title: Local dynamics coupled to hydration water determines DNA-sequence-dependent deformability.
abstract: Molecular dynamics (MD) simulations and quasielastic neutron scattering (QENS) experiments were conducted on two hydrated DNA dodecamers with distinct deformability: 5'CGCG[under AATT]̲CGCG3' and 5'CGCG[under TTAA]̲CGCG3'. The former is known to be rigid and the latter to be flexible. The mean-square displacements 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 correlates 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 the base pair steps, themselves coupled to hydration water in the minor groove.
authors.affiliation: Neutron Biophysics, Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Nakagawa
authors.affiliation: Molecular Modeling and Simulation, Quantum Beam Science Center, Japan Atomic Energy Agency, Kizugawa, Kyoto 619-0215, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Yonetani
authors.affiliation: J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Nakajima
authors.affiliation: J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Ohira-Kawamura
authors.affiliation: J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Kikuchi
authors.affiliation: J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Inamura
authors.affiliation: Neutron Biophysics, Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan and Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Kataoka
authors.affiliation: Molecular Modeling and Simulation, Quantum Beam Science Center, Japan Atomic Energy Agency, Kizugawa, Kyoto 619-0215, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Kono
mesh_terms: D004247:DNA / Q000737:chemistry*; D004548:Elasticity; D006860:Hydrogen Bonding; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009502:Neutrons; D009690:Nucleic Acid Conformation; D012542:Scattering, Radiation; D044366:Transition Temperature; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D004247:DNA