Patent ID: 7601492

Claim:
A method of detecting a polynucleotide-polypeptide interaction domain in a genome of an organism, comprising: a) crosslinking polypeptides and polynucleotides in a sample comprising genomic DNA; b) fragmenting the sample comprising the crosslinked genomic DNA to obtain polynucleotide fragments; c) immunoprecipitating a polynucleotide fragment associated with a polypeptide to obtained an enriched polynucleotide preparation; d) biotinylating polynucleotides in the enriched preparation; e) contacting the polynucleotide in the enriched preparation with a primer pair under conditions whereby the primer pair hybridizes to the polynucleotide to form a first hybridization complex, each primer comprising at least two portions, a first portion comprising a target-specific oligonucleotide that is capable of hybridizing to a target polynucleotide in the enriched preparation, and a second portion comprising a universal primer landing site, the two primers being specific for an upstream and downstream segment of the target polynucleotide, wherein the universal landing sites are not the same; f) contacting the enriched polynucleotide preparation with a substrate comprising streptavidin; g) contacting the first hybridization complex with a ligase under conditions whereby primer pairs hybridized to the polynucleotide are ligated to form a ligated probe; h) amplifying the ligated probe with universal primers to generate an amplified-labeled product; i) contacting the amplified-labeled product with an array of oligonucleotides under conditions whereby the ligated probe hybridizes to a complementary oligonucleotide in the array to form assay complexes; and j) detecting the assay complexes, wherein the presence of complexes is indicative of DNA that binds the immunoprecipitated polypeptide.