Method for the synthesis of a bifunctional complex

1. A method for synthesizing a library of bifunctional complexes comprising a reaction product and an identifier oligonucleotide, the method comprising:

performing a first synthesis round, comprising:

a) Adding a bridging molecule part to each of a plurality of reaction wells;

b) Adding a chemical entity to each of the plurality of reaction wells;

c) Adding an oligonucleotide tag to each of the plurality of reaction wells;

d) Attaching the oligonucleotide tag to the chemical entity through the bridging molecule part in each of the plurality of reaction wells, wherein the oligonucleotide tag identifies the chemical entity attached thereto;

performing a second synthesis round in each of the plurality of reaction wells, comprising

e) repeating steps b) through c), and

f) reacting the chemical entity added in step (e) with the chemical entities attached in step (d) to provide the reaction products, and attaching the oligonucleotide tag added in step (e) to the oligonucleotide tags attached in step (d) to provide the identifier oligonucleotides,

wherein the oligonucleotide identifier comprises at least two oligonucleotide tags, and the reaction product comprises at least two reacted chemical entities, each oligonucleotide tag identifying a reacted chemical entity;

g) optionally performing one or more additional synthesis rounds in each of the plurality of reaction wells by repeating steps (e) and (f); and

combining the contents of a plurality of reaction wells from step (f) or step (g) to provide the library of bifunctional complexes;

the method further comprising,

contacting one or more bifunctional complexes with a complimentary oligonucleotide comprising anti-tags capable of hybridizing with at least two of the oligonucleotide tags of the identifier oligonucleotide of the one or more bifunctional complexes.

2. The method of claim 1 , further comprising combining the contents of a plurality of reaction wells from step (d) and splitting the combined contents into a plurality of reaction wells prior to step (e).

3. The method of claim 2 , wherein the contents of a plurality of reaction wells from step (f) are combined and step (g) is omitted.

4. The method of claim 3 , wherein different chemical entities are added to each of the plurality of reaction wells in steps (b), and different oligonucleotide identifier tags are added to each of the plurality of reaction wells in step (c).

5. The method of claim 4 , wherein the reaction product is a small, non-polymeric molecule.

6. The method of claim 5 , wherein the small, non-polymeric molecule is a scaffolded molecule.

7. The method of claim 4 , wherein the library contains from 10 5 to 10 8 different bifunctional molecules, and the number of reaction wells in the first synthesis round and the second synthesis round are the same or different.

8. The method of claim 4 , wherein the complimentary oligonucleotide is attached to an attachment entity, the method further comprising

reacting the reaction product of a bifunctional complex with the attachment entity after hybridization of the identifier oligonucleotide with the complimentary oligonucleotide.

9. The method of claim 8 , wherein one or more of the anti-tags of the complimentary oligonucleotide is prepared by an extension reaction prior to reacting the reaction product of a bifunctional complex with the attachment entity.

10. The method of claim 4 , wherein the complimentary oligonucleotide comprises an assembly platform comprising a unique region that hybridizes with the at least two of the oligonucleotide tags of the identifier oligonucleotide.

11. The method of claim 10 , wherein the assembly platform is also capable of hybridizing to a second oligonucleotide.

12. The method of claim 11 , wherein the assembly platform comprises anti-tags capable of hybridizing with at least two of the oligonucleotide tags of the identifier oligonucleotide of a second bifunctional complex of the library.

13. The method of claim 12 , further comprising

reacting the reaction product of the bifunctional complex with the reaction product of the second bifunctional complex after hybridization of the identifier oligonucleotides of the bifunctional complex and second bifunctional complex with the assembly platform.

14. The method of claim 11 , wherein the oligonucleotide identifiers of the first and second bifunctional complexes are ligated by enzymatic ligation.

15. The method of claim 14 , wherein enzymatic ligation of oligonucleotide tags is performed in a single stranded state.

16. The method of claim 14 , wherein enzymatic ligation of oligonucleotide tags is performed in a double stranded state.

17. The method of claim 16 , wherein enzymatic ligation of oligonucleotide tags is performed in a double stranded state in which two oligonucleotide tags are kept together by a complementing oligonucleotide which hybridizes with ends of the two oligonucleotide tags to be ligated.

18. The method of claim 14 , wherein enzymatic ligation of oligonucleotide tags is performed by a ligase selected from the group consisting of Taq DNA ligase, T4 DNA ligase, T4 RNA ligase, T7 DNA ligase, and E. coli DNA ligase.

