Journal Article

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

Xiaohu Wang, Haichun Gao, Yufeng Shen, George M. Weinstock, Jizhong Zhou and Timothy Palzkill

in Nucleic Acids Research

Volume 36, issue 15, pages 4863-4871
Published in print September 2008 | ISSN: 0305-1048
Published online July 2008 | e-ISSN: 1362-4962 | DOI: https://dx.doi.org/10.1093/nar/gkn477

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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.

Journal Article.  5547 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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