A chiral theory of DNA supercoiling

We propose to bring together three threads of recent progress to develop anew chiral theory of DNA supercoiling. The three threads are i) theelectrostatic theory of interacting helical charge distributions, ii) themechanical theory of elastic braids, and iii) a new efficient approach toderive equilibrium equations for geometric variational problems. The newtheory will for the first time introduce explicitly chiral interactions intothe description of supercoiling, and will uncover the effects driven by theseinteractions. Specifically, we will build a theory to describe foursupercoiling situations: (i) spontaneous formation of free-ended braids,(ii) conformations of braided DNA in single-molecule manipulation experiments,and formation of writhes in (iii) torsionally stressed and (iv) initiallyrelaxed looped DNA, triggered by changing environment.In recent years systematic experimental studies of the torque response ofplectonemically supercoiled and braided DNA have been performed, while moreare anticipated. These require a quantitative theory that better accountsfor the complex DNA-DNA interactions. We will develop that theory. The mainpart of this project is theoretical, but the predictions of the theory willbe tested against new experiments that will be performed in collaborationwith the named Project Partners.