19. The method of claim 11 , wherein the oligonucleotide identifiers of a first and second bifunctional complexes are ligated by chemical ligation.

20. The method of claim 10 , wherein the assembly platform comprises a random complimentary identifier region for increasing the diversity of the library.

21. The method of claim 16 , wherein second oligonucleotides attached to different attachment entities hybridize to the random complimentary identifier region in one or more oligonucleotide hybridization steps.

22. The method of claim 4 , wherein the complimentary oligonucleotide is attached to an attachment entity and is capable of hybridizing to the identifier oligonucleotide of a first bifunctional complex and the identifier oligonucleotide of a second bifunctional complex.

23. The method of claim 22 , further comprising

reacting the reaction products of the first and second bifunctional complexes after hybridization of each of the identifier oligonucleotides with the complimentary oligonucleotide.

24. The method of claim 23 , wherein the regions of the complimentary oligonucleotide capable of hybridizing to each of the identifier oligonucleotides are prepared by an extension reaction prior to reacting the reaction products of the first bifunctional complex and the second bifunctional complex.

25. The method of claim 24 , wherein the reaction products of the first and second bifunctional complexes further react with the attachment entity attached to the complimentary oligonucleotide.

26. The method of claim 25 , wherein the reaction products of the first and second bifunctional complexes further react with an additional chemical entity.

27. The method of claim 24 , wherein the reaction products of the first and second bifunctional complexes further react with an additional chemical entity.

28. The method of claim 4 , wherein the oligonucleotide tags from one or more of steps (c), (e) and (g) are attached by enzymatic ligation.

29. The method of claim 28 , wherein enzymatic ligation of oligonucleotide tags is performed in a single stranded state.

30. The method of claim 28 , wherein enzymatic ligation of oligonucleotide tags is performed in a double stranded state.

31. The method of claim 30 , wherein enzymatic ligation of oligonucleotide tags is performed in a double stranded state in which two oligonucleotide tags are kept together by a complementing oligonucleotide which hybridizes with ends of the two oligonucleotide tags to be ligated.

32. The method of claim 28 , wherein enzymatic ligation of oligonucleotide tags is performed by a ligase selected from the group consisting of Taq DNA ligase, T4 DNA ligase, T4 RNA ligase, T7 DNA ligase, and E. coli DNA ligase.

33. The method of claim 4 , wherein the oligonucleotide tags from one or more of steps (c), (e) and (g) are attached by chemical ligation.

34. The method of claim 1 , wherein the contents of a plurality of reaction wells from step (f) are combined and step (g) is omitted.

35. The method of claim 1 , wherein different chemical entities are added to each of the plurality of reaction wells in steps (b), and different oligonucleotide identifier tags are added to each of the plurality of reaction wells in step (c).

36. The method of claim 1 , wherein the reaction product is a small, non-polymeric molecule.

37. The method of claim 36 , wherein the small, non-polymeric molecule is a scaffolded molecule.

38. The method of claim 1 , wherein at least one oligonucleotide tag of the identifier oligonucleotide is attached to the bridging molecule part, or to another oligonucleotide tag, by an enzymatic reaction, and wherein the further oligonucleotide tags are attached by chemical or enzymatic means.

39. The method of claim 1 , wherein the identifier oligonucleotide is amplifiable.

40. The method of claim 1 , wherein the complementary oligonucleotide comprising one or more anti-tags is randomly or semi-randomly designed.

41. The method of claim 1 , wherein the identifier oligonucleotide comprising one or more tags is randomly or semi-randomly designed.

42. The method of claim 1 , wherein a linker moiety of the bifunctional complexes identify a chemical reaction site of the bridging molecule having reacted with the chemical entity in step d).

43. The method of claim 42 , wherein the linker moiety of the bifunctional complexes comprises an oligonucleotide tag identifying the chemical reaction site.

44. The method of claim 1 , wherein the bifunctional complexes comprise a cleavable linker linking the reaction product and the identifier oligonucleotide.

45. The method of claim 44 , wherein the cleavable linker is selected among linkers comprising enzymatic cleavage sites, linkers comprising a chemical degradable component, and linkers cleavable by electromagnetic radiation.

46. The method of claim 1 , wherein the bifunctional complexes comprise a polyethylene glycol (PEG) linker.

47. The method of claim 1 , wherein identifier oligonucleotide tags are separated by a binding region having from 1 to 20 nucleotides.

