Breathing and bending fluctuations in DNA modeled by an open‐base‐pair kink coupled to axial compression

Abstract We develop a model designed to show that flexibility in the DNA molecule can arise from relatively improbable transient opening of base pairs. The axial direction changes at the site of an open base pair. The region between open base pairs is a double helix of hydrogen‐bonded base pairs with a slightly decreased rise per residue and a slightly increased helical winding angle. An analysis of the model yields several testable predictions. For example, we predict probability 0.026 for a base pair to be open at 25°C, a value close to that measured by hydrogen‐exchange experiments. Other predictions involve matters like the variation of persistence length with ionic strength and temperature, the variation of helical winding angle with temperature, and the kinetics of heat denaturation. An additional result of the analysis is an explanation of the high degree of local stiffness of the DNA molecule. Strong resistance to bending fluctuations is provided from two sources: increased polyelectrolyte repulsion among phosphate groups in the axially compressed stacks between open base pairs and the tendency of stacking forces to oppose opening of a base pair. Stacking forces, however, also support compression of the stacks between open base pairs, so that the net effect of stacking forces on elastic bending of DNA is small relative to the polyelectrolyte effect. If the ionic charges on the phosphate groups were absent, DNA would spontaneously fold, driven by the entropy gained when about 1% of its base pairs open.