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1: Nucleic Acids Res. 2008 Sep;36(15):4863-71. Epub 2008 Jul 24.Click here to read Click here to read Links

A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery.

Wang X, Gao H, Shen Y, Weinstock GM, Zhou J, Palzkill T.

Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.

Quantifying the binding energy in DNA-protein interactions is of critical importance to understand transcriptional regulation. Based on a simple computational model, this study describes a high-throughput percentage-of-binding strategy to measure the binding energy in DNA-protein interactions between the Shewanella oneidensis ArcA two-component transcription factor protein and a systematic set of mutants in an ArcA-P (phosphorylated ArcA) binding site. The binding energies corresponding to each of the 4 nt at each position in the 15-bp binding site were used to construct a position-specific energy matrix (PEM) that allowed a reliable prediction of ArcA-P binding sites not only in Shewanella but also in related bacterial genomes.

PMID: 18653527 [PubMed - indexed for MEDLINE]

PMCID: PMC2528174