Modified water models with scaled charges are used to investigate solvent polarity effects on
DNA structure. Several intensive molecular dynamics simulations of the DNA EcoRI …

Electrostatic potentials around DNA are obtained by solving the nonlinear Poisson‐
Boltzmann (PB) equation. The detailed charge distribution of the DNA and the different …

Revised Manuscript Received November 8, 1993® abstract: The X-ray crystalstructure of the
pure-spermine form of the left-handed Z-DNA duplex [d (CGCGCG)] 2 has been determined …

The epsilon-modified Poisson− Boltzmann (ϵ-MPB) equations (J. Phys. Chem. B, 2007, 111,
5264) have been solved on a three-dimensional grid for an all-atom geometry model of B …

Department of Biochemistry and Biophysics, Oregon State University, Corvallis,
Oregon97331 Received December 5, 1988; Revised Manuscript Received April 25, 1989 …

A theoretical study of the dynamical structure of the DNA dodecamer d (CGCGAATTCGCG)
based on 140 ps of molecular dynamics simulation including water and counterions is …

The ability to predict macromolecular conformations from sequence and thermodynamic
principles has long been coveted but generally has not been achieved. We show that …

Abstract The B̄ to Ā transition of DNA in water-ethanol solutions has been studied by
circular dichroism. The transition is reversible and co-operative and occurs within a narrow …

Z-DNA, a left-handed isoform of Watson and Crick's B-DNA, is rarely formed without the help
of high salt concentrations or negative supercoiling. However, Z-DNA-binding proteins can …

Molecular modeling is used to study the sequence dependence of conformation and stability
within helically regular duplex Z-DNA. The variations of conformation that are found are …