Effect of C5-methylation of cytosine on the UV-induced reactivity of duplex DNA: conformational and electronic factors
A Banyasz, L Esposito, T Douki, M Perron… - The Journal of …, 2016 - ACS Publications
C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in
skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of …
skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of …
Working the kinks out of nucleosomal DNA
WK Olson, VB Zhurkin - Current opinion in structural biology, 2011 - Elsevier
Condensation of DNA in the nucleosome takes advantage of its double-helical architecture.
The DNA deforms at sites where the base pairs face the histone octamer. The largest so …
The DNA deforms at sites where the base pairs face the histone octamer. The largest so …
Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond
A Balaceanu, D Buitrago, J Walther… - Nucleic acids …, 2019 - academic.oup.com
We used extensive molecular dynamics simulations to study the structural and dynamic
properties of the central d (TpA) step in the highly polymorphic d (CpTpApG) tetranucleotide …
properties of the central d (TpA) step in the highly polymorphic d (CpTpApG) tetranucleotide …
Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation
ATP Carvalho, L Gouveia, CR Kanna… - Epigenetics, 2014 - Taylor & Francis
We report a series of molecular dynamics (MD) simulations of up to a microsecond
combined simulation time designed to probe epigenetically modified DNA sequences. More …
combined simulation time designed to probe epigenetically modified DNA sequences. More …
Moving beyond Watson–Crick models of coarse grained DNA dynamics
MC Linak, R Tourdot, KD Dorfman - The Journal of Chemical Physics, 2011 - pubs.aip.org
DNA produces a wide range of structures in addition to the canonical B-form of double-
stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed …
stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed …
Revisiting DNA sequence-dependent deformability in high-resolution structures: effects of flanking base pairs on dinucleotide morphology and global chain …
DNA carries more than the list of biochemical ingredients that drive the basic functions of
living systems. The sequence of base pairs includes a multitude of structural and energetic …
living systems. The sequence of base pairs includes a multitude of structural and energetic …
[PDF][PDF] Toward a consensus view of duplex RNA flexibility
The structure and flexibility of the RNA duplex has been studied using extended molecular
dynamics simulations on four diverse 18-mer oligonucleotides designed to contain many …
dynamics simulations on four diverse 18-mer oligonucleotides designed to contain many …
Sulfur-substitution-induced base flipping in the DNA duplex
Base flipping is widely observed in a number of important biological processes. The genetic
codes deposited inside the DNA duplex become accessible to external agents upon base …
codes deposited inside the DNA duplex become accessible to external agents upon base …
Quantitative investigation of the effects of DNA modifications and protein mutations on MeCP2-MBD-DNA interactions
Q Wang, S Luo, D Xiong, X Xu, X Zhao… - International Journal of …, 2023 - Elsevier
DNA methylation as an important epigenetic marker, has gained attention for the
significance of three oxidative modifications (hydroxymethyl-C (hmC), formyl-C (fC), and …
significance of three oxidative modifications (hydroxymethyl-C (hmC), formyl-C (fC), and …
DNA duplex formation with a coarse-grained model
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of
spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the …
spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the …