48. The method of claim 47 , wherein the binding region comprises backbone modified nucleotides.

49. The method of claim 48 , wherein the backbone modified nucleotides are selected among nucleotides having a 2′-O-methyl substitution on the ribose, nucleotides having a 2′-flour substitution on the ribose, peptide nucleic acids (PNA), and nucleotides having a 2′-4′ O-methylene cyclisation of the ribose.

50. The method of claim 1 , wherein the identifier oligonucleotide tags and/or the complementary oligonucleotide anti-tags contain natural nucleotides.

51. The method of claim 50 , wherein the natural nucleobases of the nucleotides of the identifier oligonucleotide are selected from the group consisting of adenine, guanine, thymine, cytosine, 5 -methylcytosine, and uracil.

52. The method of claim 50 , wherein the natural nucleotides are selected from the group consisting of deoxyadenosine, deoxyguanosine, deoxythymidine, and deoxycytidine, and from the ribonucleotide (RNA) constituents adenosine, guanosine, uridine, cytidine, and inosine.

53. The method of claim 1 , wherein the identifier oligonucleotide tags and/or the complementary oligonucleotide anti-tags contain natural and non-natural nucleotides.

54. The method of claim 53 , wherein the natural nucleobases of the nucleotides of the identifier oligonucleotide comprise ribonucleotides selected from the group consisting of adenine, guanine, thymine, cytosine, 5-methylcytosine, and uracil.

55. The method of claim 53 , wherein the natural nucleotides comprise deoxyribonucleotides selected from the group consisting of deoxyadenosine, deoxyguanosine, deoxythymidine, and deoxycytidine, and from the ribonucleotide (RNA) constituents adenosine, guanosine, uridine, cytidine, and inosine.

56. The method of claim 53 , wherein the nucleobase of the nucleotides is selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, purine, xanthine, diaminopurine, 8-oxo-N 6 -methyladenine, 7-deazaxanthine, 7-deazaguanine, N 4 ,N 4 -ethanocytosin, N 6 ,N 6 -ethano-2,6-diamino-purine, 5-methylcytosine, 5-(C 3 -C 6 )-alkynylcytosine, 5-fluorouracil, 5-bromouracil, pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridine, isocytosine, isoguanine, and inosine.

57. The method of claim 1 , wherein the identifier oligonucleotide tags and/or the complementary oligonucleotide anti-tags comprise one or more non-natural nucleotides.

58. The method of claim 57 , wherein the ribose moieties of the non-natural nucleotides are selected from the group consisting of 2′- 0 -methyl-ribose, 2′-flour-ribose, and 2′-4′-O-methylene-ribose (LNA).

59. The method of claim 57 , wherein the internucleoside linkages of the non- natural nucleotides are selected from the group consisting of natural phosphodiester linkages, phosphorothiote linkages, phosphodithioate linkages, methylphosphonate linkages, phosphoramidate linkages, phosphotriester linkages, and non-phosphorous- containing internucleoside linkage.

60. The method of claim 57 , wherein the nucleobase of the nucleotides is selected from the group consisting of adenine, guanine, thymine, cytosine, uracil, purine, xanthine, diaminopurine, 8-oxo-N 6 -methyladenine, 7-deazaxanthine, 7-deazaguanine, N 4 ,N 4 -ethanocytosin, N 6 ,N 6 -ethano-2,6-diamino-purine, 5 -methylcytosine, 5-(C 3 -C 6 )-alkynylcytosine, 5-fluorouracil, 5-bromouracil, pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridine, isocytosine, isoguanine, and inosine.

61. The method of claim 1 , wherein identifier oligonucleotide tag backbone units are selected from the group consisting of

wherein B denotes a nucleobase.

62. The method of claim 1 , wherein the number of reaction compartments is from 5 to 5,000.

63. The method of claim 1 , wherein two synthesis rounds are performed, and the reaction product is identified by two oligonucleotide tags.

64. The method of claim 1 , wherein three synthesis rounds are performed, and the reaction product is identified by three oligonucleotide tags.

65. The method of claim 1 , wherein the complimentary oligonucleotide hybridizes with the identifier oligonucleotides of two bifunctional complexes.

66. The method of claim 1 , wherein chemical entity reactions are selected from the group consisting of an acylation reaction; an alkylation reaction; a vinylation reaction; an alkenylidation reaction; a transition metal catalyzed arylation reaction, a transition metal catalyzed hetarylation reaction, and a transition metal catalyzed vinylation reaction.

