Differential Impact of the Monovalent Ions Li+, Na+, K+, and Rb+ on DNA Conformational Properties

The present report demonstrates that the conformational properties of DNA in solution are sensitive to the type of monovalent ion. Results are based on the ability of a polarizable force field using the classical Drude oscillator to reproduce experimental solution X-ray scattering data more accurately than two nonpolarizable DNA models, AMBER Parmbsc0 and CHARMM36. The polarizable model is then used to calculate scattering profiles of DNA in the presence of four different monovalent salts, LiCl, NaCl, KCl, and RbCl, showing the conformational properties of DNA to vary as a function of ion type, with that effect being sequence-dependent. The primary conformational mode associated with the variations is contraction of the DNA minor groove width with decreasing cation size. These results indicate that the Drude polarizable model provides a more realistic representation of ion-DNA interactions than additive models that may lead to a new level of understanding of the physical mechanisms driving salt-mediated biological processes involving nucleic acids.