Use of collections of binding sites for sample profiling and other applications

• US 20040048311A1
• Filed: 01/24/2003
• Published: 03/11/2004
• Est. Priority Date: 01/24/2002
• Status: Abandoned Application

• Current Assignee: Pointilliste, Inc.
• Original Assignee: Pointilliste, Inc.
• Inventors: Ault-Riche, Dana, Kassner, Paul D.
• Application Number:
  US10/351,891
• Publication Number:
  US 20040048311A1
• Time in Patent Office: Days
• US Class Current: 435/7.1
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/149 incorporating a coding sequence
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: G01N 2458/10 Oligonucleotides as tagging agents for labelling antibodies
• CPC Class Codes: G01N 33/54306 Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/58 involving labelled substances G01N33/53 takes precedence
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins

Abstract

Provided are the use of collections of binding proteins, called capture agents, and their cognate binding partners, called tagged protein libraries, herein for profiling samples. Methods for generating the capture agents, tagged protein libraries and samples are also provided.

Claims

1. A combination, comprising:

a) an addressable collection of binding sites, comprising;

i) a plurality of capture agents, wherein each capture agent is preselected to specifically bind to a pre-selected tag; and

ii) a plurality of tagged reagents, each comprising one of the pre-selected tags, wherein;

each locus in the collection comprises the same capture agent;

the tagged reagent comprises a molecule and a tag;

each tag is pre-selected to specifically bind to a capture agent;

each tag is bound to a capture agent thereby forming a complex of the tagged reagent with the capture agent;

each locus comprises a plurality of tagged reagents; and

each of the different molecules at each locus comprises the same pre-selected tag; and

b) one or more of software comprising instructions for pattern recognition and an imager for detecting patterns.

2. The combination of claim 1 that is packaged as a kit that optionally includes instructions for profiling.

3. The combination of claim 1, wherein the capture agents and/or tags are polypeptides.

4. The combination of claim 3, wherein the polypeptides are antibodies or fragments thereof.

5. The combination of claim 4, wherein the tagged reagents comprises scFvs.

6. The combination of claim 1, wherein the tagged reagents comprise scFvs.

7. The combination of claim 1, wherein the capture agent is selected from the group consisting of capture agents that comprise a polypeptide, a nucleic acid, a carbohydrate, a lipid, a polysaccharide, a metal, an antibody, a cell membrane receptor, antiserum reactive with specific antigenic determinants, a lectin, a sugar, a polysaccharides, a cell, a cellular membranes and an organelle.

8. The combination of claim 1, wherein the tagged reagent is selected from the group consisting of tagged reagents that comprise a polypeptide, a nucleic acid, a carbohydrate, a lipid, a polysaccharide, a metal, an antibody, a cell membrane receptor, antiserum reactive with specific antigenic determinants, a lectin, a sugar, a polysaccharides, a cell, a cellular membrane and an organelle.

9. The combination of claim 1, wherein the capture agents are antibodies, and the pre-selected tags comprise polypeptides to which the capture agents bind.

10. The combination of claim 1, wherein the capture agents are arranged in an array.

11. The combination of claim 1, wherein the capture agents are linked directly or indirectly to a solid support.

12. The combination of claim 1, wherein a tagged reagent and capture agent in the collection are covalently linked.

13. The combination of claim 11, wherein the support is particulate.

14. The combination of claim 13, wherein the particles are optically encoded.

15. The combination of claim 1, wherein the capture agents are addressably tagged by linking them to electronic, chemical, optical or color-coded labels.

16. The combination of claim 10, wherein the array is addressable.

17. The combination of claim 1, wherein the tag is encoded by a nucleic acid molecule that comprises two domains:

the first domain encodes a sequence of amino acids that specifically binds to a capture agent; and

the second domain comprises a sequence of nucleic acids for amplification of genes containing the sequence of amino acids encoded by the first domain.

