Dynamic light scattering studies of internal motions in DNA. II. Clean viral DNAs

Abstract

SynopsisInternal Brownian motions of clean $29 and A-DNAs have been studied using photoncorrelation techniques a t both visible (A, = 632.8 nm) and uv (A" = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K 2 = 19 X 10' O cm-*, can in every case be satisfactorily simulated by a Rouse-Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single-strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NHIC1, or with molecular weight or GC content. The single-strand breaks have no effect a t pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints a t those pHs. The failure of either single-strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse-Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light-scattering Dapp vs K 2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light-scattering Do values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%. INTRODUCTIONThe internal Brownian motions of flexible macromolecules provide a potential means for studying their static and dynamic mechanical properties, such as flexional and torsional rigidities, structural inhomogeneities or joints, and frictional properties. For macromolecules of sufficiently great physical extent, the polarized dynamic light scattering a t high angles contains significant contributions from internal which may in some cases completely dominate the observed intensity autocorrelation functions. Unfortunately, theoretical predictions for the dynamic light scattering from very realistic models of semiflexible polymers are not yet available, so recourse must temporarily be made to oversimplified models, such as those of Rouse,6 Zimm,7 and Harris and Nevertheless, for the comparatively long wavelength fluctuations (in the distribution of polymer segments) that are actually accessible to current dynamic light Biopolymers, Vol. 19, 1451-1474 is the apparent diffusion coefficient at a given angle, T is the exponential decay time, and K is the scattering vector. Subsequent discoveryg of pronounced variations in those model parameters in the pH range 9-10 for both calf thymus DNA and an initial $29 viral DNA sample provided strong evidence for the existence of titratable joints...

Chromatin Dynamics

“…The diffusion of DNA in concentrated solutions (semidilute) has diffusion coefficients on the order of 10 −9 to 10 −8 cm 2 s −1 (98, 119), which is approximately four orders of magnitude higher than that of chromatin. Similarly, the dynamics of DNA is lower by several orders of magnitude than the diffusion constant of proteins, with diffusion constants of 10 −6 cm 2 s −1 for proteins in aqueous solution and 10 −8 to 10 −7 cm 2 s −1 in the cytoplasm (69).…”

Effects of Na+and Mg2+on the Structures of Supercoiled DNAs: Comparison of Simulations with Experiments

“…Additional dynamic light scattering (DLS) measurements were performed over the same angular range with 351.1 nm light from an Ar-ion laser. Details concerning the DLS apparatus and experimental protocols have been described (Thomas & Schurr, 1979;Thomas et al, 1980;Lin et al, 1981;Wilcoxon & Schurr, 1983;Wilcoxon, 1983;Kim et al, 1993). Intensity autocorrelation functions ( I(0)I(t) ) were determined using our locally constructed 4-bit × n digital photon correlator.…”

Cross-correlation laser scattering

“…The fluctuations in the scattering factor in this case are due to intramolecular interference changes reflecting the relative motion of segments along the DNA molecule. This internal interference depends on the scattering wavelength both by its amplitude and its correlation time (15)(16)(17)(18). Dependence that follows k2 (19) and k3 (20) was predicted theoretically.…”