Methods and compositions for high throughput identification of protein/nucleic acid binding pairs
First Claim
1. A method of identifying protein/nucleic acid binding pairs, said method comprising:
- (a) contacting a molecular beacon array comprising a plurality of distinct molecular beacon probes with a population of target nucleic acids to produce a hybridized molecular beacon array, wherein each distinct probe of said plurality comprises a different probe sequence and all of said probes of said plurality share a common first fluorescent label;
(b) contacting said hybridized molecular beacon array with a population of fluorescently labeled proteins to produce a protein bound array, where each member of said population of fluorescently labeled proteins is labeled with a second fluorescent label that makes up a FRET pair with said first fluorescent label; and
(c) detecting any FRET generated signals from said array to identify protein/nucleic acid binding pairs on said array.
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Abstract
Methods and compositions for high-throughput identification of protein/nucleic acid binding pairs are provided. In the subject methods, a nucleic acid probe array, e.g., a molecular beacon probe array, is contacted with a target nucleic acid population to produce a hybridized array. The resultant hybridized array is then contacted with a population of proteins to produce a protein bound array. Any resultant array surface bound target nucleic acid/protein complexes are then detected to identify protein/nucleic acid binding pairs. In certain embodiments, the protein and/or nucleic acid members of the identified protein/nucleic acid binding pairs are further characterized. Also provided are systems and kits for use in practicing the subject methods. The subject invention finds use in a variety of different applications.
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Citations
31 Claims
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1. A method of identifying protein/nucleic acid binding pairs, said method comprising:
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(a) contacting a molecular beacon array comprising a plurality of distinct molecular beacon probes with a population of target nucleic acids to produce a hybridized molecular beacon array, wherein each distinct probe of said plurality comprises a different probe sequence and all of said probes of said plurality share a common first fluorescent label;
(b) contacting said hybridized molecular beacon array with a population of fluorescently labeled proteins to produce a protein bound array, where each member of said population of fluorescently labeled proteins is labeled with a second fluorescent label that makes up a FRET pair with said first fluorescent label; and
(c) detecting any FRET generated signals from said array to identify protein/nucleic acid binding pairs on said array. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A system for use in identifying protein/nucleic acid binding pairs, said system comprising:
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(a) a molecular beacon array comprising a plurality of distinct molecular beacon probes, wherein each distinct probe of said plurality comprises a different probe sequence and all of said probes of said plurality share a common first fluorescent label;
(b) a labeling reagent for labeling a protein population with a second fluorescent label, wherein said first and second labels make up a FRET pair;
(c) reagents for generating a population of target nucleic adds, and (d) a fluorescence detector device. - View Dependent Claims (15, 16, 17, 18)
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19. A kit for use in identifying protein/nucleic acid binding pairs, said kit comprising:
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(a) a molecular beacon array comprising a plurality of distinct molecular beacon probes, wherein each distinct probe of said plurality comprises a different probe sequence and all of said probes of said plurality share a common first fluorescent label;
(b) a labeling reagent for labeling a protein population with a second fluorescent label, wherein said first and second labels make up a FRET pair; and
(c) reagents for generating a population of target nucleic acids. - View Dependent Claims (20, 21, 22)
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23. A substrate comprising a surface having at least one protein/nucleic acid binding pair immobilized thereon, wherein each protein/nucleic acid binding pair comprises:
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(a) a molecular beacon probe comprising a first fluorescent label;
(b) an unlabeled target nucleic acid hybridized to said molecular beacon probe; and
(c) a fluorescently labeled protein labeled with a second fluorescent label and bound to said unlabeled target nucleic acid, wherein said second fluorescent label and said first fluorescent label make up a FRET pair. - View Dependent Claims (24)
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25. A method of identifying protein/nucleic acid binding pairs, said method comprising:
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(a) contacting a nucleic acid probe array comprising a plurality of distinct probe nucleic acids with a population of target nucleic acids to produce a hybridized array, wherein each distinct probe nucleic acid of said plurality comprises a different probe sequence;
(b) contacting said hybridized array with a population of labeled proteins to produce a protein bound array; and
(c) detecting any surface bound protein/target nucleic acid complexes to identify protein/nucleic acid binding pairs on said array. - View Dependent Claims (26, 27, 28, 29)
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30. A method of identifying protein/nucleic acid binding pairs, said method comprising:
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(a) contacting a molecular beacon array comprising a plurality of distinct molecular beacon probes with a population of target nucleic acids to produce a hybridized molecular beacon array, wherein each distinct probe of said plurality comprises a different probe sequence and all of said probes of said plurality share a common first fluorescent label;
(b) contacting said hybridized molecular beacon array with at least one fluorescently labeled protein to produce a protein bound array, where said at least one fluorescently labeled protein is labeled with a second fluorescent label that makes up a FRET pair with said first fluorescent label; and
(c) detecting any FRET generated signals from said array to identify protein/nucleic acid binding pairs on said array.
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31. A method of identifying protein/nucleic acid binding pairs, said method comprising:
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(a) contacting a nucleic acid probe array comprising a plurality of distinct probe nucleic acids with a population of target nucleic acids ro produce a hybridized array, wherein each distinct probe nucleic acid of said plurality comprises a different probe sequence;
(b) contacting said hybridized array with at least one labeled protein to produce a protein bound array; and
(c) detecting any surface bound protein/target nucleic acid complexes to identify protein/nucleic acid binding pairs on said array.
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Specification