18. The combination of claim 1, wherein

each of the tags is encoded by oligonucleotides that comprises at least two regions, wherein the regions are a divider region that contains a sequence of nucleotides that comprise a sequence unique to a target library, and an polypeptide-encoding region (E) that encodes a sequence of amino acids to which a capture agent binds.

19. The combination of claim 18, wherein the divider region is 3′

of the polypeptide-encoding region.

20. The combination of claim 18, wherein the divider and E regions comprise at least about 10 nucleotides.

21. The combination of claim 20, wherein the divider and E regions comprise at least about 15 nucleotides.

22. The combination of claim 18, wherein each of the oligonucleotides further comprises a common region, wherein the common region is shared by each of the oligonucleotides in the set, and is of a sufficient length to serve as a unique priming site for amplifying nucleic acid molecules that comprise the sequence of nucleotides that comprises the common region.

23. The combination of claim 22, wherein the common region is 3′

of the polypeptide-encoding region (E) and/or of the divider region.

24. The combination of claim 1, wherein the capture agents are immobilized at discrete loci on a solid support, wherein the capture agents at each loci specifically bind to one of the preselected tagged reagents.

25. The combination of claim 24, wherein the capture agents are antibodies;

and the preselected tagged reagents comprise an polypeptide or plurality thereof to which the antibodies bind.

26. The combination of claim 1 that comprises from 3 up to 10⁶ capture agents that specifically bind to different tags.

27. The combination of claim 22, wherein the length of each of the divider, E region and common regions is at least about 14 nucleotides.

28. The combination of claim 18, wherein the length of each of the divider and E regions is independently at least about 14 nucleotides.

29. The combination of claim 28, wherein the length of each of the divider and E regions is independently at least about 16 nucleotides.

30. The combination of claim 1, wherein the tagged reagents comprise a tagged library, produced by a method comprising:

incorporating each one of a set of oligonucleotides into a nucleic acid molecule in a library of nucleic acid molecules to create a tagged library, wherein the set of oligonucleotides has the formula;

5′

-D_n-E_m-3′

wherein;

each D is a unique sequence among the set of oligonucleotides and contains at least about 10 nucleotides;

each E encodes an a sequence of amino acids that comprises a polypeptide that specifically binds to a capture agent in the collection;

each polypeptide that specifically binds is unique in the set;

each polypeptide comprises a sequence of amino acids to which a capture agent binds;

n is 0 or is an integer of 2 or higher;

m is an integer of 2 or higher; and

the oligonucleotides are single-stranded, double-stranded, and/or partially double-stranded.

31. The combination of claim 30, wherein m×

n is between about 10 to about 10¹², inclusive.

32. The combination of claim 30, wherein m×

n is between about 10 to about 10⁹, inclusive.

33. The combination of claim 30, wherein m×

n is from about 10 up to about 10⁶, inclusive.

34. The combination of claim 30, wherein the library of nucleic acid molecules encodes a library comprising scFvs or T cell receptors.

37. A system for profiling samples, comprising:

a) a combination of claim 1;

and

b) a computer system programmed with the software for pattern recognition.

38. The system of claim 37 that comprises an imager for detecting and/or digitizing the patterns.

35. The combination of 30, wherein each oligonucleotide further comprises a common region C, and comprises formula:

5′

C-D_n-E_m3′

,

wherein the common region is shared by each of the oligonucleotides in the set, and is of a sufficient length to serve as a unique priming site for amplifying nucleic acid molecules that comprise the sequence of nucleotides that comprises the common region.

36. The combination of claim 35, wherein the library of nucleic acid molecules encodes a library comprising scFvs or T cell receptors.

39. A method for profiling a sample, comprising:

a) providing an addressable collection comprising a plurality binding sites, wherein the collection comprises;

i) a plurality of capture agents, wherein each capture agent is preselected to specifically bind to a pre-selected tag; and

ii) a plurality of tagged reagents, each comprising one of the pre-selected tags, wherein;

each locus in the collection comprises the same capture agent;

the tagged reagent comprises a molecule and a tag;

each tag is a moiety pre-selected to specifically bind to a capture agent;

each tag is bound to a capture agent thereby forming a complex of the molecule with a capture agent;

each locus comprises a plurality of different molecules;

each of the different molecules at each locus comprises the same pre-selected tag;

b) contacting the collection with a sample under conditions whereby components of the sample specifically bind to binding sites of the collection; and

c) detecting binding of the components, wherein loci to which the components bind provides a profile of the sample.

