Patent ID: 7258974

Claim:
A method for determining the nucleic acid subsequence specificity of at least one putative double-stranded DNA-binding protein, which comprises: (a) providing a plurality of double-stranded nucleic acid probes which represent substantially all combinations of sequences of length N in solution or immobilized on a solid support, wherein N is at least three and substantially all combinations of sequences of length N is 4 N different sequences; (b) contacting said double-stranded nucleic acid probes with said at least one putative double-stranded DNA-binding protein under conditions in which DNA-binding proteins bind to double-stranded nucleic acid; (c) determining whether said at least one putative double-stranded DNA-binding protein has bound to a double-stranded nucleic acid sequence, thus determining if said at least one putative double-stranded DNA-binding protein is a double-stranded DNA-binding protein; (d) determining gross binding site data, wherein said gross binding site data comprises nucleic acid sequences of substantially all double-stranded nucleic acid probes, wherein said nucleic acid sequences comprise nucleic acid sequences of bound probes and unbound probes; and (e) using said gross binding site data to determine the subsequences common to the double-stranded nucleic acid probes to which said DNA-binding protein has bound in step (b); thus determining the nucleic acid subsequence specificity of the at least one DNA-binding protein.