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

作者：Wang Xiaohu; Gao Haichun; Shen Yufeng; Weinstock George M; Zhou Jizhong; Palzkill Timothy^*

来源：Nucleic Acids Research, 2008, 36(15): 4863-4871.

DOI：10.1093/nar/gkn477

Quantifying the binding energy in DNAprotein 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 DNAprotein 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.

• 出版日期2008-9
• 单位浙江大学