40. The method of claim 39, wherein the collection of addressable binding sites is produced by mixing capture agents and tagged reagents, where the each tagged reagent is specific for only one capture agent.

41. The method of claim 39, wherein the collection of addressable binding sites is produced by mixing capture agents and tagged reagents, and steps a) and b) are performed simultaneously so that sample is added with the tagged reagents to a collection of capture agents, whereby the collection of addressable binding sites with bound sample components is produced.

42. The method of claim 39, further comprising detecting or identifying the pattern of loci to which components of the sample bind.

43. The method of claim 42, wherein the pattern is produced by comparing the results from the test sample to a control.

44. The method of claim 39, wherein the profile is stored in a database.

45. A computer system or computer readable medium, comprising the database produced by the method of claim 44.

46. The method of claim 39, wherein the tag is encoded by a nucleic acid molecule that comprises two domains:

the first domain encodes a sequence of amino acids that specifically binds to a capture agent; and

the second domain comprises a sequence of nucleic acids for specific amplification of genes containing the sequence of amino acids encoded by the first domain.

47. The method of claim 39, wherein

each of the tags is encoded by oligonucleotides that comprises at least two regions, wherein the regions are a divider region that contains a sequence of nucleotides that comprise a sequence unique to a target library, and an polypeptide-encoding region (E) that encodes a sequence of amino acids to which a capture agent binds.

48. The method of claim 47, wherein the divider region is 3′

of the polypeptide-encoding region (E).

49. The method of claim 47, wherein the divider and polypeptide (E) regions comprise at least about 10 nucleotides.

50. The method of claim 49, wherein the divider and polypeptide (E) regions comprise at least about 15 nucleotides.

51. The method of claim 47, wherein each of the oligonucleotides further comprises a common region, wherein the common region is shared by each of the oligonucleotides in the set, and is of a sufficient length to serve as a unique priming site for amplifying nucleic acid molecules that comprise the sequence of nucleotides that comprises the common region.

52. The method of claim 51, wherein the common region is 3′

of the polypeptide (E)-encoding region and/or of the divider region.

53. The method of claim 39, wherein the capture agents are immobilized at discrete loci on a solid support, wherein the capture agents at each loci specifically bind to one of the preselected tagged reagents.

54. The method of claim 53, wherein the capture agents are antibodies;

and the pre-selected tags comprise a polypeptide or plurality thereof to which the antibodies bind.

55. The method of claim 54, wherein the tagged reagents further comprise scFvs or T cell receptors.

56. The method of claim 39, wherein the collection in the combination comprises from 3 up to 10⁶ capture agents that specifically bind to different tags.

57. The method of claim 47, wherein the length of each of the divider, polypeptide (E) and common regions is at least about 14 nucleotides.

58. The method of claim 48, wherein the length of each of the divider, polypeptide (E) and common regions is at least about 14 nucleotides.

59. The method of claim 39, wherein the capture agents are antibodies;

and the pre-selected tags comprise polypeptide (E)s to which the capture agents bind.

60. The method of claim 54, wherein the collection comprises up to about 10³ antibodies.

61. The method of claim 59, wherein the collection comprises up to about 10³ antibodies.

62. The method of claim 47, wherein the length of each of the divider and polypeptide (E) regions is independently at least about 14 nucleotides.

63. The method of claim 48, wherein the length of each of the divider and polypeptide (E) regions is independently at least about 14 nucleotides.

64. The method of claim 47, wherein the length of each of the divider and polypeptide (E) regions is independently at least about 16 nucleotides.

