11 papers
Sequence-dependent B-A transitions in DNA in silico: Electrostatic condensation mechanism
Alexey K. Mazur
Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties…
Relaxation of DNA curvature by single stranded breaks: Simulations and experiments
Dimitri E. Kamashev, Alexey K. Mazur
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal…
Reversible B/A Transitions in Single DNA Molecule Immersed in A Water Drop
Alexey K. Mazur
Clarification of the detailed mechanisms involved in the DNA polymorphism is an important challenge for computational molecular biophysics. This paper reports about reversible A/B…
DNA Dynamics in A Water Drop
Alexey K. Mazur
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent…
Simulated and Experimental Bending Dynamics in DNA with and without A-Tracts
Alexey K. Mazur, Dimitri E. Kamashev
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though…
Molecular Dynamics Studies of Sequence-directed Curvature in Bending Locus of Trypanosome Kinetoplast DNA
Alexey K. Mazur
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this ef…