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 in which each nucleotide is represented by one bead. The radius of the helix is regarded as an adjustable parameter. The translational coefficient 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 have also calculated a nuclear magnetic resonance relaxation time in which the coefficient for rotation about the main axis is involved. As found previously with cylindrical models, the results deviate from experimental values, indicating that the internal motion of the bases has a remarkable amplitude. An attempt to quantify the extent of internal motions is presented.