Methods and compositions for high throughput identification of protein/nucleic acid binding pairs

A system for use in identifying protein/nucleic acid binding pairs, said system comprising:

• (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.

A kit for use in identifying protein/nucleic acid binding pairs, said kit comprising:

• (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.

A substrate comprising a surface having at least one protein/nucleic acid binding pair immobilized thereon, wherein each protein/nucleic acid binding pair comprises:

• (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.

A method of identifying protein/nucleic acid binding pairs, said method comprising:

• (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.

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 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.

A method of identifying protein/nucleic acid binding pairs, said method comprising:

• (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.