Selection of fibronectin scaffolds using nucleic acid-protein fusions
First Claim
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1. A molecule comprising i) a protein comprising a fibronectin type III (Fn3) domain, wherein the Fn3 domain:
- (a) has at least one loop with a modified amino acid sequence relative to the sequence of the corresponding loop of a human Fn3 domain; and
(b) binds to a target compound that is not bound by the corresponding human Fn3 domain; and
ii) a nucleic acid, wherein the protein is bonded through a DNA-puromycin linker to the nucleic acid, and wherein the protein is encoded by said nucleic acid.
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Abstract
Disclosed herein are proteins that include an immunoglobulin fold and that can be used as scaffolds. Also disclosed herein are nucleic acids encoding such proteins and the use of such proteins in diagnostic methods and in methods for evolving novel compound-binding species and their ligands.
91 Citations
26 Claims
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1. A molecule comprising i) a protein comprising a fibronectin type III (Fn3) domain, wherein the Fn3 domain:
- (a) has at least one loop with a modified amino acid sequence relative to the sequence of the corresponding loop of a human Fn3 domain; and
(b) binds to a target compound that is not bound by the corresponding human Fn3 domain; and
ii) a nucleic acid, wherein the protein is bonded through a DNA-puromycin linker to the nucleic acid, and wherein the protein is encoded by said nucleic acid. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
- (a) has at least one loop with a modified amino acid sequence relative to the sequence of the corresponding loop of a human Fn3 domain; and
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13. A fibronectin type III (Fn3) domain scaffold-based protein that binds to a compound, selected by the method comprising the steps of:
- a) producing a population of candidate RNA molecules, each comprising a candidate (Fn3) domain scaffold-based protein sequence which differs from human Fn3 domain 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 operably linked to a DNA-puromycin linker at the 3′
end;
b) in vitro translating said candidate protein coding sequences to produce a population of candidate RNA-protein fusions;
c) contacting said population of candidate RNA-protein fusions with said compound; and
d) selecting an RNA-protein fusion, the protein portion of which has a binding affinity or specificity for said compound that is altered relative to the binding affinity or specificity of said human Fn3 for said compound. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26)
- a) producing a population of candidate RNA molecules, each comprising a candidate (Fn3) domain scaffold-based protein sequence which differs from human Fn3 domain 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 operably linked to a DNA-puromycin linker at the 3′
Specification