Correlated local bending of DNA double helix and its effect on the cyclization of short DNA fragments

We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the persistence length of DNA base pairs) cannot be described by the traditional worm-like chain (WLC) model, e.g., the observed ring closure probability is much higher than predicted. To explain these observations, DNA flexibility is investigated with explicit considerations of a new length scale base pairs, over which DNA local bend angles are correlated. In this correlated worm-like chain (C-WLC) model, a finite length correction term is analytically derived and the persistence length is found to be contour length dependent. While our model reduces to the traditional worm-like chain model when treating long DNA at length scales much larger than , it predicts that DNA becomes much more flexible at shorter sizes, which helps explain recent cyclization measurements of short DNA fragments around base pairs.