Specific Coordination Mode and Electrostatic Ion Atmosphere Effects of Divalent Cations Regulating Spatially Crossing Configurations of DNA Duplexes

摘要

The double helical structure of a DNA duplex exhibits an intrinsic trend of forming a superhelix, which preferentially induces spatially crossing configurations of intramolecular DNA duplexes. Since DNA crossovers are closely related to the regulation of various biological functions, their physical properties such as thermodynamic stability were investigated in this study by employing molecular dynamics (MD) simulations under various ionic conditions (Mg2+ concentrations of 0-120 mM). Our MD simulations indicated that specific Mg2+ coordination modes contributed to the formation and stabilization of the right-handed crossover DNA duplexes in a manner independent of the Mg2+ concentration. By contrast, the dissociation free energy of crossover DNA duplexes (Delta G(d)) was correlated with the Mg2+ concentration, which was indicated to be subject to the atomistic plasma model based on Debye-litickel theory. Thus, the distinct roles of solvated Mg2+, i.e., the specific binding and electrostatic ion atmosphere effects, were revealed to regulate the structural and thermodynamic features of spatially crossing DNA duplexes, respectively.