67. The method of claim 1 , wherein the identity of the reaction product is determined by sequencing the tags of the identifier oligonucleotide, or by sequencing the anti-tags of the complementary oligonucleotide.

68. A method for synthesizing a library of bifunctional complexes comprising a chemical entity and an identifier oligonucleotide, the method comprising:

performing a synthesis round, comprising:

a) Adding a bridging molecule part to each of a plurality of reaction wells;

b) Adding a chemical entity to each of the plurality of reaction wells;

c) Adding an oligonucleotide tag to each of the plurality of reaction wells;

d) Attaching the oligonucleotide tag to the chemical entity through the bridging molecule part in each of the plurality of reaction wells, wherein the oligonucleotide tag identifies the chemical entity attached thereto;

e) Combining the contents of a plurality of the reaction wells to provide the library of bifunctional complexes;

the method further comprising,

f) Contacting one or more bifunctional complexes with a complimentary oligonucleotide comprising an anti-tag capable of hybridizing with an oligonucleotide tag of one or more bifunctional complexes;

wherein,

1) the complimentary oligonucleotide is attached to an attachment entity, the method further comprising reacting the chemical entity of a bifunctional complex with the attachment entity after hybridization of the identifier oligonucleotide with the complimentary oligonucleotide, and wherein the anti-tag of the complimentary oligonucleotide is prepared by an extension reaction prior to reacting the chemical entity of the bifunctional complex with the attachment entity, or

2) the complimentary oligonucleotide comprises an assembly platform comprising a unique region that hybridizes with a tag of an identifier oligonucleotide, and wherein the assembly platform is also capable of hybridizing to an identifier oligonucleotide of a second bifunctional complex, the method further comprising reacting the chemical entity of the bifunctional complex with the chemical entity of the second bifunctional complex after hybridization of the identifier oligonucleotides of the bifunctional complex and second bifunctional complex with the assembly platform, wherein the region of the complimentary oligonucleotide capable of hybridizing to the identifier oligonucleotide of the second bifunctional complex is prepared by an extension reaction prior to reacting the chemical entities of the bifunctional complexes, or

3) the complimentary oligonucleotide is attached to an attachment entity and is capable of hybridizing to the identifier oligonucleotide of a first bifunctional complex and the identifier oligonucleotide of a second bifunctional complex, the method further comprising reacting the chemical entities of the first and second bifunctional complexes after hybridization of each of their identifier oligonucleotides with the complimentary oligonucleotide, wherein the regions of the complimentary oligonucleotide capable of hybridizing to each of the identifier oligonucleotides are prepared by an extension reaction prior to reacting the chemical entities of the first bifunctional complex and the second bifunctional complex.

69. The method of claim 68 , wherein the complimentary oligonucleotide is attached to an attachment entity, the method further comprising reacting the chemical entity of a bifunctional complex with the attachment entity after hybridization of the identifier oligonucleotide with the complimentary oligonucleotide, and wherein the anti-tag of the complimentary oligonucleotide is prepared by an extension reaction prior to reacting the chemical entity of the bifunctional complex with the attachment entity.

70. The method of claim 68 , wherein the complimentary oligonucleotide comprises an assembly platform comprising a unique region that hybridizes with a tag of an identifier oligonucleotide, and wherein the assembly platform is also capable of hybridizing to an identifier oligonucleotide of a second bifunctional complex, the method further comprising reacting the chemical entity of the bifunctional complex with the chemical entity of the second bifunctional complex after hybridization of the identifier oligonucleotides of the bifunctional complex and second bifunctional complex with the assembly platform, wherein the region of the complimentary oligonucleotide capable of hybridizing to the identifier oligonucleotide of the second bifunctional complex is prepared by an extension reaction prior to reacting the chemical entities of the bifunctional complexes.

71. The method of claim 68 , wherein the complimentary oligonucleotide is attached to an attachment entity and is capable of hybridizing to the identifier oligonucleotide of a first bifunctional complex and the identifier oligonucleotide of a second bifunctional complex, the method further comprising reacting the chemical entities of the first and second bifunctional complexes after hybridization of each of their identifier oligonucleotides with the complimentary oligonucleotide, wherein the regions of the complimentary oligonucleotide capable of hybridizing to each of the identifier oligonucleotides are prepared by an extension reaction prior to reacting the chemical entities of the first bifunctional complex and the second bifunctional complex.