The energetics of the BZ transition in DNA
SM Mirkin, VI Lyamichev, VP Kumarev… - Journal of …, 1987 - Taylor & Francis
The paper deals with the energetics of the transition to left-handed Z form in DNA with an
arbitrary base sequence. There is a brief outline of the statistical-mechanical model of the BZ …
arbitrary base sequence. There is a brief outline of the statistical-mechanical model of the BZ …
Z‐DNA crystallography
PS Ho, BHM Mooers - Biopolymers: Original Research on …, 1997 - Wiley Online Library
We review the effect of sequence on the structure of left‐handed Z‐DNA in single crystals.
The various substituent groups that define a nucleotide base as guanine, cytosine, thymine …
The various substituent groups that define a nucleotide base as guanine, cytosine, thymine …
DNA structure: what's in charge?
KJ McConnell, DL Beveridge - Journal of molecular biology, 2000 - Elsevier
DNA structure is well known to be sensitive to hydration and ionic strength. Recent
theoretical predictions and experimental observations have raised the idea of the intrusion …
theoretical predictions and experimental observations have raised the idea of the intrusion …
[HTML][HTML] The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation
MA Kastenholz, TU Schwartz, PH Hünenberger - Biophysical journal, 2006 - cell.com
The transition between the B and Z conformations of double-helical deoxyribonucleic acid
(DNA) belongs to the most complex and elusive conformational changes occurring in …
(DNA) belongs to the most complex and elusive conformational changes occurring in …
A-to B-DNA transition in AMBER force fields and its coupling to sugar pucker
M Zgarbová, P Jurecka, J Sponer… - Journal of Chemical …, 2018 - ACS Publications
The A/B transition is a basic element of DNA conformational change. Because of its
involvement in the sensing of the ionic conditions by DNA and in specific protein–DNA …
involvement in the sensing of the ionic conditions by DNA and in specific protein–DNA …
Effects of 5 cytosine methylation on the BZ transition in DNA restriction fragments and recombinant plasmids
J Klysik, SM Stirdivant, CK Singleton… - Journal of Molecular …, 1983 - Elsevier
Alternating (dC-dG) n regions in DNA restriction fragments and recombinant plasmids were
methylated at the 5 position of the cytosine residues by the HhaI methylase. Methylation …
methylated at the 5 position of the cytosine residues by the HhaI methylase. Methylation …
Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure
We have investigated to what extent molecular dynamics (MD) simulations can reproduce
DNA sequence-specific features, given different electrostatic descriptions and different cell …
DNA sequence-specific features, given different electrostatic descriptions and different cell …
Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson‐Boltzmann approach
TJ Robbins, JD Ziebarth, Y Wang - Biopolymers, 2014 - Wiley Online Library
The ion atmosphere created by monovalent (Na+) or divalent (Mg2+) cations surrounding a
B‐form DNA duplex were examined using atomistic molecular dynamics (MD) simulations …
B‐form DNA duplex were examined using atomistic molecular dynamics (MD) simulations …
Inclusion of ionic interactions in force field calculations of charged biomolecules–DNA structural transitions
R Klement, DM Soumpasis, EV Kitzing… - … : Original Research on …, 1990 - Wiley Online Library
The potential of mean force (PMF) approach for treating polyion–diffuse ionic cloud
interactions [DM Soumpasis (1984) Proceedings of the National Academy of Sciences USA …
interactions [DM Soumpasis (1984) Proceedings of the National Academy of Sciences USA …
The conformational effect of para-substituted C8-arylguanine adducts on the B/Z-DNA equilibrium
V Vongsutilers, DJ Phillips, BC Train, GR McKelvey… - Biophysical …, 2011 - Elsevier
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 …
electrostatic interactions, and steric effects. C8-purine substitution shifts the equilibrium …