Method and means for sorting and identifying biological information

• US 5,866,363 A
• Filed: 02/28/1991
• Issued: 02/02/1999
• Est. Priority Date: 08/28/1985
• Status: Expired due to Term

• Current Assignee: George Pieczenik
• Original Assignee: I. C. Technologies America, Inc.
• Inventors: Pieczenik, George
• Primary Examiner(s): Elliott, George C.
• Assistant Examiner(s): Brusca, John S.
• Application Number:
  US07/662,764
• Time in Patent Office: 2,896 Days
• Field of Search: 435/91, 435/69.1, 435/69.6, 435/172.3, 435/320.1, 435/69.3, 536/23.1, 935/8, 935/12, 935/81, 530/327, 530/328, 530/329, 530/330, 530/387.9
• US Class Current: 435/69.1
• CPC Class Codes: A61K 38/17 from animals; from humans enzyme inhibitors A61K38/005
• CPC Class Codes: C07K 16/00 Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies antibodies with enzymatic activity, e.g. abzymes C12N9/0002
• CPC Class Codes: C07K 16/005 constructed by phage libraries
• CPC Class Codes: C07K 16/18 against material from animals or humans
• CPC Class Codes: C12N 15/11 DNA or RNA fragments; Modified forms thereof DNA or RNA not used in recombinant technology, C07H21/00; Non-coding nucleic acids having a biological activity
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: G01N 33/53 Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/6878 in eptitope analysis

Abstract

In one aspect the invention discloses a matrix comprising a discrete population of random oligopeptides of the same length, the length being selected from about 4 to about 12 L-amino acid residues, the population comprising at least 10% of all amino acid sequences of the selected length; and a heterogeneous population of antibodies comprising antibodies capable of binding to substantially every member of the oligopeptide population.

Claims

1. A population of recombinant vectors comprising:

autonomously replicating nucleic acid sequences which nucleic acid sequences comprise a recombinant structural gene, each of the structural genes comprising an insert containing one member of an oligonucleotide population,

said oligonucleotide population comprising oligonucleotides comprising a coding region consisting of a length from about 4 to about 12 nucleotide triplets, said oligonucleotide population encoding a plurality of corresponding random peptide sequences of from about 4 to about 12 L-amino acid residues, and

wherein said recombinant structural genes are expressed upon transfer of said recombinant vectors into Escherichia coli host cells, and wherein expression of the recombinant structural genes yields polypeptides, each polypeptide comprising one of said plurality of corresponding random peptide sequences.

2. The vector population of claim 1 wherein each oligonucleotide has a coding region having a length of from 4 to 7 nucleic acid triplets.

3. The vector population of claim 1 wherein the replicating sequence is a plasmid.

4. The vector population of claim 3 wherein the plasmid is pBR322.

5. The vector population of claim 3 wherein the plasmid is pUC8.

6. The vector population of claim 1 wherein the replicating sequence is viral.

7. The vector population of claim 6, wherein the viral replicating sequence is lambda-gt 11.

8. The vector population of claim 1 wherein each of the encoded corresponding peptides forms a binding pair with an antibody that has not been elicited by immunization with said peptide or said peptide in conjugated form, said antibody being selected from the group consisting of all antibodies produced by lymphoid-derived antibody-producing cells, where the group of all antibodies together recognizes substantially all epitopic sequences.

9. The recombinant vector population of claim 1, wherein each of said members of said oligonucleotide population has a length of from about 4 to 7 nucleotide triplets and the encoded corresponding peptide sequences have a length of from 4 to 7 L-amino acid residues.

25. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 5 nucleotide triplets and the encoded corresponding peptide sequences have a length of 5 L-amino acid residues.

26. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 4 nucleotide triplets and the encoded corresponding peptide sequence has a length of 4 amino acid residues.

27. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 6 nucleotide triplets and the encoded corresponding peptide sequence has a length of 6 amino acid residues.

28. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 7 nucleotide triplets and the encoded corresponding peptide sequence has a length of 7 amino acid residues.

29. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 8 nucleotide triplets and the encoded corresponding peptide sequence has a length of 8 amino acid residues.

30. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 9 nucleotide triplets and the encoded corresponding peptide sequence has a length of 9 amino acid residues.

31. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 10 nucleotide triplets and the encoded corresponding peptide sequence has a length of 10 amino acid residues.

32. The recombinant vector population of claim 1 or 24, wherein each of said members of said oligonucleotide population has a coding region having a length of 11 nucleotide triplets and the encoded corresponding peptide sequence has a length of 11 amino acid residues.

33. The recombinant vector population of claim 1, wherein each of said members of said oligonucleotide population has a coding region having a length of 12 nucleotide triplets and the encoded corresponding peptide sequence has a length of 12 amino acid residues.

10. A population of oligonucleotides comprising double-stranded oligonucleotides comprising coding regions consisting of a length of from about 4 to about 12 nucleotide triplets, said coding regions encoding a plurality of peptide sequences of from about 4 to about 12 L-amino acid residues, said oligonucleotides also comprising 5'"'"' and 3'"'"' flanking sequences that permit said oligonucleotides to be ligated into a vector,

and wherein the sum of said peptide sequences represents at least about 10% of all possible peptide sequences of said length.

11. The oligonucleotide population of claim 10 wherein the length of the coding region of each oligonucleotide is from 4 to 7 nucleotide triplets.

12. The oligonucleotide population of claim 11 wherein the population is generated by shearing of mammalian genetic material and size fractionation.

13. The oligonucleotide population of claim 11 wherein the population is chemically synthesized from component nucleotides.

14. The oligonucleotide population of claim 10 wherein each of said encoded corresponding peptide sequences forms a binding pair with an antibody that has not been selected by immunization with said peptide sequence or said peptide sequence in conjugated form, said antibody being selected from the group consisting of all antibodies produced by lymphoid-derived antibody-producing cells, where the group contains antibodies that bind substantially all members of the discrete oligopeptide population encoded by said oligonucleotide population.

15. The oligonucleotide population of claim 10, wherein the length of the coding region is 4 nucleotide triplets.

16. The oligonucleotide population of claim 10, wherein the length of the coding region is 6 nucleotide triplets.

17. The oligonucleotide population of claim 10, wherein the length of the coding region is 7 nucleotide triplets.

18. The oligonucleotide population of claim 10, wherein the length of the coding region is 8 nucleotide triplets.

19. The oligonucleotide population of claim 10, wherein the length of the coding region is 9 nucleotide triplets.

20. The oligonucleotide population of claim 10, wherein the length of the coding region is 10 nucleotide triplets.

21. The oligonucleotide population of claim 10, wherein the length of the coding region is 11 nucleotide triplets.

22. The oligonucleotide population of claim 10, wherein the length of the coding region is 12 nucleotide triplets.

53. The oligonucleotide population of claim 10 or 49, wherein the length of the coding region of each oligonucleotide is 5 nucleotide triplets.

23. A method of producing a population of epitopic peptide sequences, comprising the steps of:

providing a population of recombinant E. coli cells, each of said cells containing at least one member of a recombinant vector population, each member of said vector population comprising substantially identical autonomously replicating nucleic acid sequences, said nucleic acid sequences comprising a recombinant structural gene, each structural gene having inserted therein one member of an oligonucleotide population wherein each member of said oligonucleotide population has a coding region having a length from about 4 to about 12 nucleotide triplets that encodes a corresponding epitopic peptide sequence of from about 4 to about 12 L-amino acid residues, and wherein each member of said oligonucleotide population is contained in said recombinant vector population and wherein the sum of said corresponding epitopic peptide sequences represents substantially all possible peptide sequences of said length; and

culturing said recombinant E. coli cells to allow expression of said recombinant structural genes such that said epitopic peptide sequences are accessible to antibody recognition.

