Patent US2499421A successfully refreshed from Google Patents.
US6258530B1
Expired / Lapsed
US
⏱️ 0.0 years remaining
Surface expression libraries of randomized peptides
Assignee: Applied Molecular Evolution Inc
•
Filing: 1994-12-30
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Granted: 2001-07-10
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Expires: 2014-12-30
Abstract
Abstract A composition of matter comprising a plurality of procaryotic cells containing a diverse population of expressible oligonucleotides operationally linked to expression elements, said expressible oligonucleotides having a desirable bias of random codon sequences.
Inventors
- 👤 William D. Huse
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-23 01:45
CPC Classifications
C; C40; C40B; C40B40/00; C40B40/02; C07; C07K; C07K14/00; C07K14/005; C07K14/435; C07K14/665; C07K14/675; C12; C12N; C12N15/00; C12N15/09; C12N15/10; C12N15/1034; C12N15/1037; C12N15/63; C12N15/66; C12N15/70; C12Q; C12Q1/00; C12Q1/68; C12Q1/6811; C07K2319/00; C12N2795/00; C12N2795/00011; C12N2795/14011; C12N2795/14111; C12N2795/14122
Claims Analysis
Total Claims: 89
Claim 1
Independent Claim
138 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, which each of said oligonucleotides is operationally linked to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids produced from random combinations of first and second oligonucleotide precursor populations having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said precursor populations being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 2
Dependent Claim
138 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, which each of said oligonucleotides is operationally linked to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids produced from random combinations of first and second oligonucleotide precursor populations having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said precursor populations being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 3
Dependent Claim
30 words
The composition of claim 1 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 4
Dependent Claim
28 words
The composition of claim 1 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is biased toward that of a predetermined sequence.
Claim 5
Dependent Claim
26 words
The composition of claim 1 , wherein said first and second oligonucleotides having random codon sequences have at least one specified codon at a predetermined position.
Claim 6
Dependent Claim
12 words
The composition of claim 1 , wherein said cells are E. coli.
Claim 7
Dependent Claim
23 words
The composition of claim 1 , wherein said expressible oligonucleotides are expressed as gVIII-peptide fusion proteins on the surface of a filamentous bacteriophage.
Claim 8
Dependent Claim
157 words
A kit for the preparation of vectors useful for the expression of a diverse population of random peptides from combined first and second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said kit comprising two vectors: a first filamentous bacteriophage vector having: a cloning site for said first oligonucleotides and a pair of restriction sites for operationally combining first oligonucleotides with second oligonucleotides; and a second filamentous bacteriophage vector having a cloning site for said second oligonucleotides and a pair of restriction sites complementary to those on said first vector, one or both vectors containing expression elements and the major coat protein of a filamentous bacteriophage capable of being operationally linked to said combined first and second oligonucleotides wherein said expression elements direct the expression of said combined first and second oligonucleotides as fusion proteins with said major coat protein of said filamentous bacteriophage or as a soluble peptide.
Claim 9
Dependent Claim
157 words
A kit for the preparation of vectors useful for the expression of a diverse population of random peptides from combined first and second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said kit comprising two vectors: a first filamentous bacteriophage vector having: a cloning site for said first oligonucleotides and a pair of restriction sites for operationally combining first oligonucleotides with second oligonucleotides; and a second filamentous bacteriophage vector having a cloning site for said second oligonucleotides and a pair of restriction sites complementary to those on said first vector, one or both vectors containing expression elements and the major coat protein of a filamentous bacteriophage capable of being operationally linked to said combined first and second oligonucleotides wherein said expression elements direct the expression of said combined first and second oligonucleotides as fusion proteins with said major coat protein of said filamentous bacteriophage or as a soluble peptide.
Claim 10
Dependent Claim
30 words
The kit of claim 7 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 11
Dependent Claim
28 words
The kit of claim 7 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 12
Dependent Claim
30 words
The kit of claim 7 , wherein said first and second oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 13
Dependent Claim
15 words
The kit of claim 7 , wherein said pair of restriction sites are Fok I.
