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Nucleic Acids Research Advance Access originally published online on July 24, 2008
Nucleic Acids Research 2008 36(15):4863-4871; doi:10.1093/nar/gkn477
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Nucleic Acids Research, 2008, Vol. 36, No. 15 4863-4871
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Gene Regulation, Chromatin and Epigenetics

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

Xiaohu Wang1, Haichun Gao2,3, Yufeng Shen4, George M. Weinstock4, Jizhong Zhou2 and Timothy Palzkill1,*

1Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, 2Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA, 3College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, P. R. China and 4Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA

*To whom correspondence should be addressed. Tel: +1 713 798 5609; Fax: +1 713 798 7375; Email: timothyp{at}bcm.tmc.edu

Received May 8, 2008. Revised June 11, 2008. Accepted July 8, 2008.

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.


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