Selection of nucleic acid-based sensor domains within nucleic acid switch platform
First Claim
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1. A method of screening a library of nucleic acids for a nucleic acid that binds a ligand, wherein each member of said library comprises:
- (a) an aptamer that potentially binds the ligand; and
,(b) a functional domain,the method comprising;
(1) contacting the library of nucleic acids with the ligand, under conditions that allow binding of the ligand to the aptamer of one or more members of the library in solution;
(2) isolating nucleic acids that form complexes with the ligand; and
,(3) determining, for each nucleic acids isolated in (2), if any, whether binding of the ligand to said aptamer favors a conformational change in the functional domain from a first ligand-free conformation to a second ligand-bound conformation,wherein the functional domain is not a ribozyme or a catalytic RNA, or wherein step (2) is not effectuated by denaturing polyacrylamide gel electrophoresis (PAGE) or a chromatography-based selection system, or both.
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Abstract
The invention relates to a method (preferably a high throughput method) for screening for functional aptamer-regulated, ligand-responsive nucleic acids, or “ampliSwitches,” and uses thereof. The subject method not only applies to large molecules, such as proteins, but also applies to relatively small ligands, such as those with molecular weight of no more than 5 kDa, 3 kDa, or 1 kDa.
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36 Claims
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1. A method of screening a library of nucleic acids for a nucleic acid that binds a ligand, wherein each member of said library comprises:
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(a) an aptamer that potentially binds the ligand; and
,(b) a functional domain, the method comprising; (1) contacting the library of nucleic acids with the ligand, under conditions that allow binding of the ligand to the aptamer of one or more members of the library in solution; (2) isolating nucleic acids that form complexes with the ligand; and
,(3) determining, for each nucleic acids isolated in (2), if any, whether binding of the ligand to said aptamer favors a conformational change in the functional domain from a first ligand-free conformation to a second ligand-bound conformation, wherein the functional domain is not a ribozyme or a catalytic RNA, or wherein step (2) is not effectuated by denaturing polyacrylamide gel electrophoresis (PAGE) or a chromatography-based selection system, or both. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36)
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Specification