65. The method of claim 39, wherein the tagged reagents comprise a tagged library, produced by a method comprising:

incorporating each one of a set of oligonucleotides into a nucleic acid molecule in a library of nucleic acid molecules to create a tagged library, wherein the set of oligonucleotides has the formula;

5′

-D_n-E_m-3′

wherein;

each D is a unique sequence among the set of oligonucleotides and contains at least about 10 nucleotides;

each E encodes an a sequence of amino acids that comprises a polypeptide that specifically binds to a capture agent in the collection;

each polyeptide that specifically binds to a capture agent is unique in the set;

each polyeptide that specifically binds to a capture agents comprises a sequence of amino acids to which a capture agent binds;

n is 0 or is an integer of 2 or higher;

m is an integer of 2 or higher; and

the oligonucleotides are single-stranded, double-stranded, and/or partially double-stranded.

66. The method of claim 65, wherein the library of nucleic acid molecules encodes a library comprising scFvs or T cell receptors.

67. The method of claim 65, wherein m×

n is between about 10 to about 10¹², inclusive.

68. The method of claim 65, wherein m×

n is between about 10 to about 10⁹, inclusive.

69. The method of claim 65, wherein m×

n is from about 10 up to about 10⁶, inclusive.

70. The method of claim 65, wherein each oligonucleotide further comprises a common region C, and comprises formula:

5′

C-D_n-E_m3′

,

wherein the common region is shared by each of the oligonucleotides in the set, and is of a sufficient length to serve as a unique priming site for amplifying nucleic acid molecules that comprise the sequence of nucleotides that comprises the common region.

71. The method of claim 70, wherein the library of nucleic acid molecules encodes a library comprising scFvs or T cell receptors.

72. The method of claim 39, wherein the capture agents and/or tags are polypeptides.

73. The method of claim 72, wherein the polypeptides comprise antibodies or fragments thereof.

74. The method of claim 73, wherein the tagged reagents comprise scFvs or T cell receptors.

75. The method of claim 39, wherein the tagged reagents comprise scFvs.

76. The method of claim 39, wherein the capture agent is selected from the group consisting of a agents that comprise a polypeptide, a nucleic acid, a carbohydrate, a lipid, a polysaccharide, a metal, an antibody, a cell membrane receptor, antiserum reactive with specific antigenic determinants, a lectin, a sugar, a polysaccharides, a cell, a cellular membranes and an organelle.

77. The method of claim 39, wherein the tag is selected from the group consisting of a polyeptide tags that comprise a polypeptide to which a capture agent binds, a nucleic acid, a carbohydrate, a lipid, a polysaccharide, a metal, an antibody, a cell membrane receptor, antiserum reactive with specific antigenic determinants, a lectin, a sugar, a polysaccharides, a cell, a cellular membranes and an organelle.

78. The method of claim 39, wherein the capture agents are arranged in an array.

79. The method of claim 39, wherein the capture agents are linked directly or indirectly to a solid support.

80. The method of claim 39, wherein a tagged reagent and capture agent in the collection are covalently linked.

81. The method of claim 79, wherein the support is particulate.

82. The method of claim 81, wherein the particles are optically encoded.

83. The method of claim 78, wherein the array is addressable.

84. A method for preparing a capture system that displays a collection of binding sites, comprising:

a) providing an addressable collection of a plurality of capture agents, wherein each capture agent is pre-selected to specifically bind to a pre-selected tag, wherein;

each locus in the collection comprises the same capture agent;

b) providing a plurality of tagged reagents, each comprising one of the pre-selected tags, wherein;

each tagged reagent comprises a molecule and a tag; and

each tag is a moiety pre-selected to specifically bind to a capture agent;

c) contacting the plurality of tagged reagents to the addressable collection of the plurality of capture agents to form a capture system that displays a diverse collection of binding sites, wherein;

each tag is bound to a capture agent thereby forming a complex of the molecule with the capture agent;

each locus comprises a plurality of different molecules; and

each of the different molecules at each locus comprises the same pre-selected tag, thereby preparing a capture system that displays a diverse collection of binding sites.

