Methods for producing a paired tag from a nucleic acid sequence and methods of use thereof

• US 20060024681A1
• Filed: 10/29/2004
• Published: 02/02/2006
• Est. Priority Date: 10/31/2003
• Status: Abandoned Application

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Agencourt Bioscience Corporation (Danaher Corporation)
• Inventors: Smith, Douglas R., McKernan, Kevin J., Malek, Joel A.
• Application Number:
  US10/978,224
• Publication Number:
  US 20060024681A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor

Abstract

Methods for producing a paired tag from a nucleic acid sequence are provided in which the paired tag comprises the 5′ end tag and 3′ end tag of the nucleic acid sequence. In one embodiment, the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition sites. In another embodiment, the nucleic acid sequence further comprises restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease. Methods of using paired tags are also provided. In one embodiment, paired tags are used to characterize a nucleic acid sequence. In a particular embodiment, the nucleic acid sequence is a genome. In one embodiment, the characterization of a nucleic acid sequence is karyotyping. Alternatively, in another embodiment, the characterization of a nucleic acid sequence is mapping of the sequence. In a further embodiment, a method is provided for identifying nucleic acid sequences that encode at least two interacting proteins.

Claims

1. A method for producing a paired tag from a first nucleic acid sequence fragment, without cloning, comprising the steps of:

a) joining the 5′ and

3′

ends of a first nucleic acid sequence fragment via a first linker such that the first linker is located between the 5′

end and the 3′

end of the first nucleic acid sequence fragment in a circular nucleic acid molecule;

b) cleaving the circular nucleic acid molecule, thereby producing a second nucleic acid fragment comprising paired tag wherein a 5′

end tag of the first nucleic acid sequence fragment is joined to a 3′

end tag of the first nucleic acid sequence fragment via the first linker.

2. The method of claim 1, wherein:

a) the linker comprises at least two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

b) the circular nucleic acid molecule is cleaved with a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site to thereby producing the paired tag.

3. (canceled)

4. The method of claim 1 wherein step a) comprises the steps of:

a) joining the 5′ and

3′

ends of a first nucleic acid sequence fragment to at least one adapter;

b) cleaving the adapter(s), thereby producing a second nucleic acid sequence fragment with compatible ends; and

c) circularizing the second nucleic acid sequence fragment such that a 5′

end of the first nucleic acid sequence fragment is joined to a 3′

end of the first nucleic acid sequence fragment via a first linker derived from the adapter(s), thereby producing a circular nucleic acid molecule.

5. The method of claim 4, wherein:

a) the adapter comprises at least two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

b) the adapter comprises a restriction endonuclease recognition site specific for a rare cutting restriction endonuclease;

c) cleaving the adapter joined to the nucleic acid sequence fragment with a rare cutting restriction endonuclease to produce the compatible ends; and

d) cleaving the circular nucleic acid molecule with a restriction endonuclease that cleaves distally to the restriction endonuclease recognition site.

6. (canceled)

7. The method of claim 1 further comprising the steps of:

c) joining a second linker to the 5′ and

3′

ends of the second nucleic acid sequence fragment; and

d) amplifying the second nucleic acid fragment using an oligonucleotide complementary to a sequence present in the second linker.

8. The method of claim 1 further comprising the steps of:

c) joining the 5′ and

3′

ends of a second nucleic acid sequence fragment via a second linker such that the second linker is located between the 5′

end and the 3′

end of the second nucleic acid sequence fragment in a second circular nucleic acid molecule; and

d) amplifying a nucleic acid sequence fragment from the second circular nucleic acid molecule using two oligonucleotides complementary to sequences present in the second linker.

9. The method of claim 8, wherein the second linker comprises a recognition site for a rare-cutting restriction endonuclease, and the second circular nucleic acid molecule is cleaved using a rare-cutting restriction endonuclease that recognizes the site in the second linker.

10. The method of claim 7, wherein:

a) the first linker comprises at least two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

b) the first circular nucleic acid molecule is cleaved with a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site.

11-12. -12. (canceled)

13. The method of claim 12, wherein the second nucleic acid fragment is purified by affinity capture using a reagent specific for the first linker prior to amplification, wherein the reagent is selected from the group consisting of biotin a sequence capable of forming a triple helix and a recognition site for a DNA binding protein.

