Orientation relaxation of DNA restriction fragments and the internal mobility of the double helix

Abstract

The orientation relaxation of 15 DNA restriction fragments (43-4361 base-pairs) is characterized by measurements of linear dichroism using high electric field pulses. The off-field relaxation of fragments of 84 base-pairs or less can be described by single exponentials, which are related to the transverse rotational diffusion of the helix. Fragments of 95 base-pairs or greater exhibit an additional fast component with time constants .apprx. 100 ns for fragments of .apprx. 100 base-pairs, increasing with chain length to .apprx. 700 ns for a fragment with 258 base-pairs. The amplitude of this process increases from virtually zero at low fields (.apprxeq. 10 kV) to a substantial limit contribution at high fields. Electric fields may induce stretching of the DNA fragments from a weakly bent to a more straight form and that the fast component reflects the internal mobility of the DNA chain. The slow off-field components of the orientation are discussed in terms of different models. The data up to helix lengths of .apprx. 400 base-pairs can be described by the weakly bending rod model from Hearst using 3.4 .ANG. rise/base-pair and 13 .ANG. axial radius of the helix. Both the weakly bending rod according to Hearst and the wormlike chain according to Hagerman and Zimm provide a persistence length of 500 .ANG.. The on-field relaxation is slower than the corresponding off-field process at low field strengths, but the on-field process is accelerated substantially at high electric fields. These observations are compared with model calculations of Schwarz.