8th Liquid Matter Conference September 6-10, 2011 Wien, Austria ...

P4.8Fri 911:10-14:00Helix specific electrostatics in DNA braids and supercoilsRuggero Cortini, 1 Alexei Kornyshev, 1 Dominic Lee, 1 and Sergey Leikin 21 Imperial College, Exhibition Road, SW7 2AZ, London, United Kingdom2 Eunice Kennedy Shriver National Institute of Child Health and Human Development,Bethesda, Ud States of AmDNA supercoiling in vivo is important in plasmids and during the DNA replication process. So far,many theoretical studies of supercoils have focused on the elastic properties of DNA, the inclusionof steric forces and the electrostatic contribution from treating the DNA as a uniformly charged rod.However, overlooking the helical shape of the charged patterns formed by DNA and its counterionsneglects physics that could be important, here. Firstly, electrostatic interactions between helicalcharge patterns cause attraction [1], provided that the DNA charge is sufficiently neutralized bycounter-ions. Secondly, helix specific interactions provide a torque causing tilt, in one direction,between two DNA fragments [1]. Indeed, in braids and supercoils, such a torque breaks positivenegativesupercoil symmetry. In the first part of our study we consider a braid formed by twoDNA molecules modeled as charged helices, where we include base pair dependent distortionsin the helical structure. We show that electrostatic forces may lead to spontaneous braiding, andestimate the DNA pairing energy for a braid [2]. The pairing is more energetically favourablefor homologous pairs (same base pair text) than for nonhomologous ones. Therefore, this mightexplain pairing between only homologues observed in NaCl solution [3]. Next, we construct asimple model for a closed loop supercoil, including the chiral electrostatic interactions. There arevery interesting effects, at sufficient charge neutralization and groove localization of counter-ions.i. ) Positive super-coils are more energetically favourable than negative ones. ii. ) A transitionbetween loosely and tightly wound supercoils as one moves from negative to positive values of thesupercoiling density. iii. ) In positive super-coils the chiral interaction underwinds DNA. [1]A. A.Kornyshev et Al, Rev. Mod. Phys. , 79, 943 [2] R. Cortini et Al, submitted to Biophysical Journal[3]C. Danilowicz et Al, PNAS USA, 106, 198248