Claim 14
Dependent Claim
163 words
A cloning system for expressing random peptides from diverse populations of combined first and second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said system comprising: a set of first vectors having a diverse population of first oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences, and a set of second vectors having a diverse population of second oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences operationally linked to the major coat protein of a filamentous bacteriophage, wherein said first and second vectors each have a pair of restriction sites so as to allow the operational combination of first and second oligonucleotides into a contiguous oligonucleotide having a desirable bias of random codon sequences and wherein said vectors are filamentous bacteriophage vectors which direct the expression of said contiguous oligonucleotides as a fusion protein with said major coat protein or as a soluble peptide.
Claim 15
Dependent Claim
163 words
A cloning system for expressing random peptides from diverse populations of combined first and second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said system comprising: a set of first vectors having a diverse population of first oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences, and a set of second vectors having a diverse population of second oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences operationally linked to the major coat protein of a filamentous bacteriophage, wherein said first and second vectors each have a pair of restriction sites so as to allow the operational combination of first and second oligonucleotides into a contiguous oligonucleotide having a desirable bias of random codon sequences and wherein said vectors are filamentous bacteriophage vectors which direct the expression of said contiguous oligonucleotides as a fusion protein with said major coat protein or as a soluble peptide.
Claim 16
Dependent Claim
31 words
The cloning system of claim 12 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 17
Dependent Claim
29 words
The cloning system of claim 12 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 18
Dependent Claim
31 words
The cloning system of claim 12 , wherein said first and second oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 19
Dependent Claim
21 words
The cloning system of claim 12 , wherein said first and second vectors are combined through a pair of restriction sites.
Claim 20
Dependent Claim
16 words
The cloning system of claim 12 , wherein said pair of restriction sites are Fok I.
Claim 21
Dependent Claim
113 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, wherein each of said oligonucleotides is operationally linked to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 22
Dependent Claim
113 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, wherein each of said oligonucleotides is operationally linked to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 23
Dependent Claim
23 words
The composition of claim 18 , wherein said expressible oligonucleotides are expressed as gVIII-peptide fusion proteins on the surface of said filamentous bacteriophage.
Claim 24
Dependent Claim
41 words
The composition of claim 18 , wherein said diverse population of oligonucleotides having a desirable bias of random codon sequences are produced from the combination of diverse populations of first and second oligonucleotides having a desirable bias of random codon sequences.
Claim 25
Dependent Claim
27 words
The composition of claim 18 , wherein the desirable bias of random codon sequences of said oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 26
Dependent Claim
25 words
The composition of claim 18 , wherein the desirable bias of random codon sequences of said oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 27
Dependent Claim
27 words
The composition of claim 18 , wherein said oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 28
Dependent Claim
82 words
A plurality of filamentous bacteriophage vectors containing a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers and being operationally linked to (i) expression elements, (ii) a suppressible stop codon and (iii) the major coat protein of a filamentous bacteriophage which are expressible as fusion proteins with said major coat protein in a suppressor host or as soluble peptides in a non-suppressor host.
Claim 29
Dependent Claim
82 words
A plurality of filamentous bacteriophage vectors containing a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers and being operationally linked to (i) expression elements, (ii) a suppressible stop codon and (iii) the major coat protein of a filamentous bacteriophage which are expressible as fusion proteins with said major coat protein in a suppressor host or as soluble peptides in a non-suppressor host.
Claim 30
Dependent Claim
22 words
The vectors of claim 24 , wherein said oligonucleotides are expressible as gVIII-peptide fusion proteins on the surface of said filamentous bacteriophage.
Claim 31
Dependent Claim
27 words
The vectors of claim 24 , wherein the desirable bias of random codon sequences of said oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 32
Dependent Claim
25 words
The vectors of claim 24 , wherein the desirable bias of random codon sequences of said oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 33
Dependent Claim
27 words
The vectors of claim 24 , wherein said oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 34
Dependent Claim
42 words
A composition of matter, comprising a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids produced from random combinations of two or more oligonucleotide precursor populations having a desirable bias of random codon sequences.
Claim 35
Dependent Claim
42 words
A composition of matter, comprising a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids produced from random combinations of two or more oligonucleotide precursor populations having a desirable bias of random codon sequences.
