CIRCULARIZATION OF SMALL DNAS IN THE PRESENCE OF ETHIDIUM - A THEORETICAL-ANALYSIS

A rigorous theory is developed for ethidium binding to linear and circ ular DNAs and for the ratios of topoisomers produced upon ligation of an equilibrium population of noncovalently closed circles in the prese nce of ethidium. Assuming an unwinding angle phi(E) = 26 degrees for i ntercalated ethidium, optimum values of the intrinsic binding constant , K-E = 7.16 X 10(4)M(-1), the intrinsic twist, l(0) = 23.746 turns, a nd twist energy parameter, E(t) = 5250, are obtained by fitting the pr esent theory to the data of Shore and Baldwin [(1993) Journal of Molec ular Biology, Vol. 170, pp. 983-1007] for a 247 base pair DNA. A very good fit is achieved with these optimum values, but a poor fit results when the parameters estimated by Shore and Baldwin are employed in th e same theory. Three assumptions employed in the analysis of Shore and Baldwin are found to be not strictly valid. Adoption of the present s ubstantially larger E(t) value as representative of their short DNAs w ould allow the E(t) vs N data of Shore and Baldwin to conform to the s hape predicted by Shimada and Yamakawa [(1985) Journal of Molecular Bi ology, Vol. 184, pp. 319-329] and Frank-Kamenetskii et al. [(1985) Jou rnal of Biomolecular Structure and Dynamics, Vol. 2, pp. 1005-1012], a nd would imply that all of their DNAs exist in a substantially stiffer than normal state. (C) 1994 John Wiley & Sons, Inc.