The Effect of environment on the conformational transition of DNA studied by molecular dynamics simulations

分子動力学によるDNAコンフォメーション変化における周辺環境の影響

藤井 聡*; 河野 秀俊; 郷 信広*; 皿井 明倫*

Fujii, Satoshi*; Kono, Hidetoshi; Go, Nobuhiro*; Sarai, Akinori*

Sequence-dependent conformational properties of DNA play important roles in various biological processes. For example, interactions of proteins with DNA sequences are known to be affected by the conformational properties of DNA. Proteins such as TATA-box binding protein and catalytic protein DNaseI induce the DNA conformation to bent form and A-form at recognition sites, respectively. It has been known that these conformational transitions are induced by the environment: variations in ionic strength and identity, sequence, water activity, and ligand/protein binding all can modulate DNA structure. In this study, we analyzed how the sequence and water activity influence the DNA conformations using molecular dynamics simulations.