Claim 36
Independent Claim
198 words
A method of constructing a diverse population of filamentous bacteriophage vectors having combined first and second oligonucleotides encoding a desirable bias of amino acids, said oligonucleotides being synthesized from nucleotide monomers and having a desirable bias of random codon sequences capable of expressing said combined oligonucleotides as random peptides fused to the major coat protein of a filamentous bacteriophage or as soluble peptides, comprising the steps of: (a) operationally linking sequences from a diverse population of first oligonucleotides having a desirable bias of random codon sequences encoding said desirable bias of amino acids to expression elements within a first filamentous bacteriophage vector; (b) operationally linking sequences from a diverse population of second oligonucleotides having a desirable bias of random codon sequences encoding said desirable bias of amino acids to said major coat protein of said filamentous bacteriophage within a second filamentous bacteriophage vector; and (c) combining the filamentous bacteriophage vector products of steps (a) and (b) under conditions where said populations of first and second oligonucleotides are joined together into a population of combined vectors wherein said joined first and second oligonucleotides are capable of being expressed as fusion proteins with said coat protein or as soluble peptides.
Claim 37
Independent Claim
198 words
A method of constructing a diverse population of filamentous bacteriophage vectors having combined first and second oligonucleotides encoding a desirable bias of amino acids, said oligonucleotides being synthesized from nucleotide monomers and having a desirable bias of random codon sequences capable of expressing said combined oligonucleotides as random peptides fused to the major coat protein of a filamentous bacteriophage or as soluble peptides, comprising the steps of: (a) operationally linking sequences from a diverse population of first oligonucleotides having a desirable bias of random codon sequences encoding said desirable bias of amino acids to expression elements within a first filamentous bacteriophage vector; (b) operationally linking sequences from a diverse population of second oligonucleotides having a desirable bias of random codon sequences encoding said desirable bias of amino acids to said major coat protein of said filamentous bacteriophage within a second filamentous bacteriophage vector; and (c) combining the filamentous bacteriophage vector products of steps (a) and (b) under conditions where said populations of first and second oligonucleotides are joined together into a population of combined vectors wherein said joined first and second oligonucleotides are capable of being expressed as fusion proteins with said coat protein or as soluble peptides.
Claim 38
Dependent Claim
30 words
The method of claim 30 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 39
Dependent Claim
28 words
The method of claim 30 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 40
Dependent Claim
30 words
The method of claim 30 , wherein said first and second oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 41
Dependent Claim
17 words
The method of claim 30 , wherein steps (a) through (c) are repeated two or more times.
Claim 42
Independent Claim
189 words
A method of selecting a peptide which binds a ligand binding protein from a population of random peptides, comprising: (a) operationally linking to expression elements within a first filamentous bacteriophage vector a diverse population of first oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (b) operationally linking to the major coat protein of a filamentous bacteriophage within a second filamentous bacteriophage vector a diverse population of second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (c) combining the filamentous bacteriophage vector products of steps (a) and (b) under conditions where said populations of first and second oligonucleotides are joined together into a population of combined vectors; (d) introducing said population of combined vectors into a compatible host under conditions sufficient for expressing said population of random peptides as fusion proteins with said major coat protein of said filamentous bacteriophage or as soluble peptides; and (e) identifying a peptide which binds to said ligand binding protein.
Claim 43
Independent Claim
189 words
A method of selecting a peptide which binds a ligand binding protein from a population of random peptides, comprising: (a) operationally linking to expression elements within a first filamentous bacteriophage vector a diverse population of first oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (b) operationally linking to the major coat protein of a filamentous bacteriophage within a second filamentous bacteriophage vector a diverse population of second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (c) combining the filamentous bacteriophage vector products of steps (a) and (b) under conditions where said populations of first and second oligonucleotides are joined together into a population of combined vectors; (d) introducing said population of combined vectors into a compatible host under conditions sufficient for expressing said population of random peptides as fusion proteins with said major coat protein of said filamentous bacteriophage or as soluble peptides; and (e) identifying a peptide which binds to said ligand binding protein.
Claim 44
Dependent Claim
30 words
The method of claim 35 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 45
Dependent Claim
28 words
The method of claim 35 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 46
Dependent Claim
30 words
The method of claim 35 , wherein said first and second oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 47
Dependent Claim
17 words
The method of claim 35 , wherein steps (a) through (c) are repeated two or more times.
