A semiflexible chain model of local denaturation in double-stranded DNA

Double-stranded DNA (dsDNA) is known to form a locally denatured structure ("bubble") below its denaturation temperature (T(c)). We have investigated the physical behavior of the bubbles using a model of dsDNA as two wormlike chains containing interacting complementary base pairs. The model incorporates two biologically relevant features, i.e., semiflexibility of the strand and overdamping nature of aqueous background. Computer simulations using the Langevin equation are performed to examine the size distribution and dynamics of bubbles. The results show that the entropy associated with semiflexibility of DNA sensitively affects the size distribution and lifetime of bubble. In particular, the lifetime grows with bubble size m as m(2.7) at temperature close to T(c), which is consistent with our analysis based on a stochastic model of bubble size dynamics.