14-16. -16. (canceled)

17. A method for characterizing a paired tag from a first nucleic acid sequence fragment, without cloning, comprising the steps of:

a) joining the 5′ and

3′

ends of a first nucleic acid sequence fragment to a linker such that the linker is located between the 5′

end and the 3′

end of the first nucleic acid sequence fragment in a circular nucleic acid molecule;

b) cleaving the circular nucleic acid molecule, thereby producing a second nucleic acid sequence fragment wherein a 5′

end tag of the first nucleic acid sequence fragment is joined to a 3′

end tag of the first nucleic acid sequence fragment via the linker;

c) amplifying the second nucleic acid fragment; and

d) characterizing the 5′ and

3′

end tags of the amplified second nucleic acid fragments.

18. A method for characterizing a nucleic acid sequence, without cloning, comprising the steps of:

a) fragmenting a nucleic acid sequence thereby producing a plurality of first nucleic acid sequence fragments having a 5′

end and a 3′

end;

b) joining the 5′ and

3′

ends of each first nucleic acid sequence fragment to a first linker such that the first linker is located between the 5′

end and the 3′

end of each first nucleic acid sequence fragment in a circular nucleic acid molecule;

c) cleaving the circular nucleic acid molecules, thereby producing a plurality of second nucleic acid sequence fragments wherein a subset of the fragments comprise a paired tag derived from each first nucleic acid sequence fragment joined via the first linker;

d) joining a second linker to the 5′ and

3′

ends of the second nucleic acid sequence fragments;

e) amplifying the second nucleic acid fragments using an oligonucleotide complementary to a sequence present in the second linker; and

f) characterizing the 5′ and

3′

end tags of the amplified second nucleic acid fragments.

19. A method for characterizing a nucleic acid sequence, without cloning, comprising the steps of:

a) fragmenting a nucleic acid sequence thereby producing a plurality of first nucleic acid sequence fragments having a 5′

end and a 3′

end;

b) joining the 5′ and

3′

ends of each first nucleic acid sequence fragment to a first linker such that the first linker is located between the 5′

end and the 3′

end of each first nucleic acid sequence fragment in a circular nucleic acid molecule;

c) cleaving the circular nucleic acid molecules, thereby producing a plurality of second nucleic acid sequence fragments wherein a subset of the fragments comprise a paired tag derived from each first nucleic acid sequence fragment joined via the first linker;

d) joining the 5′ and

3′

ends of each second nucleic acid sequence fragment via a second linker such that the second linker is located between the ends of each second nucleic acid sequence fragment to form a plurality of second circular nucleic acid molecules;

e) amplifying the second circular nucleic acid molecules two oligonucleotides complementary to sequences present in the second linker, thereby producing a plurality of amplified nucleic acid fragments; and

f) characterizing the 5′ and

3′

end tags of the plurality of amplified nucleic acid fragments.

20. A method for characterizing a nucleic acid sequence, without cloning, comprising the steps of:

a) fragmenting a nucleic acid sequence thereby producing a plurality of first nucleic acid sequence fragments having a 5′

end and a 3′

end;

b) joining the 5′ and

3′

ends of each first nucleic acid sequence fragment to a first linker such that the first linker is located between the 5′

end and the 3′

end of each first nucleic acid sequence fragment in a circular nucleic acid molecule;

c) cleaving the circular nucleic acid molecules, thereby producing a plurality of second nucleic acid sequence fragments wherein a subset of the fragments comprise a paired tag derived from each first nucleic acid sequence fragment joined via the first linker;

d) joining the 5′ and

3′

ends of each second nucleic acid sequence fragment via a second linker such that the second linker is located between the ends of each second nucleic acid sequence fragment to form a plurality of second circular nucleic acid molecules;

e) cleaving the second circular nucleic acid molecules;

f) amplifying the cleaved second circular nucleic acid molecules using two oligonucleotides complementary to sequences present in the second linker as PCR primers thereby producing a plurality of amplified nucleic acid fragments; and

g) characterizing the 5′ and

3′

end tags of the plurality of amplified nucleic acid fragments.

21. The method of claim 20, wherein the second linker comprises a recognition site for a rare-cutting restriction endonuclease, and the second circular nucleic acid molecule is cleaved using a rare-cutting restriction endonuclease that recognizes the recognition site for a rare-cutting restriction endonuclease in the second linker.

22. The method of claim 20, wherein the second circular nucleic acid molecules are cleaved non specifically.

23. The method of claim 17, wherein:

a) the first linker comprises at least two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

b) the first circular nucleic acid molecules are cleaved with a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site.

24. The method of claim 10, wherein the restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site are immediately adjacent to the ends of the first nucleic acid sequence fragments.

