Shape and energetics of DNA plectonemes

The mechanics of DNA at length scales of few hundred nanometers is described by a fluctuating elastic rod model. In this paper we couple the fluctuating rod model with a variational method for describing plectonemes to unravel the mechanics of some recent single molecule experiments. We are able to reproduce some features seen in these experiments which analyze plectoneme formation in DNA under tension by continuously twisting it and tracking its end-to-end distance, torque, etc., as a function of the added link. Our model accounts for configurational entropy and electrostatics in the plectoneme. We find that configurational entropy makes a significant contribution to the mechanics of the plectoneme while electrostatics (in the presence of monovalent counterions) plays a relatively minor role.