Temperature dependence of the dynamic light scattering of linear phi 29 DNA: implications for spontaneous opening of the double-helix.

Abstract

AbstractThe apparent diffusion coefficient Dapp(K) of a single sample of linear ϕ29 DNA (Mr = 11.5 × 106) has been measured as a function of K2 from 0.21 × 1010 to 20 × 1010 cm−2 at a variety of temperatures from −0.5 to +70°C. Dapp(K) scales closely as T/η at every value of K2. All of these data are simulated by a particular Rouse‐Zimm model comprised of a constant number of subchains with constant rms subchain extension b = 1057 Å and an apparent subchain diffusion coefficient Dplat that scales at T/η from −0.5 to +70°C. It is inferred from these results that any temperature dependence of the flexural and torsional rigidities of DNA must be rather weak. A less firm inference is that these rigidities actually increase slightly with temperature, possibly in proportion to T, which is weak T dependence in this context. These findings eliminate the possibility that spontaneous transient opening of the DNA structure has any significant effect on the flexural and torsional rigidities of the DNA filament. A review of the most pertinent available data from other experiments concerning spontaneous transient opening of the DNA is presented. The formaldehyde kinetics data do not unequivocally implicate an open base‐pair intermediate and provide only an upper limit to the fraction of open base pairs. An alternative nonopening model with a protonated doorway state is proposed to accommodate the hydrogen‐exchange data. It is concluded that there is presently no incontrovertible evidence for a fraction of unstacked open base pairs greater than about 10−4.