Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter

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Abstract
The magnitude and uniformity of the torsion elastic constant (.alpha.) of linear pBR322 DNA and supercoiled pBR322 DNAs with high-twist (.sigma. = -0.083) and normal-twist (.sigma. = -0.48) are measured in 0.1 M NaCl as a function of added chloroquine/base-pair ratio (chl/bp) by studying the fluorescence polarization anisotropy (FPA) of intercalated ethidium dye. The time-resolved FPA is measured by using a picosecond dye laser for excitation and time-correlated single-photon counting detection. A general theory is developed for the binding of ligands that unwind superhelical DNAs, and the simultaneous binding of two different intercalators is treated in detail. The equilibrium constant (K) for binding chloroquine to linear pBR322 DNA and the number (r) of bound chloroquines per base pair are determined from the relative amplitude ratio of the slow (normally intercalated) and fast (free) components in the decay of the (probe) ethidium fluroescence intensity as a function of chl/bp. For chloroquine binding to supercoiled pBR322 DNAs, the intrinsic binding constant is assumed to be the same as for the linear DNA, but the twist energy parameter ET (N times the free energy to change the linking number from 0 to 1 in units of kBT) is regarded as adjustable. Using the best-fit ET, the binding ratios r are calculated for each chl/bp ratio. Twist energy parameters are also determined for ethidium binding to these supercoiled DNAs by competitive dialysis. For chloroquine binding, we obtain ET = 360 and 460 respectively for the normal-twist and high-twist supercoiled DNAs. For ethidium binding the corresponding values are ET = 280 .+-. 70 and 347 .+-. 50. Like other dye-binding values, these are substantially lower than those obtained by ligation methods. In the absence of chloroquine, the torsion constants of all three DNAs are virtually identical, .alpha. = (5.0 .+-. 0.4) .times. 10-12 dyn .cntdot. cm. For linear pBR322 DNA, the magnitude and uniformity of .alpha. remain unaltered by intercalated chloroquine up to r = 0.19. This finding argues that the FPA is not significantly relaxed by diffusion of any kinks or solitons. If .alpha.d denotes the torsion constant between a dye and a base pair and .alpha.0 that between two base pairs, then our data imply that .alpha.d/.alpha.0 lies in the range 0.65-1.64, with a most probable value of 1.0. For the supercoiled DNAs, .alpha. remains uniform, but its magnitude decreases significantly with increasing intercalated chloroquine through the point where the effective superhelix density vanishes and even up to substantial positive superhelix densities. The signficiant difference in observed FPA dynamics between the relaxed (by intercalator) supercoiled DNAs and the linear DNA with the same amount of bound chloroquine profoundly contradicts any notion that the local structures and dynamics of such species are equivalent. At very high chl/bp ratios both linear and supercoiled DNAs exhibit evidence of substantial structural changes. The torsion constant increases for the linear DNA but drops for the supercoiled DNAs, which are substnatially positively twisted (.sigma. .gtoreq. 0.06) at that point.