Two Intercalation
Mechanisms of Oxazole
Yellow Dimer (YOYO-1) into DNA
10.3390/molecules26123748 · doi-reference
Characterization
of the Binding of the Fluorescent Dyes YO and YOYO to DNA by Polarized
Light Spectroscopy
10.1021/ja00098a004 · doi-reference
Single-molecule kinetics and footprinting
of DNA bis-intercalation: the paradigmatic case of Thiocoraline
10.1093/nar/gkv087 · doi-reference
Structural perturbations in DNA caused
by bis-intercalation
of ditercalinium visualised by atomic force microscopy
10.1093/nar/gkf409 · doi-reference
Kinetic studies
of anthracycline-DNA
interaction by fluorescence stopped flow confirm a complex association
mechanism
10.1021/bi00427a038 · doi-reference
The kinetics of
YOYO-1 intercalation into single molecules
of double-stranded DNA
10.1016/j.bbrc.2010.11.015 · doi-reference
Identification
and hydropathic characterization of structural features affecting
sequence specificity for doxorubicin intercalation into DNA double-stranded
polynucleotides
10.1093/nar/26.20.4721 · doi-reference
Interaction
of doxorubicin with polynucleotides. A spectroscopic study
10.1021/bi401687v · doi-reference
New insights
into the mechanism of the DNA/doxorubicin interaction
10.1021/jp411429g · doi-reference
Deoxyribonucleic
acid binding studies on several new anthracycline antitumor antibiotics.
Sequence preference and structure-activity relationships of marcellomycin
and its analogues as compared to adriamycin
10.1021/bi00585a028 · doi-reference
Induction of stable transcriptional blockage sites
by adriamycin: GpC specificity of apparent adriamycin-DNA adducts
and dependence on iron(III) ions
10.1021/bi00475a032 · doi-reference
Structural comparison
of anticancer drug-DNA complexes: adriamycin and daunomycin
10.1021/bi00462a016 · doi-reference
Ionic effects
on the elasticity of single DNA molecules
10.1073/pnas.94.12.6185 · doi-reference
Bubble nucleation and cooperativity
in DNA melting
10.1016/j.jmb.2004.02.072 · doi-reference
A polarized
view on DNA under tension
10.1063/1.5004019 · doi-reference
Designer Catalyst-Enabled Regiodivergent Histone Acetylation
10.1021/jacs.5c01699 · doi-reference
Mechanism for verification of mismatched and homoduplex
DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations
10.1002/prot.25077 · doi-reference
Stacking
Free Energies of All DNA
and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed
Using Recently Revised AMBER Parameters and Compared with Experiment
10.1021/ct501170h · doi-reference
The GB/SA Continuum
Model for Solvation. A Fast Analytical Method for the Calculation
of Approximate Born Radii
10.1021/jp961992r · doi-reference
DNA Elasticity from
Short DNA to Nucleosomal DNA
10.1021/acs.jpcb.5b03006 · doi-reference
Elasticity of DNA
and the effect of dendrimer binding
10.1140/epje/i2013-13068-1 · doi-reference
Stiff Chains
and Filaments under Tension
10.1021/ma00124a044 · doi-reference
3DNA: a software package for the analysis, rebuilding
and visualization of three-dimensional nucleic acid structures
10.1093/nar/gkg680 · doi-reference
Torsional stress can regulate the
unwrapping of two outer half superhelical
turns of nucleosomal DNA
10.1073/pnas.2020452118 · doi-reference
Estimation
of Absolute and Relative Entropies of Macromolecules Using the Covariance
Matrix
10.1016/0009-2614(93)89366-p · doi-reference
Free Energy Landscape of H2A-H2B
Displacement From Nucleosome
10.1016/j.jmb.2022.167707 · doi-reference
The weighted
histogram analysis method for free energy calculations on biomolecules.
I. The method
10.1002/jcc.540130812 · doi-reference
Adaptively
biased molecular dynamics
of free energy calculations
10.1063/1.2844595 · doi-reference
Settle: An analytical
version of the SHAKE and RATTLE
algorithm for rigid water models
10.1002/jcc.540130805 · doi-reference
Rattle:
A “velocity” version of the shake algorithm for molecular
dynamics calculations
10.1016/0021-9991(83)90014-1 · doi-reference
Numerical
integration of the cartesian
equations of motion of a system with constraints: molecular dynamics
of n-alkanes
10.1016/0021-9991(77)90098-5 · doi-reference
Isothermal-isobaric molecular dynamics
using stochastic velocity rescaling
10.1063/1.3073889 · doi-reference
Canonical
sampling through velocity
rescaling
10.1063/1.2408420 · doi-reference
A smooth particle
mesh Ewald method
10.1063/1.470117 · doi-reference
Particle mesh
Ewald: An N·log(N)
method for Ewald sums in large systems
10.1063/1.464397 · doi-reference
Comparison
of simple potential functions for simulating liquid water
10.1063/1.445869 · doi-reference
Determination of
alkali and halide monovalent ion parameters
for use in explicitly solvated biomolecular simulations
10.1021/jp8001614 · doi-reference
Parmbsc1:
a refined force field for DNA simulations
10.1038/nmeth.3658 · doi-reference
GENESIS 1.1: A hybrid-parallel
molecular dynamics simulator with enhanced sampling algorithms on
multiple computational platforms
10.1002/jcc.24874 · doi-reference
GENESIS: a hybrid-parallel
and multi-scale molecular dynamics simulator with enhanced sampling
algorithms for biomolecular and cellular simulations
10.1002/wcms.1220 · doi-reference
