the library comprises from about 10 3 to about 10 12 different small non-peptide molecules.

34. The library of claim 33 , wherein the library comprises small non-peptide molecules that are linear, branched, cyclic or scaffolded molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles; monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons; monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles; monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles; monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles; monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles; and monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

35. The library of claim 34 , wherein the library comprises linear small non-peptide molecules.

36. The library of claim 35 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

37. The library of claim 35 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

38. The library of claim 35 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

39. The library of claim 35 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

40. The library of claim 35 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

41. The library of claim 35 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

42. The library of claim 35 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

43. The library of claim 34 , wherein the library comprises branched small non-peptide molecules.

44. The library of claim 43 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

45. The library of claim 43 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

46. The library of claim 43 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

47. The library of claim 43 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

48. The library of claim 43 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

49. The library of claim 43 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

50. The library of claim 43 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

51. The library of claim 34 , wherein the library comprises cyclic small non-peptide molecules.

52. The library of claim 51 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

53. The library of claim 51 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

54. The library of claim 51 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

55. The library of claim 51 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

56. The library of claim 51 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

57. The library of claim 51 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

58. The library of claim 51 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

59. The library of claim 34 , wherein the library comprises scaffolded small non-peptide molecules.

60. The library of claim 59 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

61. The library of claim 59 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

62. The library of claim 59 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

63. The library of claim 59 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

64. The library of claim 59 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

65. The library of claim 59 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

66. The library of claim 59 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

67. The library of claim 33 , wherein each and both strands of the double stranded identifier oligonucleotide comprises sequences identifying the small non-peptide molecule.

68. The library of claim 67 , wherein the library comprises small non-peptide molecules that are linear, branched, cyclic or scaffolded molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles; monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons; monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles; monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles; monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles; monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles; and monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

69. The library of claim 68 , wherein the library comprises linear small non-peptide molecules.

70. The library of claim 69 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

71. The library of claim 69 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

72. The library of claim 69 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

73. The library of claim 69 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

74. The library of claim 69 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

75. The library of claim 69 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

76. The library of claim 69 , wherein the library comprises linear small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

77. The library of claim 68 , wherein the library comprises branched small non-peptide molecules.

78. The library of claim 77 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

79. The library of claim 77 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

80. The library of claim 77 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

81. The library of claim 77 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

82. The library of claim 77 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

83. The library of claim 77 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

84. The library of claim 77 , wherein the library comprises branched small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

85. The library of claim 68 , wherein the library comprises cyclic small non-peptide molecules.

86. The library of claim 85 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

87. The library of claim 85 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

88. The library of claim 85 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

89. The library of claim 85 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

90. The library of claim 85 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

91. The library of claim 85 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

92. The library of claim 85 , wherein the library comprises cyclic small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

93. The library of claim 68 , wherein the library comprises scaffolded small non-peptide molecules.

94. The library of claim 93 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic carbocycles.

95. The library of claim 93 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons.

96. The library of claim 93 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional nonaromatic heterocycles.

97. The library of claim 93 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic heterocycles.

98. The library of claim 93 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic carbocycles.

99. The library of claim 93 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monocyclic, bicyclic, tricyclic and polycyclic aromatic carbocycles.

100. The library of claim 93 , wherein the library comprises scaffolded small non-peptide molecules comprising one or more structures selected from the group consisting of monofunctional, difunctional, trifunctional and oligofunctional aromatic heterocycles.

101. The library of claim 67 , wherein the library comprises small non-peptide molecules linked to a nucleotide or nucleotide analog derivatived on its nucleobase or on its ribose or deoxyribose unit.

102. The library of claim 101 , wherein the small non-peptide molecules are linked to the derivatived nucleotide or nucleotide analog through a linker.

103. The library of claim 102 , wherein the linker comprises an aliphatic chain.

104. The library of claim 102 , wherein the linker comprises a polyether.

105. The library of claim 104 , wherein the polyether is a polyethylene glycol.

106. The library of claim 67 , wherein the library comprises small non-peptide molecules linked to the double stranded identifier oligonucleotide through a linker comprising a double stranded, a partially double stranded, or a single stranded natural or unnatural oligonucleotide.