Templated molecules and methods for using such molecules
First Claim
Patent Images
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, whereinat 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.
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Abstract
The present invention relates to a method for synthesising templated molecules. In one aspect of the invention, the templated molecules are linked to the template which templated the synthesis thereof. The invention allows the generation of libraries which can be screened for e.g. therapeutic activity.
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Citations
106 Claims
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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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106)
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
- or 3′
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11. The library according to claim 9, wherein at least one derivatized nucleotide or derivatized nucleotide analog is located internally in the identifier oligonucleotide.
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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.
- -, 4′
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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.
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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.
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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
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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.
- or 3′
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18. The library according to claim 16, wherein at least one derivatized nucleotide or derivatized nucleotide analog is located internally in the identifier oligonucleotide.
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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.
- -, 4′
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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.
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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.
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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.
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23. The library according to claim 22, wherein the polyether is polyethyleneglycol.
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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.
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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.
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26. The library according to claim 25, wherein at least one derivatized nucleotide or derivatized nucleotide analog is selected from the group consisting of
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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.
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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.
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29. The library according to claim 28, wherein the polyether is polyethyleneglycol.
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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.
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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.
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32. The library according to claim 31, wherein at least one derivatized nucleotide or derivatized nucleotide analog is selected from the group consisting of
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33. The library of claim 1, wherein the library comprises from about 103 to about 1012 different small non-peptide molecules.
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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.
- monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons;
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35. The library of claim 34, wherein the library comprises linear small non-peptide molecules.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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43. The library of claim 34, wherein the library comprises branched small non-peptide molecules.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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51. The library of claim 34, wherein the library comprises cyclic small non-peptide molecules.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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59. The library of claim 34, wherein the library comprises scaffolded small non-peptide molecules.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
- monocyclic, bicyclic, tricyclic, polycyclic and bridged polycyclic hydrocarbons;
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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.
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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.
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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.
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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.
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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.
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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.
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93. The library of claim 68, wherein the library comprises scaffolded small non-peptide molecules.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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102. The library of claim 101, wherein the small non-peptide molecules are linked to the derivatived nucleotide or nucleotide analog through a linker.
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103. The library of claim 102, wherein the linker comprises an aliphatic chain.
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104. The library of claim 102, wherein the linker comprises a polyether.
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105. The library of claim 104, wherein the polyether is a polyethylene glycol.
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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.
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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.
Specification
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Current AssigneeNuevolution A/S (Amgen Inc.)
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Original AssigneeNuevolution A/S (Amgen Inc.)
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InventorsPedersen, Henrik, Gouliaev, Alex Haahr, Franch, Thomas, Sams, Christian Klarner, Olsen, Eva Kampmann, Slok, Frank Abilgaard, Husemoen, Gitte Nystrup, Felding, Jakob, Hyldtoft, Lene, Norregaard-Madsen, Mads, Godskesen, Michael Anders, Glad, Sanne Schroder, Thisted, Thomas, Freskgard, Per-Ola, Holtmann, Anette
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Primary Examiner(s)Riley, Jezia
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Application NumberUS15/293,102Publication NumberTime in Patent Office1,328 DaysField of Search506 16, 506 18US Class CurrentCPC Class CodesC07B 2200/11 Compounds covalently bound ...C07D 405/04 directly linked by a ring-m...C07H 19/06 Pyrimidine radicalsC07H 19/10 with the saccharide radical...C07H 19/16 Purine radicalsC07H 19/20 with the saccharide radical...C07H 21/00 Compounds containing two or...C07H 23/00 Compounds containing boron,...C12N 15/1058 Directional evolution of li...C12N 15/1068 Template (nucleic acid) med...C12P 19/34 Polynucleotides, e.g. nucle...C40B 40/00 Libraries per se, e.g. arra...