The complete bending energy function for nicked DNA

Department of Physics and Astronomy, University of California at Los Angeles - Los Angeles, CA 90095-1547, USA

^a zocchi@physics.ucla.edu

Received: 6 November 2010
Accepted: 25 February 2011

Abstract

We derive an analytic expression for the bending elastic energy of short DNA molecules, valid in the entire range from low to high energies. The elastic energy depends on three parameters: the length of the molecule (2L), the bending modulus B, and a critical torque τ_c at which the molecule develops a kink. In the kinked state, the elastic energy is linear in the kink angle, i.e. the torque at the kink is constant (= τ_c). τ_c depends (weakly) on the sequence around the nick, but is about 27 pN×nm. We measure it for a specific sequence, through experiments where the elastic energy of constrained DNA molecules is directly measured.