Large-amplitude fast motions in double-stranded DNA driven by solvent thermal fluctuations.

The nature of the internal dynamics of double-stranded DNA in aqueous environment remains to be established. We consider the motions to stem from thermal fluctuations/dissipations of the harmonic modes of beads (bases and sugars) in a cylindrical geometry that are tracked through the stochastic Langevin trajectories; these are characterized by parameters obtained from published data. The present approach has allowed a comparative study of the dynamics for DNA lengths in the range of 20-600 base pairs.

Maintenance of open DNA base pairs through histone acetylated lysine-purine interaction leading to transcriptional activation: a proposed mechanism.

Post-translational acetylation of lysines of the histone N-terminal tails is known to induce transcriptional activation, and thus plays a major role in gene regulation. A mechanism for this effect is suggested by our recent finding that the initial 'solvation' network, which is formed around the purines of base pairs immediately following their opening, has the tendency to be preserved. The experiments involved studying the solvation of nucleosides in water-alcohol mixtures; these systems model the hydrophobic/hydrophilic effects that participate in the interaction between histone-tail amino acid residues and nucleosomal DNA base pairs following their opening by the action of DNA-binding proteins in conjunction with remodeling complexes.