HYDRODYNAMIC PROPERTIES OF A DOUBLE-HELICAL MODEL FOR DNA

The translational and rotational diffusion coefficients of very short DNA fragments have been calculated using a double-helical bead model i n which each nucleotide is represented by one bead. The radius of the helix is regarded as an adjustable parameter. The translational coeffi cient and the perpendicular rotation coefficient agree very well with experimental values for oligonuclotides with 8, 12, and 20 base pairs, for a single value of the helical radius of about 10 Angstrom. We hav e also calculated a nuclear magnetic resonance relaxation time in whic h the coefficient for rotation about the main axis is involved. As fou nd previously with cylindrical models, the results deviate from experi mental values, indicating that the internal motion of the bases has a remarkable amplitude. An attempt to quantify the extent of internal mo tions is presented.