Base Pair Openings and Temperature Dependence of DNA Flexibility

The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.

Figure 1

The quantity $Q$ (left $y$ axis), as extracted from measurements of magnetic birefringence (circles, adapted from 9), and calculated (i) on the basis of Eq. (7) (dashed curve), (ii) from the heterogeneous KP model (full line); the dotted curve shows a $1/T$ behavior for comparison. Also shown (right $y$ axis) is the measured melting fraction for a similar sample [18] (dotted line) and as calculated from a 290 kb sequence of bos taurus [19] (thin full line).

Figure 2

Some average properties of the bovine sequence [19]. Left $y$-scale: the average size (in bps) of intact clusters (dash-dotted curve); the inverse of the melting fraction (dotted curve). Right $y$ scale: the melting fraction $\Theta$ (solid curve) and the conditional probability $P_0/\Theta$ that if a base pair is in the open state, the next one will also be in the open state (dashed curve); note that the latter quantity is much larger than $\Theta$ (bubble aggregation tendency).

Figure 3

Persistence length obtained by cyclization of DNA fragments (filled squares, open circles, redrawn from Ref. 7). The solid curve shows the estimate obtained from the inhomogeneous KP chain with stiff and soft joints distributed according to (5) and probabilities from a PBD calculation. Also shown is a $1/T$ reference curve (dotted line), and the melting fraction (dashed line, right $y$ axis) obtained from the PBD calculation.