RNA molecules play a key role in countless biochemical processes. RNA interactions, which
are of highly diverse nature, are determined by the fact that RNA is a highly negatively …

Hydrating water molecules are believed to be an inherent part of the RNA structure and
have a considerable impact on RNA conformation. However, the magnitude and mechanism …

We have carried out an extended reference set of explicit solvent molecular dynamics
simulations (63 simulations with 8.4 μs of simulation data) of canonical A-RNA duplexes …

Nanosecond length simulations applying the particle mesh Ewald method within AMBER 4.1
on canonical A-form and B-form geometries of d [CCAACGTTGG] 2, r [CCAACGUUGG] 2 …

The biological functions of RNA range from gene regulation through catalysis and depend
critically on its structure and flexibility. Conformational variations of flexible, non-base-paired …

As a result of important methodological advances, the number of molecular dynamics (MD)
simulations related to RNA systems has become significant, and simulations on more than …

We present an extensive molecular dynamics study (0.6 μs in total) on three A-RNA
duplexes. The dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) …

The roles that metal ions play in the structure and dynamics of RNA molecules are long-
standing problems that have been studied extensively but are still not well understood. Here …

A full understanding of RNA-mediated biology would require the knowledge of three-
dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D …

When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2′-O-methyl RNA
residues enhance the duplex stabilities, and this makes it possible to create much better …