Model solvent effects, related to DNA stability in water, are explored with molecular
dynamics (MD) simulations:(i) hydrophobicity and (ii) salt modulated electrostatic effects …

Background Most biological processes involve water, and the interactions of biomolecules
with water affect their structure, function and dynamics. Scope of review This review …

The interaction of nucleic acids with metal cations, particularly magnesium, plays an
important role in stabilizing their tertiary structure. An accurate quantitative description of …

An explicit ion, implicit water solvent model for molecular dynamics was developed and
tested with DNA and RNA simulations. The implicit water model uses the finite difference …

We calculate the water and ion spatial distributions around charged oligonucleotides using
a renormalized three-dimensional reference interaction site theory coupled with the HNC …

Intermolecular potentials to describe the interaction between nucleic acid bases and water
are derived using ab initio calculations with a double-zeta plus one polarization function …

We report observation and photoelectron spectroscopic characterization of sodium
cationization on four doubly deprotonated mononucleotide dianions Na+·[dNMP-2H] 2–(N …

Because proteins and DNA interact with each other and with various small molecules in the
presence of water molecules, we cannot ignore their hydration when discussing their …

The ionic atmosphere around a nucleic acid regulates its stability in aqueous salt solutions.
One major source of complexity in biological activities involving nucleic acids arises from the …

The interactions between Na+ or Mg2+ ions with different parts of single-stranded RNA
molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in …