25. (canceled)

26. The method of claim 19, wherein the second nucleic acid fragment is purified from other nucleic acid fragments by affinity capture using a reagent specific for the first linker prior to amplification, wherein said reagent is selected from the group consisting of biotin a sequence capable of forming a triple helix and a recognition site for a DNA binding protein.

27-29. -29. (canceled)

30. The method of claim 20, wherein the nucleic acid sequence is a genome.

31. The method of claim 30, wherein the method karyotypes or sequences the genome.

32. (canceled)

33. A composition comprising nucleic acid sequence elements arranged in the following order:

linker 1--5′

end tag--linker 2--3′

end tag--linker 3

wherein the 5′

end tag and the 3′

end tag comprise a paired tag derived from a single contiguous nucleic acid sequence fragment.

34. (canceled)

35. The composition of claim 33, wherein linker 2 comprises:

a) at least two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site, and is oriented in such a way that one of the sites directs cleavage within the 5′

end tag or at the junction of linker 1 and the 5′

end tag, and the other site directs cleavage within the 3′

end tag or at the junction of linker 3 and the 3′

end tag; and

/or

b) at least one recognition site for a rare-cutting restriction endonuclease located between the two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site.

36. The composition of claim 33, wherein linker 1 and linker 3 are the same sequence in reverse orientation.

37. The composition of claim 33, wherein the composition is amplified using oligonucleotides complementary to sequences present in linker 1 and linker 3.

38. The composition of claim 33, wherein linker 1 and linker 3 are derived by cleavage of a circular nucleic acid molecule with a rare-cutting restriction endonuclease comprising a recognition site between linker 1 and linker 3.

39. A composition comprising a circular nucleic acid molecule, wherein sequence elements are arranged in the following circular order:

40. (canceled)

41. The composition of claim 39, wherein linker 2 comprises:

a) at least two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site, and are oriented in such a way that one of the sites directs cleavage within the 5′

end tag or at the junction of the 5′

end tag and linker 2 and, and the other site directs cleavage within the 3′

end tag or at the junction of the 3′

end tag and linker 2; and

/or

b) at least one recognition site for a rare-cutting restriction endonuclease located between the two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site.

42. The composition of claim 39, wherein linker 2 is palindromic.

43. The composition of claim 39, wherein linker 2 comprises a recognition site for a rare-cutting restriction endonuclease.

44. The composition of claim 39, wherein the composition is amplified isothermally using oligonucleotide primers complementary to sequences in either linker 1 or linker 2, or in both linker 1 and linker 2.

45. (canceled)

46. A method for producing a paired tag from a nucleic acid sequence, wherein the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition site, comprising the steps of:

a) cleaving the restriction endonuclease recognition sites using the restriction endonuclease that is specific for the restriction endonuclease recognition sites, thereby producing a 5′

end tag and a 3′

end tag from the nucleic acid sequence; and

b) joining the 5′

end tag with the 3′

end tag from the nucleic acid sequence;

thereby producing a paired tag from the nucleic acid sequence.

47. The method of claim 46, wherein the nucleic acid sequence further comprises at least two restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease.

48. A method for characterizing a nucleic acid sequence comprising the steps of:

a) fragmenting a nucleic acid sequence thereby producing a plurality of nucleic acid sequence fragments having a 5′

end and a 3′

end;

b) introducing into the 5′

end and into the 3′

end of each nucleic acid sequence fragment;

(i) a restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(ii) a restriction endonuclease recognition site specific for a rare cutting restriction endonuclease;

thereby producing modified nucleic acid sequence fragments;

c) cleaving the restriction endonuclease recognition site specific for a rare cutting restriction endonuclease in each modified nucleic acid sequence fragment with the rare cutting restriction endonuclease, thereby producing a plurality of nucleic acid sequence fragments having compatible ends;

d) maintaining the fragments having compatible ends under conditions in which the compatible ends intramolecularly ligate, thereby producing a plurality of circularized nucleic acid sequences comprising two restriction endonuclease recognition sites specific for restriction endonucleases that cleave the nucleic acid sequence fragment distally to the restriction endonuclease recognition sites;

e) cleaving the circularized nucleic acid sequences at the restriction endonuclease recognition sites with the restriction endonucleases specific for the restriction endonuclease recognition sites, thereby producing a plurality of paired tags comprising a 5′

end tag and a 3′

end tag of the nucleic acid sequence fragment; and

f) characterizing the paired tags;

thereby characterizing the nucleic acid sequence.

