The role of the dispersion energy and electrostatic energy on the geometry and stability of
the B-DNA helix was investigated. Both molecular dynamics simulations with empirical force …

The effects of monovalent (Na+) and divalent (Mg++) cations on the temperature and
breadth of the helix–coil transition of phage DNA have been investigated. The experimental …

DNA is a negatively charged biopolymer composed of monomeric nucleotides each carrying
on average a net (− 1) charge concentrated in the region of the phosphate backbone. In …

We performed three 3-ns molecular dynamics simulations of d (CGCGAATTCGCG) 2 using
the AMBER 8 package to determine the effect of salt concentration on DNA conformational …

The dependence of the effective force on the distance between two DNA molecules was
directly computed from a set of extensive all-atom molecular dynamics simulations. The …

The high charge density of nucleic acids and resulting ion atmosphere profoundly influence
the conformational landscape of RNA and DNA and their association with small molecules …

Z-DNA duplexes are a particularly complicated test case for current force fields. We
performed a set of explicit solvent molecular dynamics (MD) simulations with various …

The dielectric behavior of solvent water around DNA is elicited in terms of Kirkwood−
Grunwald theory from a 14 ns molecular dynamics trajectory of B-DNA developed in a …

Nucleic acids are highly charged polyanionic molecules; thus, the ionic conditions are
crucial for nucleic acid structural changes such as bending. We use the tightly bound ion …

Canonical, right-handed B-DNA can be transformed into noncanonical, left-handed Z-DNA
in vitro at high salt concentrations or in vivo under physiological conditions. The molecular …