We present a systematic study of the long-timescale dynamics of the Drew–Dickerson
dodecamer (DDD: d(CGCGAATTGCGC) 2 ) a prototypical B-DNA duplex. Using our newly …

We present a multi-laboratory effort to describe the structural and dynamical properties of
duplex B-DNA under physiological conditions. By processing a large amount of atomistic …

… In principle, if there are m states for each inter base pair distribution, we should expect m 6
states at the bps level (ie for bimodality m = 2 we could expect 64 different stiffness matrices …

The structure of B-DNA, the physiological form of the DNA molecule, has been a central
topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was …

We used extensive molecular dynamics simulations to study the structural and dynamic
properties of the central d(TpA) step in the highly polymorphic d(CpTpApG) tetranucleotide. …

The rules governing sequence-specific DNA–protein recognition are under a long-standing
debate regarding the prevalence of base versus shape readout mechanisms to explain …

Although chemically close to DNA, RNA can adopt a wide range of structures from regular
helices to complex globular conformations, showing a complexity similar to that of proteins. …

We have used a variety of theoretical and experimental techniques to study the role of four
basic amino acids–Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid–on the structure…

Last generation of force-fields are raising expectations on the quality of molecular dynamics
(MD) simulations of DNA, as well as to the belief that theoretical models can substitute …

Sequence-dependent properties of the DNA duplex have been accurately described using
extensive molecular dynamics simulations. The RNA duplex meanwhile─which is typically …