Understanding the structural and dynamic consequences of DNA epigenetic modifications : Computational insights into cytosine methylation and hydroxymethylation

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• Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

  2014cited by this paper
• A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line

  2014cited by this paper
• DNA conformational flexibility study using phosphate backbone neutralization model.

  2014cited by this paper
• Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

  2014influential reference
• B-DNA structure and stability: the role of hydrogen bonding, π-π stacking interactions, twist-angle, and solvation.

  2014cited by this paper
• B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands

  2013cited by this paper
• GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

  2013cited by this paper
• Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine

  2013cited by this paper
• Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

  2013cited by this paper
• 5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics.

  2013cited by this paper
• Insights into intrastrand cross-link lesions of DNA from QM/MM molecular dynamics simulations.

  2012cited by this paper
• Frontiers in molecular dynamics simulations of DNA.

  2012cited by this paper
• The Role of Methylation in the Intrinsic Dynamics of B- and Z-DNA

  2012cited by this paper
• CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI

  2012cited by this paper
• Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions.

  2011cited by this paper
• B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

  2011cited by this paper
• Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

  2011cited by this paper
• Recognition of methylated DNA through methyl-CpG binding domain proteins

  2011cited by this paper
• Effect of CpG methylation on DNA binding protein: molecular dynamics simulations of the homeodomain PITX2 bound to the methylated DNA.

  2011cited by this paper
• Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

  2010cited by this paper
• Origins of specificity in protein-DNA recognition.

  2010cited by this paper
• Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome

  2009cited by this paper
• UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications

  2009cited by this paper
• A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

  2009cited by this paper
• Mammalian cytosine methylation at a glance

  2009cited by this paper
• Epigenetics

  2009cited by this paper
• Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures

  2009cited by this paper
• The mammalian epigenome.

  2007cited by this paper
• Sequence-dependent DNA deformability studied using molecular dynamics simulations

  2007cited by this paper
• Cancer epigenomics: DNA methylomes and histone-modification maps

  2007cited by this paper
• Canonical sampling through velocity rescaling.

  2007cited by this paper
• Dynamics of B-DNA on the microsecond time scale.

  2007cited by this paper
• Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

  2007cited by this paper
• Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition.

  2005cited by this paper
• DNA methylation and human disease

  2005influential reference
• Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.

  2005cited by this paper
• The influence of intercalator binding on DNA triplex stability: correlation with effects on A‐tract duplex structure

  2004cited by this paper
• DNA deformability at the base pair level.

  2004cited by this paper
• DNA basepair step deformability inferred from molecular dynamics simulations.

  2003cited by this paper
• Sequence-dependent DNA structure: a database of octamer structural parameters.

  2003cited by this paper
• 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.

  2003cited by this paper
• The Influence of the Thymine C5 Methyl Group on Spontaneous Base Pair Breathing in DNA*

  2002cited by this paper
• DNA methylation and chromatin – unraveling the tangled web

  2002cited by this paper
• Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts.

  2002cited by this paper
• Structural effects of cytosine methylation on DNA sugar pucker studied by FTIR.

  2002cited by this paper
• A-tract DNA disfavours triplex formation.

  2002cited by this paper
• Structural basis of DNA flexibility.

  2001cited by this paper
• How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

  2000cited by this paper
• Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: evidence for a secondary long-lived open state of the base pair.

  2000cited by this paper
• DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.

  1998cited by this paper
• Sp1 binding is inhibited by (m)Cp(m)CpG methylation.

  1997cited by this paper
• Molecular dynamics simulations highlight the structural differences among DNA: DNA, RNA:RNA, and DNA:RNA hybrid duplexes

  1997cited by this paper
• Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins

  1995cited by this paper
• B-DNA twisting correlates with base-pair morphology.

  1995cited by this paper
• A smooth particle mesh Ewald method

  1995cited by this paper
• CpG-rich islands and the function of DNA methylation

  1986cited by this paper
• Molecular dynamics with coupling to an external bath

  1984cited by this paper
• Comparison of simple potential functions for simulating liquid water

  1983cited by this paper
• Efficient diffuse function‐augmented basis sets for anion calculations. III. The 3‐21+G basis set for first‐row elements, Li–F

  1983cited by this paper
• Structure of a B-DNA dodecamer: conformation and dynamics.

  1981cited by this paper
• Polymorphic transitions in single crystals: A new molecular dynamics method

  1981cited by this paper
• The influence of polarization functions on molecular orbital hydrogenation energies

  1973cited by this paper
• Self‐Consistent Molecular‐Orbital Methods. IX. An Extended Gaussian‐Type Basis for Molecular‐Orbital Studies of Organic Molecules

  1971cited by this paper
• Effects of Cytosine Hydroxymethylation on Dna Strand Separation

  year unknowncited by this paper
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  year unknowncited by this paper

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  2023cites this paper
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  2023cites this paper