LIBRARIES FOR GENOMIC SELEX

An increasing number of proteins are being identified that regulate ge ne expression by binding specific nucleic acids in vivo. A method term ed genomic SELEX facilitates the rapid identification of networks of p rotein-nucleic acid interactions by identifying within the genomic seq uences of an organism the highest affinity sites for any protein of th e organism. As with its progenitor, SELEX of random-sequence nucleic a cids, genomic SELEX involves iterative binding, partitioning, and ampl ification of nucleic acids. The two methods differ in that the variabl e region of the nucleic acid library for genomic SELEX is derived from the genome of an organism. We have used a quick and simple method to construct Escherichia coil, Saccharomyces cerevisiae, and human genomi c DNA PCR libraries that can be transcribed with T7 RNA polymerase. We present evidence that the libraries contain overlapping inserts start ing at most of the positions within the genome, making these libraries suitable for genomic SELEX.