With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their
experimentally determined structures using molecular dynamics simulations initialized in the …

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 …

Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an
atomic level of detail the conformational changes undergone by proteins. The application of …

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al.
AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were …

Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …

Molecular dynamics (MD) simulations became a leading tool for investigation of structural
dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force …

Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent
transient opening events (fraying). Accurate modeling of this process is important because of …

In recent years, researchers have identified certain RNAs as druggable targets for small
molecules to treat several human pathologies. However, these regulatory RNAs are …

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last
decades, base stacking has been extensively studied by experimental and theoretical …