Claim 48
Independent Claim
208 words
A method for determining the nucleic acid sequence encoding a peptide which binds a ligand binding protein which is selected from a population of random peptides, comprising: (a) operationally linking to expression elements within a first filamentous bacteriophage vector a diverse population of first oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (b) operationally linking to the major coat protein of a filamentous bacteriophage within a second filamentous bacteriophage vector a diverse population of second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (c) combining the vector products of steps (a) and (b) under conditions where said populations of first and second oligonucleotides are joined together into a population of combined vectors; (d) introducing said population of combined vectors into a compatible host under conditions sufficient for expressing said population of random peptides as fusion proteins with said major coat protein of said filamentous bacteriophage or as soluble peptides; (e) identifying a peptide which binds to said ligand binding protein; (f) isolating the nucleic acid encoding said peptide; and (g) sequencing said nucleic acid.
Claim 49
Independent Claim
208 words
A method for determining the nucleic acid sequence encoding a peptide which binds a ligand binding protein which is selected from a population of random peptides, comprising: (a) operationally linking to expression elements within a first filamentous bacteriophage vector a diverse population of first oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (b) operationally linking to the major coat protein of a filamentous bacteriophage within a second filamentous bacteriophage vector a diverse population of second oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers; (c) combining the vector products of steps (a) and (b) under conditions where said populations of first and second oligonucleotides are joined together into a population of combined vectors; (d) introducing said population of combined vectors into a compatible host under conditions sufficient for expressing said population of random peptides as fusion proteins with said major coat protein of said filamentous bacteriophage or as soluble peptides; (e) identifying a peptide which binds to said ligand binding protein; (f) isolating the nucleic acid encoding said peptide; and (g) sequencing said nucleic acid.
Claim 50
Dependent Claim
30 words
The method of claim 40 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 51
Dependent Claim
28 words
The method of claim 40 , wherein the desirable bias of random codon sequences of said first and second oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 52
Dependent Claim
30 words
The method of claim 40 , wherein said first and second oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 53
Dependent Claim
17 words
The method of claim 40 , wherein steps (a) through (c) are repeated two or more times.
Claim 54
Independent Claim
85 words
A method of constructing a diverse population of filamentous bacteriophage vectors containing oligonucleotides having a desirable bias of random codon sequences which are expressible as fusion proteins with a major coat protein of a filamentous bacteriophage in a suppressor host or as soluble peptides in a non-suppressor host, comprising operationally linking a diverse population of oligonucleotides having a desirable bias of random codon sequences to (i) expression elements, (ii) to a suppressible stop codon and (iii) to said major coat protein of a filamentous bacteriophage.
Claim 55
Independent Claim
85 words
A method of constructing a diverse population of filamentous bacteriophage vectors containing oligonucleotides having a desirable bias of random codon sequences which are expressible as fusion proteins with a major coat protein of a filamentous bacteriophage in a suppressor host or as soluble peptides in a non-suppressor host, comprising operationally linking a diverse population of oligonucleotides having a desirable bias of random codon sequences to (i) expression elements, (ii) to a suppressible stop codon and (iii) to said major coat protein of a filamentous bacteriophage.
Claim 56
Dependent Claim
22 words
The method of claim 45 , wherein said oligonucleotides are expressible as gVIII-peptide fusion proteins on the surface of said filamentous bacteriophage.
Claim 57
Dependent Claim
27 words
The method of claim 45 , wherein the desirable bias of random codon sequences of said oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 58
Dependent Claim
25 words
The method of claim 45 , wherein the desirable bias of random codon sequences of said oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 59
Dependent Claim
27 words
The method of claim 45 , wherein said oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 60
Independent Claim
143 words
A method of selecting a peptide which binds a ligand binding protein from a population of random peptides, comprising: (a) operationally linking to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage a diverse population of oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, said expression elements contained in a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein in a suppressor host or as soluble peptides in a non-suppressor host; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; and (c) identifying a peptide which binds to said ligand binding protein.
Claim 61
Independent Claim
143 words
A method of selecting a peptide which binds a ligand binding protein from a population of random peptides, comprising: (a) operationally linking to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage a diverse population of oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, said expression elements contained in a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein in a suppressor host or as soluble peptides in a non-suppressor host; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; and (c) identifying a peptide which binds to said ligand binding protein.
Claim 62
Dependent Claim
25 words
The method of claim 50 , wherein said population of random peptides are expressed as gVIII-peptide fusion proteins on the surface of said filamentous bacteriophage.
Claim 63
Dependent Claim
26 words
The method of claim 50 , wherein the desirable bias of random codon sequences of said oligonucleotides is unbiased with respect to amino acids encoded thereby.
