Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium
K Hart, N Foloppe, CM Baker, EJ Denning… - Journal of chemical …, 2012 - ACS Publications
The B-form of DNA can populate two different backbone conformations: BI and BII, defined
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …
Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”
F Mocci, A Laaksonen - Soft Matter, 2012 - pubs.rsc.org
Nucleic acids are highly charged polyelectrolytes. Their interactions with counterions are of
great importance for their structural stability, conformational behaviour and biological …
great importance for their structural stability, conformational behaviour and biological …
DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson–Crick pairing near graphite surfaces
Single-and double-stranded DNA are increasingly being paired with surfaces and
nanoparticles for numerous applications, such as sensing, imaging, and drug delivery …
nanoparticles for numerous applications, such as sensing, imaging, and drug delivery …
Theoretical study on steric effects of DNA phosphorothioation: B-helical destabilization in Rp-phosphorothioated DNA
YC Zhang, J Liang, P Lian, Y Han, Y Chen… - The Journal of …, 2012 - ACS Publications
Phosphorothioation, with sulfur replacing a nonbridging oxygen of phosphate, has surfaced
in bacterial DNA electrophoresis. To understand structural characteristics of the thio …
in bacterial DNA electrophoresis. To understand structural characteristics of the thio …
Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy
A-tracts in DNA are generally associated with reduced nucleosome occupancy relative to
other sequences, such that the longer the A-tract, the less likely that nucleosomes are found …
other sequences, such that the longer the A-tract, the less likely that nucleosomes are found …