title: DNA base pair hybridization and water-mediated metastable structures studied by molecular dynamics simulations.
abstract: The base pair hybridization of a DNA segment was studied using molecular dynamics simulation. The results show the obvious correlation between the probability of successful hybridization and the accessible surface area to water of two successive base pairs, including the unpaired base pair adjacent to paired base pair and this adjacent paired base pair. Importantly, two metastable structures in an A-T base pair were discovered by the analysis of the free energy landscape. Both structures involved addition of a water molecule to the linkage between the two nucleobases in one base pair. The existence of the metastable structures provide potential barriers to the Watson-Crick base pair, and numerical simulations show that those potential barriers can be surmounted by thermal fluctuations at higher temperatures. These studies contribute an important step toward the understanding of the mechanism in DNA hybridization, particularly the effect of temperature on DNA hybridization and polymerase chain reaction. These observations are expected to be helpful for facilitating experimental bio/nanotechnology designs involving fast hybridization.
authors: Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
authors: Wenpeng
authors: W
authors: Qi
authors: Bo
authors: B
authors: Song
authors: Xiaoling
authors: X
authors: Lei
authors: Chunlei
authors: C
authors: Wang
authors: Haiping
authors: H
authors: Fang
mesh_terms: D020029:Base Pairing; D017403:In Situ Hybridization / Q000379:methods; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT / Q000737:chemistry / Q000378:metabolism; D011336:Probability; D014867:Water / Q000737:chemistry* / Q000378:metabolism
chemical_list: D014867:Water; D011067:Poly dA-dT