Fluorescein mercuric acetate as a probe of the dynamic structure of double-helical DNA

Fluorescein mercuric acetate causes the unwinding of DNA and binds to the separated bases. The kinetics of this unwinding process were studied using both untreated DNA and sonicated DNA at various pH values (6.8--9.3) and Na+ concentrations (10--250 mM). The unwinding process is explained by assuming a nucleation in the middle of DNA (as a function of time) as well as at the helix ends (immediately after addition of this reagent) and the subsequent growth of the nuclei. The frequency of the nucleation in the middle of DNA appears to be markedly affected by pH and Na+ concentration. In contrast, the reaction rate of this reagent with heat-denatured DNA was almost insensitive to these environmental variables. The growth rate of the unwinding nuclei in double-stranded DNA also appears insensitive. The most important implication of this study is that in the low pH range (6.8--7.5) the reactivity of thermally-induced locally open regions in the middle of double-helical DNA toward this reagent appears much higher than that of heat-denatured DNA. Since this reagent is negatively charged, these findings are discussed in view of its electrostatic interaction with the locally open regions.