49-50. -50. (canceled)

51. A method for characterizing a nucleic acid sequence comprising the steps of:

a) fragmenting a nucleic acid sequence thereby producing a plurality of nucleic acid sequence fragments having a 5′

end and a 3′

end;

b) introducing into the 5′

end and into the 3′

end of each nucleic acid sequence fragment a restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site, thereby producing a plurality of modified nucleic acid sequence fragments;

c) cloning the modified nucleic acid sequence fragments, thereby producing cloned nucleic acid sequence fragments;

d) cleaving the restriction endonuclease recognition sites at the 5′

end and the 3′

end of the cloned nucleic acid sequence fragments using the restriction endonuclease that is specific for the restriction endonuclease recognition sites, thereby producing a 5′

end tag and a 3′

end tag of each cloned nucleic acid sequence fragment;

e) joining the 5′

end tag to the 3′

end tag of each cloned nucleic acid sequence fragment thereby producing a plurality of paired tags; and

f) characterizing the paired tags;

thereby characterizing the nucleic acid sequence.

52. The method of claim 51, wherein step b) comprises step c).

53. A method for identifying nucleic acid sequences that encode at least two interacting proteins comprising the steps of:

a) combining;

(i) a first vector comprising;

(1) a nucleic acid sequence that encodes a first protein that interacts with a second protein; and

(2) a first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(ii) a second vector comprising;

(1) a nucleic acid sequence that encodes the second protein; and

(2) a second restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

thereby producing a combination;

b) maintaining the combination under conditions in which the first protein and the second protein are expressed and interact;

c) joining the first vector with the second vector, thereby forming a contiguous nucleic acid sequence that comprises;

(i) the nucleic acid sequence that encodes a first protein that interacts with a second protein;

(ii) the first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

(iii) the nucleic acid sequence that encodes the second protein; and

(iv) the second restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

d) cleaving the first restriction endonuclease recognition site and the second restriction endonuclease recognition site in the contiguous nucleic acid sequence with restriction endonucleases that cleave the contiguous nucleic acid sequence distally to the restriction endonuclease recognition sites, thereby producing a paired tag comprising 5′

end tag and a 3′

end tag of the contiguous nucleic acid sequence; and

e) sequencing the paired tag,

thereby identifying nucleic acid sequences that encode at least two interacting proteins.

54. A method for identifying nucleic acid sequences that encode at least two interacting proteins comprising the steps of:

a) combining;

(i) a first vector comprising;

(1) a nucleic acid sequence that encodes a first protein that interacts with a second protein; and

(2) a first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(ii) a second vector comprising;

(1) a nucleic acid sequence that encodes the second protein; and

(2) a second restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

thereby producing a combination;

b) maintaining the combination under conditions in which the first protein and the second protein are expressed and interact;

c) joining the first vector with the second vector, thereby forming a contiguous nucleic acid sequence that comprises;

(i) the nucleic acid sequence that encodes a first protein that interacts with a second protein;

(ii) the first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

(iii) the nucleic acid sequence that encodes the second protein; and

(iv) the second restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

d) sequencing the contiguous nucleic acid sequence;

thereby identifying nucleic acid sequences that encode at least two interacting proteins.

55. The method of claim 53, wherein the method, after step d) and before step e), further comprises the step of:

d′

) joining the 5′

end tag to the 3′

end tag, thereby producing a paired tag.

56. The method of claim 55, wherein the method identifies a plurality of nucleic acid sequences that encode at least two interacting proteins, the method comprising a plurality of first vectors and a plurality of second vectors, wherein the method further comprises the step of:

d″

) joining the paired tags.

57. A method for identifying nucleic acid sequences that encode at least two interacting proteins comprising the steps of:

a) combining;

(i) a first vector comprising;

(1) a nucleic acid sequence that encodes a first protein that interacts with a second protein;

(2) a first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(3) a second restriction endonuclease recognition site; and

(ii) a second vector comprising;

(1) a nucleic acid sequence that encodes the second protein;

(2) a third restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(3) a fourth restriction endonuclease recognition site;

thereby producing a combination;

b) maintaining the combination under conditions in which the first protein and the second protein are expressed and interact;

c) joining the first vector with the second vector, thereby forming a contiguous nucleic acid sequence that comprises;

(i) the nucleic acid sequence that encodes a first protein that interacts with a second protein;

(ii) the first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

(iii) the second restriction endonuclease recognition site;

(iv) the nucleic acid sequence that encodes the second protein;

(v) the third restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(vi) the fourth restriction endonuclease recognition site;

d) cleaving the second restriction endonuclease recognition site and the fourth restriction endonuclease recognition site in the contiguous nucleic acid sequence with restriction endonucleases thereby producing compatible ends in the contiguous nucleic acid sequence;

e) maintaining the contiguous nucleic acid sequence under conditions in which the compatible ends in the contiguous nucleic acid sequence intramolecularly ligate, thereby producing a circularized nucleic acid sequence; and

f) sequencing the circularized nucleic acid sequence;

thereby identifying nucleic acid sequences that encode at least two interacting proteins.