85. The method of claim 84, wherein the diversity of the binding sites is selected from the group consisting of 10², 10³, 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹ and 10¹².

86. The method of claim 84, wherein the capture agents are antibodies, and the pre-selected tags comprise polyepeptides to which the capture agents bind.

87. The method of claim 86, wherein the tagged reagent comprises a polypeptide.

88. The method of claim 87, wherein the polypeptide comprises a scFv.

89. The method of claim 87, wherein the polypeptide comprises a T cell receptor (TCR) or fragment thereof.

90. The method of claim 84, wherein the addressable collection is positionally addressable;

and

each locus comprises a spot on a solid support.

91. The method of claim 90, wherein the solid support comprises a well or pit or plurality thereof on the surface.

92. The method of claim 90, wherein the solid support is selected from the group consisting of plates, beads, microbeads, whiskers, combs, hybridization chips, membranes, single crystals, ceramics and self-assembling monolayers.

93. The method of claim 90, wherein the solid support is selected from the group consisting of silicon, celluloses, metal, polymeric surfaces and radiation grafted supports.

94. The method of claim 93, wherein the solid support is selected from the group consisting of gold, nitrocellulose, polyvinyidiene fluoride (PVDF), radiation grafted polytetrafluoroethylene, polystyrene, glass and activated glass.

95. The method of claim 84, wherein the addressable collection of capture agents are addressably tagged by linking them to electronic, chemical, optical or color-coded labels.

96. The method of claim 84, wherein the tag is encoded by a nucleic acid molecule that comprises two domains:

the first domain encodes a sequence of amino acids that specifically binds to a capture agent; and

the second domain comprises a sequence of nucleic acids for specific amplification of genes containing the sequence of amino acids encoded by the first domain.

97. The method of claim 84, wherein

each of the tags is encoded by oligonucleotides that comprises at least two regions, wherein the regions are a divider region that contains a sequence of nucleotides that comprise a sequence unique to a target library, and a polypeptide-encoding region that encodes a sequence of amino acids to which a capture agent binds.

98. The method of claim 84, wherein each of the oligonucleotides further comprises a common region, wherein the common region is shared by each of the oligonucleotides in the set, and is of a sufficient length to serve as a unique priming site for amplifying nucleic acid molecules that comprise the sequence of nucleotides that comprises the common region.

99. The method of claim 84, wherein the tagged reagents comprise a tagged library, produced by a method comprising:

incorporating each one of a set of oligonucleotides into a nucleic acid molecule in a library of nucleic acid molecules to create a tagged library, wherein the set of oligonucleotides has the formula;

5′

-D_n-E_m-3′

wherein;

each D is a unique sequence among the set of oligonucleotides and contains at least about 10 nucleotides;

each E encodes an a sequence of amino acids that comprises an polypeptide that specifically binds to a capture agent in the collection;

each epitope is unique in the set;

each epitope is a sequence to which a capture agent binds;

n is 0 or is an integer of 2 or higher;

m is an integer of 2 or higher; and

the oligonucleotides are single-stranded, double-stranded, and/or partially double-stranded.

100. The method of claim 99, wherein the library of nucleic acid molecules encodes a library comprising scFvs or T cell receptors.

101. The method of claim 99, wherein m×

n is between about 10 to about 10¹², inclusive.

102. The method of claim 99, wherein m×

n is between about 10 to about 10⁹, inclusive.

103. The method of claim 99, wherein m×

n is from about 10 up to about 10⁶, inclusive.

104. The method of claim 99, wherein each oligonucleotide further comprises a common region C, and comprises formula:

5′

C-D_n-E_m3′

,

wherein the common region is shared by each of the oligonucleotides in the set, and is of a sufficient length to serve as a unique priming site for amplifying nucleic acid molecules that comprise the sequence of nucleotides that comprises the common region.

105. The method of claim 104, wherein the library of nucleic acid molecules encodes a library comprising scFvs or T cell receptors.

