The B form of DNA exists in equilibrium with the Z form and is mainly affected by sequence,
electrostatic interactions, and steric effects. C8-purine substitution shifts the equilibrium …

We have analyzed the non-covalent interactions observed in the Z-DNA structure by
examining structures retrieved from the nucleic database (NDB) and by using high level ab …

Abstract Modified Poisson-Boltzmann (MPB) equations have been numerically solved to
study ionic distributions and mean electrostatic potentials around a macromolecule of …

We present an analytical, Green-function-based model for the electric potential of DNA in
solution, treating the surrounding solvent with the Debye-Huckel approximation. The partial …

Understanding how DNA molecules interact with other biomolecules is related to how they
utilize their functions and is therefore critical for understanding their structure–function …

DNA carries an inherent polymorphism, which surfaces under various external conditions.
While B-form remains predominant under normal physiological conditions for most of the …

An explicit ion, implicit water solvent model for molecular dynamics was developed and
tested with DNA and RNA simulations. The implicit water model uses the finite difference …

The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double
helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long …

Alternating pyrimidine-purine sequences typically form Z-DNA, with the pyrimidines in the
anti and purines in the syn conformations. The observation that dC and dT nucleotides can …

We calculate the water and ion spatial distributions around charged oligonucleotides using
a renormalized three-dimensional reference interaction site theory coupled with the HNC …