58. A method for identifying nucleic acid sequences that encode at least two interacting proteins comprising the steps of:

a) combining;

(i) a first vector comprising;

(1) a nucleic acid sequence that encodes a first protein that interacts with a second protein;

(2) a first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(3) a second restriction endonuclease recognition site; and

(ii) a second vector comprising;

(1) a nucleic acid sequence that encodes the second protein;

(2) a third restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site; and

(3) a fourth restriction endonuclease recognition site;

thereby producing a combination;

b) maintaining the combination under conditions in which the first protein and the second protein are expressed and interact;

c) joining the first vector with the second vector, thereby forming a contiguous nucleic acid sequence that comprises;

(i) the nucleic acid sequence that encodes a first protein that interacts with a second protein;

(ii) the first restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

(iii) the second restriction endonuclease recognition site;

(iv) the nucleic acid sequence that encodes the second protein; and

(v) the third restriction endonuclease recognition site specific for a restriction endonuclease that cleaves the nucleic acid sequence fragment distally to the restriction endonuclease recognition site;

(vi) a fourth restriction endonuclease recognition site;

d) cleaving the second restriction endonuclease recognition site and the fourth restriction endonuclease recognition site in the contiguous nucleic acid sequence with restriction endonucleases, thereby producing compatible ends in the contiguous nucleic acid sequence;

e) maintaining the contiguous nucleic acid sequence under conditions in which the compatible ends in the contiguous nucleic acid sequence intramolecularly ligate, thereby producing a circularized nucleic acid sequence;

f) cleaving the first restriction endonuclease recognition site and the third restriction endonuclease recognition site in the circularized nucleic acid sequence with restriction endonucleases that cleave the circularized nucleic acid sequence distally to the restriction endonuclease recognition sites, thereby producing a paired tag comprising a 5′

end tag and a 3′

end tag of the circularized nucleic acid sequence; and

g) sequencing the paired tag;

thereby identifying nucleic acid sequences that encode at least two interacting proteins.

59. The method of claim 58, wherein the method identifies a plurality of nucleic acid sequences that encode at least two interacting proteins, wherein the method comprises a plurality of first vectors and a plurality of second vectors and wherein the method further comprises the steps of:

f′

) joining the paired tags; and

f″

) sequencing the joined paired tags;

thereby identifying a plurality of nucleic acid sequences that encode at least two interacting proteins.

60. The method of claim 54, wherein the joining step is site-specific intermolecular recombination.

61-62. -62. (canceled)

63. The method of claim 57, wherein cleaving the second restriction endonuclease recognition site and cleaving the fourth restriction endonuclease recognition site in the contiguous nucleic acid sequence releases a fragment containing a recombined site-specific recombinase recognition site between the nucleic acid sequence that encodes a sequence from the first protein and a sequence from the second protein that interact with each other.

64-69. -69. (canceled)

70. The method of claim 1, wherein step (a) is performed by emulsion ligation.

71. The method of claim 17, wherein step (a) is performed by emulsion ligation.

72. The method of claim 18, wherein step (b) is performed by emulsion ligation.

73. The method of claim 19, wherein steps (b) and (d) are performed by emulsion ligation.

74. The method of claim 20, wherein steps (b) and (d) are performed by emulsion ligation.

75. The method of claim 46, wherein step (b) is performed by emulsion ligation.

76. The method of claim 48, wherein the conditions in which the compatible ends intramolecularly ligate in step (d) are conditions suitable for emulsion ligation.

77. The method of claim 51, wherein step (e) is performed by emulsion ligation.

78. The method of claim 55, wherein step (d′

) is performed by emulsion ligation.

79. The method of claim 57, wherein the conditions in which the compatible ends in the contiguous nucleic acid sequence intramolecularly ligate in step (e) are conditions suitable for emulsion ligation.

80. The method of claim 58, wherein the conditions in which the compatible ends in the contiguous nucleic acid sequence intramolecularly ligate in step (e) are conditions suitable for emulsion ligation.

81. The method of claim 59, where step (f′

) is performed by emulsion ligation.