Local dynamics coupled to hydration water determines DNA-sequence-dependent deformability
中川 洋; 米谷 佳晃; 中島 健次; 河村 聖子; 菊地 龍弥; 稲村 泰弘; 片岡 幹雄; 河野 秀俊
Nakagawa, Hiroshi; Yonetani, Yoshiteru; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya; Inamura, Yasuhiro; Kataoka, Mikio; Kono, Hidetoshi
Molecular dynamics (MD) simulations and Quasi-Elastic Neutron Scattering (QENS) experiments were conducted on hydrated two DNA dodecamers with distinct deformability; 5'CGCGAATTCGCG3' and 5'CGCGTTAACGCG3'. The former is known to be rigid and the latter to be flexible. The mean-square displacements (MSDs) of DNA dodecamers exhibit so-called dynamical transition around 200-240 K for both sequences. To investigate the DNA sequence dependent dynamics, the dynamics of DNA and hydration water above the transition temperature were examined using both MD simulations and QENS experiments. The fluctuation amplitude of the AATT central tetramer is smaller, and its relaxation time is longer, than that observed in TTAA, suggesting that the AT step is kinetically more stable than TA. The sequence-dependent local base pair step dynamics correlate with the kinetics of breaking the hydrogen bond between DNA and hydration water. The sequence dependent DNA base pair step fluctuations appear above the dynamical transition temperature. Together with these results, we conclude that DNA deformability is related to the local dynamics of base pair step, themselves coupled to hydration water in the minor groove.
使用言語 : English
掲載資料名 : Physical Review E
: 90
: 2
ページ数 : p.022723_1 - 022723_11
発行年月 : 2014/08
出版社名 : American Physical Society
特許データ :
論文URL :
キーワード : no keyword
使用施設 :
広報プレスリリース : DNAの曲がりやすさにも遺伝子発現情報が含まれている; J-PARCにおける中性子準弾性散乱実験とシミュレーション計算により、DNAと水和水の運動の観測に成功
: 遺伝子発現の仕組みをDNAの曲がりやすさから理解する; 中性子準弾性散乱で配列依存的なDNAの揺らぎを観測[/]
受委託・共同研究相手機関 :
登録番号 : AA20140206
抄録集掲載番号 : 42001450
論文投稿番号 : 15076
Accesses  (From Jun. 2, 2014)
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分野:Physics, Fluids & Plasmas
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