title: Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments.
abstract: DNA sequence analyzing and base pair separation techniques have attracted much attention, such as denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and capillary electrophoresis. However, details of sequence separation mechanisms in electrophoresis are not clarified enough. Understanding and controlling flow characteristics of DNA are important not only for fundamental research but also for further developments of bio-nano technologies. In the present study, we theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B-DNA decamer 5'-dCGTATATATA-3'. Consequently, it is found that water molecules that concentrate on dissociated base pairs form hydrated structures and change the diffusivity of DNA decamers. The diffusion coefficients are affected by the substitution of GC for AT because of the different manner of interactions between the base molecules and water solvent. This result predicts a possibility of base pair separation according to differences in the diffusivity.
authors.affiliation: Department of Mechanical Science and Bioengineering, Graduate School of Engineering Scienece, Osaka University, Osaka, Japan. doi@me.es.osaka-u.ac.jp
authors.forename: Kentaro
authors.initials: K
authors.lastname: Doi
authors.forename: Takamasa
authors.initials: T
authors.lastname: Uemura
authors.forename: Satoyuki
authors.initials: S
authors.lastname: Kawano
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004058:Diffusion; D006860:Hydrogen Bonding; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009841:Oligonucleotides / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D012997:Solvents / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D012997:Solvents