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 review molecular dynamics simulations of nucleic acids, including those completed from
1995 to 2000, with a focus on the applications and results rather than the methods. After the …

We present a comprehensive software package, 3DNA, for the analysis, reconstruction and
visualization of three‐dimensional nucleic acid structures. Starting from a coordinate file in …

Background: The collagen triple helix is a unique protein motif defined by the supercoiling of
three polypeptide chains in a polyproline II conformation. It is a major domain of all collagen …

In both DNA and RNA, stretches of guanine bases can form stable four-stranded helices in
the presence of sodium or potassium ions. Sequences with a propensity to form guanine …

Despite structural differences between the right-handed conformations of A-RNA and B-
DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their …

The Escherichia coli catabolite activator protein (CAP) activates transcription at P lac, P gal,
and other promoters through interactions with the RNA polymerase α subunit carboxyl …

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 …

Water distributions around phosphate groups in 59 B-, A-, and Z-DNA crystal structures were
analyzed. It is shown that the waters are concentrated in six hydration sites per phosphate …

The crystal structure of the RNA duplex [r (CCCCGGGG)] 2 has been refined to 1.46 Å
resolution with room temperature synchrotron diffraction data. This represents the highest …