Method for selection of proteins using RNA-protein fusions
First Claim
Patent Images
1. A method for generating a DNA molecule which encodes a desired protein, comprising the steps of:
- a) providing a population of candidate RNA molecules, each of which comprises a translation initiation sequence and a start codon operably linked to a candidate protein coding sequence and each of which is covalenty bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence said peptide acceptor being a molecule that can be added to the C-terminus of protein chain by the catalytic activity of a ribosomal peptidyl transferae;
b) in vitro translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of candidate RNA-protein fusions;
c) selecting from said population a desired RNA-protein fusion based on fusion binding or activity; and
d) generating from said RNA portion of said selected fusion a DNA molecule, thereby generating a DNA molecule which encodes said desired protein.
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Abstract
Described herein are methods and reagents for the selection of protein molecules that make use of RNA-protein fusions.
298 Citations
46 Claims
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1. A method for generating a DNA molecule which encodes a desired protein, comprising the steps of:
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a) providing a population of candidate RNA molecules, each of which comprises a translation initiation sequence and a start codon operably linked to a candidate protein coding sequence and each of which is covalenty bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence said peptide acceptor being a molecule that can be added to the C-terminus of protein chain by the catalytic activity of a ribosomal peptidyl transferae;
b) in vitro translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of candidate RNA-protein fusions;
c) selecting from said population a desired RNA-protein fusion based on fusion binding or activity; and
d) generating from said RNA portion of said selected fusion a DNA molecule, thereby generating a DNA molecule which encodes said desired protein. - View Dependent Claims (9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41)
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2. A method for generating a DNA molecule which encodes a protein having an altered function relative to a reference protein, comprising the steps of:
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a) producing a population of candidate RNA molecules from a population of candidate DNA templates, said candidate RNA molecules each having a candidate protein coding sequence which differs from the reference protein coding sequence, said RNA molecules each comprising a translation initiation sequence and a start codon operably linked to said candidate protein coding sequence and each being covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of RNA-protein fusions;
c) selecting from said population an RNA-protein fusion having an altered function based on fusion binding or activity; and
d) generating from said RNA portion of said selected fusion a DNA molecule, thereby generating a DNA molecule which encodes said protein having said altered function.
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3. A method for the selection of a desired RNA, comprising the steps of:
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a) providing a population of candidate RNA molecules, each of which comprises a translation initiation sequence and a start codon operably linked to a candidate protein coding sequence and each of which is covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of candidate RNA-protein fusions; and
c) selecting from said population a desired RNA-protein fusion based on fusion binding or activity, thereby selecting said desired RNA. - View Dependent Claims (4, 5)
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6. A method for the selection of a DNA molecule which encodes a desired protein, comprising the steps of:
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a) providing a population of candidate RNA molecules, each of which comprises a translation initiation sequence and a start codon operably linked to a candidate protein coding sequence and each of which is covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of candidate RNA-protein fusions;
c) generating a DNA copy of the RNA of said population of candidate RNA-protein fusions; and
d) selecting from said population a desired fusion based on fusion binding or activity, thereby selecting a DNA molecule which encodes said desired protein. - View Dependent Claims (8, 12, 13, 14)
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7. A method for the selection of a DNA molecule which encodes a protein having an altered function relative to a reference protein, comprising the steps of:
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a) producing a population of candidate RNA molecules from a population of candidate DNA templates, said candidate RNA molecules each having a candidate protein coding sequence which differs from the reference protein coding sequence, said RNA molecules each comprising a translation initiation sequence and a start codon operably linked to said candidate protein coding sequence and each being covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of RNA-protein fusions;
c) generating a DNA copy of the RNA of said population of RNA-protein fusions; and
d) selecting from said population a fusion having an altered function based on fusion binding or activity, thereby selecting a DNA molecule which encodes said protein having said altered function.
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42. A method for generating a DNA molecule which encodes a desired protein, comprising the steps of:
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a) providing a population of candidate RNA molecules, each of which comprises a translation initiation sequence and a start codon operably linked to a candidate protein coding sequence and each of which is covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro or in situ translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of candidate RNA-protein fusions;
c) selecting from said population a desired RNA-protein fusion based on fusion binding or activity; and
d) generating from said RNA portion of said selected fusion a DNA molecule, thereby generating a DNA molecule which encodes said desired protein.
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43. A method for generating a DNA molecule which encodes a protein having an altered function relative to a reference protein, comprising the steps of:
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a) producing a population of candidate RNA molecules from a population of candidate DNA templates, said candidate RNA molecules each having a candidate protein coding sequence which differs from the reference protein coding sequence, said RNA molecules each comprising a translation initiation sequence and a start codon operably linked to said candidate protein coding sequence and each being covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vito or in situ translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of RNA-protein fusions;
c) selecting from said population an RNA-protein fusion having an altered function based on fusion binding or activity; and
d) generating from said RNA portion of said selected fusion a DNA molecule, thereby generating a DNA molecule which encodes said protein having said altered function.
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44. A method for the selection of a desired RNA, comprising the steps of:
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a) providing a population of candidate RNA molecules, each of which comprises a translation initiation sequence and a start codon operably linked to a candidate protein coding sequence and each of which is covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro or in situ translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of candidate RNA-protein fusions; and
c) selecting from said population a desired RNA-protein fusion based on fusion binding or activity, thereby selecting said desired RNA.
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45. A method for the selection of a DNA molecule which encodes a desired protein, comprising the steps of:
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a) providing a population of candidate RNA molecules, each of which comprises a translation initiation sequence and a start codon operably linked to a candidate protein coding sequence and each of which is covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro or in situ translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of candidate RNA-protein fusions;
c) generating a DNA copy of the RNA of said population of candidate RNA-protein fusions; and
d) selecting from said population a desired fusion based on fusion binding or activity, thereby selecting a DNA molecule which encodes said desired protein.
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46. A method for the selection of a DNA molecule which encodes a protein having an altered function relative to a reference protein, comprising the steps of:
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a) producing a population of candidate RNA molecules from a population of candidate DNA templates, said candidate RNA molecules each having a candidate protein coding sequence which differs from the reference protein coding sequence, said RNA molecules each comprising a translation initiation sequence and a start codon operably linked to said candidate protein coding sequence and each being covalently bonded to a peptide acceptor at the 3′
end of said candidate protein coding sequence, said peptide acceptor being a molecule that can be added to the C-terminus of a growing protein chain by the catalytic activity of a ribosomal peptidyl transferase;
b) in vitro or in situ translating said candidate protein coding sequences of said candidate RNA molecules to produce a population of RNA-protein fusions;
c) generating a DNA copy of the RNA of said population of RNA-protein fusions; and
d) selecting from said population a fusion having an altered function based on fusion binding or activity, thereby selecting a DNA molecule which encodes said protein having said altered function.
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Specification