The elastic energy of sharply bent nicked DNA

¹  Department of Physics and Astronomy, University of California Los Angeles Los Angeles, CA 90095-1547, USA
²  Department of Chemistry and Biochemistry, and the California Nanosystems Institute, University of California Los Angeles - Los Angeles, CA 90095-1547, USA

Corresponding author: zocchi@physics.ucla.edu

Received: 19 February 2010
Accepted: 24 March 2010

Abstract

We obtain measurements of the elastic energy of short (18–30 bp) molecules of ds DNA constrained into a sharply bent conformation, using a thermodynamic method with the DNA in solution. We consider the case where there is one nick in the ds DNA, and find that the system develops a kink at a critical torque ≈ 27 pN × nm. In this regime the elastic energy is linear in the end-to-end distance (EED). For smaller torques the DNA is smoothly bent and described by the worm-like–chain energy, which is also approximately linear in the EED, but with a different slope. Thus we access both the high and low elastic energy regimes, and the transition between the two.