Claim 64
Dependent Claim
25 words
The method of claim 50 , wherein the desirable bias of random codon sequences of said oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 65
Dependent Claim
27 words
The method of claim 50 , wherein said oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 66
Independent Claim
164 words
A method of determining the nucleic acid sequence encoding a peptide which binds a ligand binding protein which is selected from a population of random peptides, comprising: (a) operationally linking to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage each member of a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, wherein said expression elements are contained within a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein in a suppressor host or as soluble peptides in a non-suppressor host; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; (c) identifying a peptide which binds to said ligand binding protein; (d) isolating the nucleic acid encoding said peptide; and (e) sequencing said nucleic acid.
Claim 67
Independent Claim
164 words
A method of determining the nucleic acid sequence encoding a peptide which binds a ligand binding protein which is selected from a population of random peptides, comprising: (a) operationally linking to (i) expression elements, (ii) a suppressible stop codon and (iii) to the major coat protein of a filamentous bacteriophage each member of a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding a desirable bias of amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, wherein said expression elements are contained within a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein in a suppressor host or as soluble peptides in a non-suppressor host; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; (c) identifying a peptide which binds to said ligand binding protein; (d) isolating the nucleic acid encoding said peptide; and (e) sequencing said nucleic acid.
Claim 68
Dependent Claim
25 words
The method of claim 55 , wherein said population of random peptides are expressed as gVIII-peptide fusion proteins on the surface of said filamentous bacteriophage.
Claim 69
Dependent Claim
27 words
The method of claim 55 , wherein the desirable bias of random codon sequences of said oligonucleotides is unbiased with respect to the amino acids encoded thereby.
Claim 70
Dependent Claim
25 words
The method of claim 55 , wherein the desirable bias of random codon sequences of said oligonucleotides is diverse but biased toward a predetermined sequence.
Claim 71
Dependent Claim
27 words
The method of claim 55 , wherein said oligonucleotides having a desirable bias of random codon sequences have at least one specified codon at a predetermined position.
Claim 72
Dependent Claim
98 words
A filamentous bacteriophage vector comprising two non-identical copies of a gene encoding a filamentous bacteriophage gVIII coat protein, said non-identical copies encoding gVIII coat proteins having substantially the same amino acid sequence but having different nucleotide sequences, wherein said gVIII coat proteins are expressed on the surface of a filamentous bacteriophage and wherein one copy of said gene encoding a gVIII coat protein encodes a non-gVIII signal sequence and a suppressible stop codon for directing surface expression of an oligonucleotide as a gVIII fusion protein in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 73
Dependent Claim
98 words
A filamentous bacteriophage vector comprising two non-identical copies of a gene encoding a filamentous bacteriophage gVIII coat protein, said non-identical copies encoding gVIII coat proteins having substantially the same amino acid sequence but having different nucleotide sequences, wherein said gVIII coat proteins are expressed on the surface of a filamentous bacteriophage and wherein one copy of said gene encoding a gVIII coat protein encodes a non-gVIII signal sequence and a suppressible stop codon for directing surface expression of an oligonucleotide as a gVIII fusion protein in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 74
Dependent Claim
24 words
The vector of claim 60 , wherein said vector has the same or substantially the same sequence shown in FIG. 5 (SEQ ID NO:1).
Claim 75
Dependent Claim
22 words
The vector of claim 61 , wherein said one copy of said gene is expressed on the surface of said filamentous bacteriophage.
Claim 76
Dependent Claim
71 words
A filamentous bacteriophage vector comprising two copies of a gene encoding a filamentous bacteriophage gVIII coat protein, wherein one copy of said gene is operationally linked to expression elements, an oligonucleotide, a non-gVIII signal sequence and to a suppressible stop codon, wherein said oligonucleotide is expressed as a gVIII-peptide fusion protein on the surface of said filamentous bacteriophage in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 77
Dependent Claim
71 words
A filamentous bacteriophage vector comprising two copies of a gene encoding a filamentous bacteriophage gVIII coat protein, wherein one copy of said gene is operationally linked to expression elements, an oligonucleotide, a non-gVIII signal sequence and to a suppressible stop codon, wherein said oligonucleotide is expressed as a gVIII-peptide fusion protein on the surface of said filamentous bacteriophage in a suppressor host or as a soluble peptide in a non-suppressor host.