24. A population of recombinant vectors comprising:

substantially identical autonomously replicating nucleic acid sequences comprising a recombinant structural gene, each structural gene having inserted therein a member of an oligonucleotide population, wherein each member of said oligonucleotide population has a coding region having a length from about 4 to about 12 nucleotide triplets that encodes a corresponding peptide sequence of from about 4 to about 12 L-amino acid residues, and wherein the sum of corresponding peptide sequences encoded by said oligonucleotide population represents at least about 10% of all possible peptide sequences of said length,

and wherein each member of said oligonucleotide population is contained in said recombinant vector population; and

wherein the recombinant structural genes are expressed upon transfer of said recombinant vectors into Escherichia coli host cells, and wherein expression of said recombinant structural genes yields polypeptides, each polypeptide comprising said corresponding peptide sequence.

34. A method of producing a population of epitopic peptide sequences, comprising the steps of:

providing a population of recombinant E. coli cells, each of said cells containing at least one member of a recombinant vector population, each member of said vector population comprising substantially identical autonomously replicating nucleic acid sequences, said nucleic acid sequences comprising a recombinant structural gene, each structural gene having inserted therein one member of an oligonucleotide population wherein each member of said oligonucleotide population has a length from about 4 to about 12 nucleotide triplets that encodes a corresponding epitopic peptide sequence of from about 4 to about 12 L-amino acid residues, and wherein each member of said oligonucleotide population is contained in said recombinant vector population and wherein the sum of said corresponding epitopic peptide sequences represents at least about 10% of all possible peptide sequences of said length; and

culturing said recombinant E. coli cells to allow expression of said recombinant structural genes such that said epitopic peptide sequences are accessible to antibody recognition.

35. A peptide population obtained from the process of claim 34.

36. A population of peptides wherein each member of said population has a length of from about 4 to about 12 amino acid residues, and wherein said population contains at least about 10% of all possible peptide sequences of said length.

37. The peptide population of claim 36, wherein each member has a length of from 4 to 7 amino acid residues.

38. The peptide population of claim 36, wherein each member has a length of 5 amino acid residues.

39. The peptide population of claim 36, wherein each member has a length of 4 amino acid residues.

40. The peptide population of claim 36, wherein each member has a length of 6 amino acid residues.

41. The peptide population of claim 36, wherein each member has a length of 7 amino acid residues.

42. The peptide population of claim 36, wherein each member has a length of 8 amino acid residues.

43. The peptide population of claim 36, wherein each member has a length of 9 amino acid residues.

44. The peptide population of claim 36, wherein each member has a length of 10 amino acid residues.

45. The peptide population of claim 36, wherein each member has a length of 11 amino acid residues.

46. The peptide population of claim 36, wherein each member has a length of 12 amino acid residues.

47. A population of binding pairs comprising:

a population of peptides, each member of said population having a length of from about 4 to about 12 amino acid residues, wherein said population represents at least about 10 percent of all possible peptide sequences of said length, wherein substantially every member of said peptide population is bound to an antibody.

48. A matrix comprising the population of binding pairs of claim 47.

81. The population of claim 47 or 77, wherein each peptide has a length of 4 amino acid residues.

82. The population of claim 47 or 77, wherein each peptide has a length of 5 amino acid residues.

83. The population of claim 47 or 77, wherein each peptide has a length of 6 amino acid residues.

84. The population of claim 47 or 77, wherein each peptide has a length of 7 amino acid residues.

85. The population of claim 47 or 77, wherein each peptide has a length of 8 amino acid residues.

86. The population of claim 47 or 77, wherein each peptide has a length of 9 amino acid residues.

87. The population of claim 47 or 77, wherein each peptide has a length of 10 amino acid residues.

88. The population of claim 47 or 77, wherein each peptide has a length of 11 amino acid residues.

89. The population of claim 47 or 77, wherein each peptide has a length of 12 amino acid residues.

49. A population of oligonucleotides comprising double stranded oligonucleotides that comprise coding regions consisting of a length of from about 4 to about 12 nucleotide triplets said coding regions encoding a plurality of peptides consisting of random sequences of from about 4 to about 12 L-amino acid residues, said oligonucleotides comprising 5'"'"' and 3'"'"' flanking sequences that permit said oligonucleotide to be ligated into a vector.

50. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is from about 4 to 7 nucleotide triplets.

51. The oligonucleotide population of claim 50, which is generated by random shearing of mammalian genetic material and size fractionation.

52. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 4 nucleotide triplets.

54. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 6 nucleotide triplets.

55. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 7 nucleotide triplets.

56. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 8 nucleotide triplets.

57. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 9 nucleotide triplets.

58. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 10 nucleotide triplets.

59. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 11 nucleotide triplets.

60. The oligonucleotide population of claim 49, wherein the length of the coding region of each oligonucleotide is 12 nucleotide triplets.

61. The oligonucleotide population of claim 49, which is chemically synthesized from component nucleotides or codons.

62. The peptide population of claim 61, comprising a number of peptide sequences of said length having sufficient conformational similarity with an epitope of a test species such that an antibody that binds the epitope of the test species also binds a member of said peptide population.

63. The peptide population of claim 61, comprising substantially all peptide sequences of said length.

64. The oligonucleotide population of claim 49, wherein each of said corresponding peptide sequences forms a binding pair with an antibody.

65. The oligonucleotide population of claim 49, wherein a number of the encoded plurality of peptides has sufficient conformational similarity with an epitope of a test species such that an antibody that binds to the epitope of the test species also binds a peptide of the encoded plurality of peptides.

66. The oligonucleotide population of claim 49, which encodes substantially all possible peptide sequences of said length.

67. A peptide population comprising peptides consisting of random sequences of from about 4 to about 12 amino acid residues.

68. The peptide population of claim 67, wherein each member has a length of 4 amino acid residues.

69. The peptide population of claim 67, wherein each member has a length of 5 amino acid residues.

70. The peptide population of claim 67, wherein each member has a length of 6 amino acid residues.

71. The peptide population of claim 67, wherein each member has a length of 7 amino acid residues.

72. The peptide population of claim 67, wherein each member has a length of 8 amino acid residues.

73. The peptide population of claim 67, wherein each member has a length of 9 amino acid residues.

74. The peptide population of claim 67, wherein each member has a length of 10 amino acid residues.

75. The peptide population of claim 67, wherein each member has a length of 11 amino acid residues.

76. The peptide population of claim 67, wherein each member has a length of 12 amino acid residues.

77. A population of binding pairs comprising:

a peptide population comprising peptides consisting of random sequences of from about 4 to about 12 amino acid residues, wherein substantially every member of said peptide population is bound to an antibody.

78. A matrix comprising the population of binding pairs of claim 77.

79. The binding pair population of claim 77, wherein said population of peptides comprises a number of peptides of said length having sufficient conformational similarity with an epitope of a test species such that an antibody that binds to the epitope of the test species also binds a member of said peptide population.

80. The binding pair population of claim 77, wherein said population of peptides comprises substantially all peptides of said length.

90. A method of producing a population of epitopic peptide sequences, comprising:

providing a population of recombinant Escherichia coli cells, each of said cells containing at least one member of a recombinant vector population, each member of said vector population comprising autonomously replicating nucleic acid sequences, said nucleic acid sequences comprising a recombinant structural gene, each structural gene containing an insert comprising a member of an oligonucleotide population, said oligonucleotide population comprising oligonucleotides comprising a coding region consisting of a length from about 4 to about 12 nucleotide triplets, said oligonucleotide population encoding a plurality of epitopic peptides consisting of random sequences of from about 4 to about 12 L-amino acid residues; and

culturing said recombinant Escherichia coli cells to allow expression of said recombinant structural genes such that said epitopic peptide sequences are accessible to antibody recognition.

91. The method of claim 90, wherein said oligonucleotide population encodes a number of peptide sequences of said length having sufficient conformational similarity with an epitope of a test species such that an antibody that binds to the epitope of the test species also binds a peptide of the encoded plurality of peptides.

92. The method of claim 90, wherein the oligonucleotide population encodes substantially all peptides of said length.