Nonlocal structural effects of water on DNA homology recognition.

The mechanism behind mutual recognition of homologous DNA sequences prior to genetic recombination is one of the remaining puzzles in molecular biology. Leading models of homology recognition, based on classical electrostatics, neglect the short-range nonlocal screening effects arising from structured water around DNA, and hence may only provide insight for relatively large separations between interacting DNAs. We elucidate the role of the effects of the nonlocal dielectric response of water on DNA-DNA interaction and show that these can dramatically enhance the driving force for recognition.

Electric field of DNA in solution: who is in charge?

In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a substantial electric field in its vicinity, which is screened by buffer electrolyte at longer distances from the DNA. Such field has been explored so far predominantly within the scope of a primitive model of the electrolytic solution, not considering more complicated structural effects of the water solvent. In this paper we investigate the distribution of electric field around DNA using linear response nonlocal electrostatic theory, applied here for helix-specific charge distributions, and compare the predictions of such theory with specially performed fully atomistic large scale molecular dynamics simulations. The main finding of this study is that oscillations in the electrostatic potential distribution are present around DNA, caused by the overscreening effect of structured water. Surprisingly, electrolyte ions at physiological concentrations do not strongly disrupt these oscillations, and rather distribute according to these oscillating patterns, indicating that water structural effects dominate the short-range electrostatics. We also show that (i) structured water adsorbed in the grooves of DNA lead to a positive electrostatic potential core, (ii) the Debye length some 10 {\AA} away from the DNA is reduced, effectively renormalised by the helical pitch of the DNA, and (iii) Lorentzian contributions to the nonlocal dielectric function of water, effectively reducing the dielectric constant close to the DNA, enhances the overall electric field. The impressive agreement between the atomistic simulations and the developed theory substantiates the use of nonlocal electrostatics when considering solvent effects in molecular processes in biology.