Abstract
It is required that flow characteristics of DNAs can be precisely controlled for development of bio-nano technologies. Recently, many experimental methods for DNA base-pair analysis have been proposed. Denaturing Gradient Gel Electrophoresis (DGGE) method is widely used to determine the base sequences of DNAs. In this study, we theoretically analyze the flow dynamics of DNA fragments using molecular dynamics (MD) simulations. Two types of 10 base-pairs DNA (5'-TTTTTTTTGG-3'), a rigidly bonding type and a partly dissociated one, are prepared for the simulations. As a result, the relationship between the hydrated structures and the fluidity of DNA has been clarified. Water molecules which concentrate around O and N atoms in base molecules are concerned with the hydrated structures and reduce the fluidity of the DNA fragments.
