Effects of Probe-Related Correlations on Local Electrostatic Potentials Around DNA

In this work, we perform a test of effectiveness and accuracy of using different approximations to interpret NMR paramagnetic relaxation enhancements experiment to measure local electrostatic potentials for DNA at ionic strengths from 0.138 to 0.938 M in KCl salt solution with PROXYL spin probes. Continuum Poisson-Boltzmann (PB) theory, multiscale Brownian dynamics, and all-atom molecular dynamics simulations are carried out to predict and interpret local potentials. Local potentials around DNA demonstrate strong salt dependence. Experimental results are in good agreement at 0.138 M ionic strength with continuum theory and simulation. Compared to experiment, the PB and multiscale simulation methods overestimate local potentials in magnitude at medium to high salt concentration. We find that the overestimate is mainly caused by ignoring the probe-probe and probe-ions correlations in the proximity of DNA. The probe-related correlations can be up to 0.4 kcal/mol in certain regions. Comparisons of the experiment and the calculations emphasize not only the importance of orientations of probes but also the probe-related correlations in determination of near-surface-zone potentials.