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

Internal Brownian motions of clean ?29 and λ-DNAs have been studied using photon-correlation techniques at both visible (λ₀ = 632.8 nm) and uv (λ₀ = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K² = 19 × 10¹⁰ cm^?2, 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 NH₄Cl, or with molecular weight or GC content. The single-strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at 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 D_app vs K² curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light-scattering D₀ values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.