Torsional Rigidities of Weakly Strained DNAs

¹ University of Washington

^* To whom correspondence should be addressed. E-mail: schurr{at}chem.washington.edu.

Submitted on April 22, 2006
Revised on June 7, 2006
Accepted on 21 August 2006

	Abstract

Measurements on unstrained linear and weakly strained large (340 bp) circular DNAs yield torsional rigidities in the range, C = 170-230 fJ fm. However, larger values in the range, C = 270-420 fJ fm, are typically obtained from measurements on sufficiently small (247 base-pairs) circular DNAs, and values in the range, C = 300-450 fJ fm, are obtained from experiments on linear DNAs under tension. A new method is proposed to estimate torsional rigidities of weakly supercoiled circular DNAs. Monte Carlo simulations of the supercoiling free energies of solution DNAs, and also of the structures of surface confined supercoiled plasmids, were performed using different trial values of C. The results are compared with experimental measurements of the twist energy parameter,E_T, that governs the supercoiling free energy and also with AFM images of surface confined plasmids. The results clearly demonstrate that C-values in the range, 170-230 fJ fm, are compatible with the experimental observations, whereas values in the range, C 269 fJ fm, are incompatible with those same measurements. These results strongly suggest that the secondary structure of DNA is altered by either sufficient coherent bending strain or sufficient tension so as to enhance its torsional rigidity.

Key Words: Monte Carlo simulations, supercoiling free energy, surface confined DNAs, twist energy parameter, writhe