Claim 78
Dependent Claim
113 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, which each of said oligonucleotides is operationally linked to expression elements and to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids produced from random combinations of first and second oligonucleotide precursor populations having a desirable bias of random codon sequences encoding unbiased amino acids, said precursor populations being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage.
Claim 79
Dependent Claim
113 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, which each of said oligonucleotides is operationally linked to expression elements and to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids produced from random combinations of first and second oligonucleotide precursor populations having a desirable bias of random codon sequences encoding unbiased amino acids, said precursor populations being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage.
Claim 80
Dependent Claim
91 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, wherein each of said oligonucleotides is operationally linked to expression elements and to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage.
Claim 81
Dependent Claim
91 words
A composition of matter comprising a plurality of cells containing a diverse population of expressible oligonucleotides, wherein each of said oligonucleotides is operationally linked to expression elements and to the major coat protein of a filamentous bacteriophage, said expressible oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, and wherein said expression elements direct the expression of said oligonucleotides from a filamentous bacteriophage vector as a fusion protein with said major coat protein of said filamentous bacteriophage.
Claim 82
Dependent Claim
50 words
A plurality of filamentous bacteriophage vectors containing a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers and being operationally linked to expression elements and the major coat protein of a filamentous bacteriophage.
Claim 83
Dependent Claim
50 words
A plurality of filamentous bacteriophage vectors containing a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers and being operationally linked to expression elements and the major coat protein of a filamentous bacteriophage.
Claim 84
Independent Claim
70 words
A method of constructing a diverse population of filamentous bacteriophage vectors containing oligonucleotides having random codon sequences which are unbiased with respect to the amino acids encoded thereby and which are expressible as fusion proteins with a major coat protein of a filamentous bacteriophage, comprising operationally linking a diverse population of oligonucleotides having unbiased random codon sequences to expression elements and to the major coat protein of a filamentous bacteriophage.
Claim 85
Independent Claim
70 words
A method of constructing a diverse population of filamentous bacteriophage vectors containing oligonucleotides having random codon sequences which are unbiased with respect to the amino acids encoded thereby and which are expressible as fusion proteins with a major coat protein of a filamentous bacteriophage, comprising operationally linking a diverse population of oligonucleotides having unbiased random codon sequences to expression elements and to the major coat protein of a filamentous bacteriophage.
Claim 86
Independent Claim
122 words
A method of selecting a peptide which binds a ligand binding protein from a population of random peptides, comprising: (a) operationally linking to expression elements and to the major coat protein of a filamentous bacteriophage a diverse population of oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, said expression elements contained in a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; and (c) identifying a peptide which binds to said ligand binding protein.
Claim 87
Independent Claim
122 words
A method of selecting a peptide which binds a ligand binding protein from a population of random peptides, comprising: (a) operationally linking to expression elements and to the major coat protein of a filamentous bacteriophage a diverse population of oligonucleotides synthesized from nucleotide monomers and having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, said expression elements contained in a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; and (c) identifying a peptide which binds to said ligand binding protein.
Claim 88
Independent Claim
143 words
A method of determining the nucleic acid sequence encoding a peptide which binds a ligand binding protein which is selected from a population of random peptides, comprising: (a) operationally linking to expression elements and to the major coat protein of a filamentous bacteriophage each member of a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, wherein said expression elements are contained within a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; (c) identifying a peptide which binds to said ligand binding protein; (d) isolating the nucleic acid encoding said peptide; and (e) sequencing said nucleic acid.
Claim 89
Independent Claim
143 words
A method of determining the nucleic acid sequence encoding a peptide which binds a ligand binding protein which is selected from a population of random peptides, comprising: (a) operationally linking to expression elements and to the major coat protein of a filamentous bacteriophage each member of a diverse population of oligonucleotides having a desirable bias of random codon sequences encoding completely random amino acids, said population of oligonucleotides being synthesized from nucleotide monomers, wherein said expression elements are contained within a filamentous bacteriophage vector which directs expression of the oligonucleotides as fusion proteins with said major coat protein; (b) introducing said population of vectors into a compatible host under conditions sufficient for expressing said population of random peptides; (c) identifying a peptide which binds to said ligand binding protein; (d) isolating the nucleic acid encoding said peptide; and (e) sequencing said nucleic acid.
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