ArticleEpigenetics2014
Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation.
Article in Epigenetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 49 citations in OpenAlex.
- Amplification-free cancer diagnosis based on inhibition of Cas12a activity by site-specific 5mC-modified cfDNA.Nucleic acids research · 2025Article
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- DNA methylation induces subtle mechanical alteration but significant chiral selectivity.Chemical communications (Cambridge, England) · 2023Article
- Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases.Polymers · 2023Review
- The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation.Frontiers in molecular biosciences · 2023Review
- Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields.Life (Basel, Switzerland) · 2022Article
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- Abnormal methylation in theQRB discovery · 2022Article
- Cytosine base modifications regulate DNA duplex stability and metabolism.Nucleic acids research · 2021Article
- DNA methylation and noncoding RNA in OA: Recent findings and methodological advances.Osteoarthritis and cartilage open · 2021Article
- Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer.Journal of molecular modeling · 2021Article
- Combined use of murine double minute-2 promoter methylation and serum AFP improves diagnostic efficiency in hepatitis B virus-related hepatocellular carcinoma.International journal of medical sciences · 2020Observational
- Systematic screening identifies a 2-gene signature as a high-potential prognostic marker of undifferentiated pleomorphic sarcoma/myxofibrosarcoma.Journal of cellular and molecular medicine · 2020Article
- Promoter hypermethylation of theJHEP reports : innovation in hepatology · 2019Article
- How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study.Journal of molecular modeling · 2018Article
- Effect of Methylation on Local Mechanics and Hydration Structure of DNA.Biophysical journal · 2018Article
- Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs.Frontiers in chemistry · 2018Article
- Methyl-Cytosine-Driven Structural Changes Enhance Adduction Kinetics of an Exon 7 fragment of the p53 Gene.Scientific reports · 2017Article
- Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains.Nucleic acids research · 2016Article
- Theoretical modelling of epigenetically modified DNA sequences.F1000Research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.