Extension of torsionally stressed DNA by external force

• Published in: Biophysical journal Vol. 73; no. 1; pp. 123 - 132
• Main Authors: Vologodskii, A.V., Marko, J.F.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.07.1997
• Subjects: Computer Simulation; DNA - chemistry; Models, Structural; Monte Carlo Method; Nucleic Acid Conformation; Osmolar Concentration; Stress, Mechanical; Torque
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/S0006-3495(97)78053-6

Metropolis Monte Carlo simulation was used to study the elasticity of torsionally stressed double-helical DNA. Equilibrium distributions of DNA conformations for different values of linking deficit, external force, and ionic conditions were simulated using the discrete wormlike chain model. Ionic conditions were specified in terms of DNA effective diameter, i.e., hard-core radius of the model chain. The simulations show that entropic elasticity of the double helix depends on how much it is twisted. For low amounts of twisting (less than about one turn per twist persistence length) the force versus extension is nearly the same as in the completely torsionally relaxed case. For more twisting than this, the molecule starts to supercoil, and there is an increase in the force needed to realize a given extension. For sufficiently large amounts of twist, the entire chain is plectonemically supercoiled at low extensions; a finite force must be applied to obtain any extension at all in this regime. The simulation results agree well with the results of recent micromanipulation experiments.