Structure and dynamics of M13mp19 circular single‐strand DNA: Effects of ionic strength

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Abstract
Dynamic and static light scattering, CD, and optical melting experiments have been conducted on M13mp19 viral circular single-strand DNA as a function of NaCl concentration. Over the 10,000-fold range in concentration from 100 μM to 1.0M NaCl, the melting curves and CD spectra indicate an increase in base stacking and stability of stacked regions with increased salt concentration. Analysis of dynamic light scattering measurements of the single-strand DNA solutions as a function of K2 from 1.56 to 20 × 1010 cm−2 indicates the collected autocorrelation functions are biexponential, thus revealing the presence of two decaying dynamic components. These components are taken to correspond to (1) global translational motions of the molecular center of mass and (2) motions of the internal molecular subunits. From the evaluated relaxation rates of these components, diffusion coefficients D0 and Dplat are determined. The center of mass translational diffusion coefficient D0, varies in a nonmonotonic manner, by 10%, from 3.75 × 10−8 to 3.39 × 10−8 cm2/s over the NaCl concentration range from 100 μM to 1.0M. Likewise, the radius of gyration RG, obtained from static light scattering experiments, varies by 15% from 699 to 830 Å over the same NaCl range. Dplat, the diffusion coefficient of the internal subunits, displays a different dependence on the NaCl concentration and decreases, by nearly 22% in a titratable fashion, from 12.46 × 10−8 to 10.26 × 10−8 cm2/s, when the salt is increased from 100 μM to 1.0M. A semiquantitative interpretation of these results is provided by analysis of the light scattering data in terms of the circular Rouse–Zimm chain. Rouse–Zimm model parameters are estimated from the experimental results, assuming the circular chains are composed of a fixed number of Gaussian segments, N + 1 = 15. The rms displacement of the internal segments, b, is estimated to be the smallest (442 Å) in 100 mM NaCl. Increases of b to 467 Å in 100 μM and 524 Å in 1.0M NaCl are observed. Meanwhile, the hypothetical friction factor of the internal subunits, f, progressively increases as the NaCl concentration is raised. It is inferred from the evaluated Rouse–Zimm model parameters that both the static flexibility of the circular chain and diffusive displacements of the internal subunits decrease with increases in NaCl concentration from 100 mM to 1.0M. These decreases directly contract the salt-dependent behavior of double-stranded DNA, where greater flexibility is observed when the Na+ concentration is increased. The melting and CD measurements indicate the decrease in flexibility and internal motions is due to the formation of nucleotide stacking in the higher NaCl environments. In 100 μM NaCl, where stacking is highly unfavored, a significant electrostatic contribution to the persistence length likely acts to stiffen the molecule. It appears the observable changes in the internal dynamics of M13mp19 single-strand DNA are associated with increases in base stacking that occur from 100 μM to 1.0M NaCl, which apparently induce relatively small perturbations in the overall global tertiary conformation of the DNA.