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Sequence-Dependent Twist-Stretch Coupling in DNA

Timothée Lionnet ^* and Filip Lanka 

^* Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique,UMR 8550, Ecole Normale Supérieure, 75005 Paris, France; and Institut de Mathématiques B, Ecole Polytechnique Fédérale de Lausanne, Station 8, CH-1015 Lausanne, Switzerland

Correspondence: Address reprint requests and inquiries to Filip Lanka, E-mail: filip.lankas{at}epfl.ch.

Recent single-molecule micromanipulation experiments on DNA subject to small distortion revealed positive coupling between DNA stretching and twisting—for instance, DNA elongates when overtwisted. Here we propose a method to calculate the twist-stretch coupling constant specific to a DNA fragment of a given sequence. The method employs a sequence-dependent dinucleotide force field and is based on constrained minimization of the fragment's deformation energy. Using a force field inferred from atomistic molecular dynamics simulations, we obtain the twist-stretch coupling for random sequence to be 0.30 nm/turn, close to experimental values. An exhaustive calculation for all oligomers of nine basepairs yields values between 0.14 and 0.45 nm/turn, positively correlated with the contents of pyrimidine-purine steps in the sequence. Our method is simple to use and allows one to explore the hypothesis that some sequences may be optimized for twist-stretch coupling.