A BEAD-SPRING MODEL AND MEAN FIELD THEORY BASED RE-CALCULATION REVEALS UNCERTAINTY OF ROUSE-TYPE DNA DYNAMICS IN DILUTE SOLUTION

Abstract

Double-stranded DNA (dsDNA) is one of the most used model polymers in studying polymer dynamics. Some recent studies with the experimental data via fluorescence correlation spectroscopy (FCS) proposed that the end-monomer dynamics of dsDNA in dilute solution should be fallen into Rouse-type at intermediate times. This viewpoint is inconsistent with the classical polymer dynamics, therefore arousing controversy. To have a further looking clearly at what else meaning could be revealed from the original data of the FCS measurements, we made a re-calculation by two methods: one is based on Lodge and Wu's model (LWM) modified from the classical bead-spring model, in which parameters used in modeling are needed to be adjusted; and another is a mean field theory (MFT) for semiflexible chain with no parameter fitting needed. In LWM, we find not so weak hydrodynamic interactions (HI) which is not expected in Rouse theory, and the scaling of mean square displacement (MSD) is between Rouse-type and Zimm-type. MFT can reproduce experimental data well at larger time scales, whereas also gives rather different picture in intermediate regime — a dynamical scaling between Rouse-like and Zimm-like rather than Rouse-like scaling is found, indicating there may be sample problems or limitations in the setup for the experiment.