106. A positionally addressable collection of binding sites, comprising:

a) a plurality of capture agents bound to a solid support, wherein;

each capture agent is preselected to specifically bind to a pre-selected tag; and

each locus that comprises the capture agents is within 1 mm or less from a neighboring locus; and

b) a plurality of tagged reagents, each comprising one of the pre-selected tags, wherein;

each locus in the collection comprises the same capture agent;

the capture agents at each locus are different;

the tagged reagent comprises a molecule and a tag;

each tag is re-selected to specifically bind to a capture agent;

each tag is bound to a capture agent thereby forming a complex of the tagged reagent with the capture agent;

each locus comprises a plurality of tagged reagents; and

each of the different molecules at each locus comprises the same pre-selected tag.

107. The method of claim 106, wherein the molecules in the tagged reagents are selected from the group consisting of a polypeptide, a nucleic acid, a carbohydrate, a lipid, a polysaccharide, a metal, an antibody, a cell membrane receptor, antiserum reactive with specific antigenic determinants, a lectin, a sugar, a polysaccharides, a cell, a cellular membranes and an organelle.

108. The method of claim 106, wherein the molecules are antibodies or binding fragments thereof.

109. The method of claim 106, wherein the molecules are scFvs.

110. The method of claim 106, wherein the diversity of the molecules is 10¹² or higher.

111. The method of claim 106, wherein the diversity of the molecules is 10¹³ or higher.

112. The method of claim 106, wherein the diversity of the molecules is 10¹⁴ or higher.

113. The method of claim 106, wherein the diversity of the molecules is 10¹⁵ or higher.

114. The method of claim 106, wherein the capture agents are antibodies or fragments thereof;

and the tags comprise sequences of amino acids to which the antibodies bind.

115. The method of claim 109, wherein the capture agents are antibodies or fragments thereof;

and the tags comprise sequences of amino acids to which the antibodies bind.

116. A method for screening samples, comprising:

a) providing the collection of binding sites of claim 106;

b) contacting the collection of binding sites with a sample under conditions whereby components of the sample specifically bind to binding sites of the collection;

c) removing components of the sample which are not bound to the collection of binding sites; and

d) identifying components that are bound to the collection of binding sites.

117. The method of claim 116, wherein steps a) through d) are repeated one or a plurality of times with a sub-set of tagged molecules identified from step d) until diversity of tagged reagents is reduced to a predetermined number.

118. The method of claim 116, wherein the sample is selected from the group consisting of cell lystates, cells, blood, plasma, serum, cerebrospinal fluid, synovial fluid, urine, sweat, tissues, organs, soil, water, viruses, bacteria, fungi algae, protozoa and components thereof.

119. The method of claim 116, wherein capture agents are antibodies;

and the pre-selected tagged reagents comprise a polypeptide or plurality thereof to which the antibodies bind.

120. The method of claim 116 that comprises from 3 up to 10⁶ capture agents that specifically bind to different tags.

121. The method of claim 106, wherein the tagged reagents comprise scFvs.

122. The method of claim 106, wherein the tagged reagents comprise T cell receptors.

124. The method of claim 117, wherein the predetermined number is about 1 or about 5, or about 10 or about 100, or about 500 or about 1000.

125. The method of claim 115, wherein the identified components are candidate therapeutic compounds, are diagnostic or prognostic of a disease or condition or a target for a therapeutic.

123. A combination, comprising:

a) an addressable collection of binding sites, comprising;

i) a plurality of capture agents, wherein each capture agent is preselected to specifically bind to a pre-selected tag; and

ii) a plurality of tagged reagents, each comprising one of the pre-selected tags, wherein;

each locus in the collection comprises the same capture agent;

the tagged reagent comprises a biological particle and a tag;

each tag is pre-selected to specifically bind to a capture agent;

each tag is bound to a capture agent thereby forming a complex of the tagged reagent with the capture agent;

each locus comprises a plurality of tagged reagents; and

each of the different molecules at each locus comprises the same pre-selected tag; and

b) one or more of software comprising instructions for pattern recognition and an imager for detecting patterns.