title: The thermodynamics and kinetics of a nucleotide base pair.
abstract: The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.
authors.affiliation: Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China.
authors.forename: Yujie
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China.
authors.forename: Sha
authors.initials: S
authors.lastname: Gong
authors.affiliation: Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Physics, Wuhan University, Wuhan, Hubei, People's Republic of China.
authors.forename: Wenbing
authors.initials: W
authors.lastname: Zhang
mesh_terms: D020029:Base Pairing; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D013816:Thermodynamics; D044366:Transition Temperature
chemical_list: D012313:RNA