Estimation of the persistence length of DNA from the torsion elastic constant and supercoiling free energy: effect of ethylene glycol.
Two different methods are proposed to estimate the persistence length ( P) of DNA from the measured torsion elastic constant (alpha) and the twist energy parameter ( E T ) that governs the supercoiling free energy. The first method involves Monte Carlo simulations and reversible-work calculations of E T for model DNAs that possess the measured alpha and selected trial values of P. Comparison of the computed E T values with the experimental value allows estimation of P (or equivalently the bending elastic constant (kappa beta)) by interpolation. A far simpler, though less accurate, alternative is to solve a previously conjectured analytical relation connecting E T , alpha, kappa beta (or P), and an unknown "constant" ( B). The present simulations are used to ascertain the optimum value of B and to assess the validity and accuracy of that relation. Within the simulation errors, P values obtained from the measured alpha and E T via this analytical expression agree with those determined from the simulations and E T values reckoned from the input alpha and kappa beta by this analytical expression agree with the corresponding simulated values. Although B is found to be insensitive to variation in alpha, it appears to decline slightly with increasing kappa beta. The original analytical expression is modified to take this apparent variation of B with kappa beta into account. By using this modified analytical relation to estimate P (from the measured alpha and E T ) or E T (from the input alpha and kappa beta), much closer agreement is obtained respectively with the values of P or E T obtained from the simulations. As specific examples, these methods are applied to determine P in 0 and 20 w/v % ethylene glycol, which has been shown to induce a structural transition in duplex DNA.
Rangel
David P
DP
Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
Fujimoto
Bryant S
BS
Schurr
J Michael
JM
D004278:DNA, Superhelical / Q000737:chemistry*; D004548:Elasticity / Q000187:drug effects*; D019855:Ethylene Glycol / Q000494:pharmacology*; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation / Q000187:drug effects; D015203:Reproducibility of Results; D013816:Thermodynamics; D054159:Torsion, Mechanical
D004278:DNA, Superhelical; D019855:Ethylene Glycol