ArticleNucleic acids research2021
Structural dynamics of double-stranded DNA with epigenome modification.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 26 citations in OpenAlex.
- Contrasting effects of different molecular crowding environments on base-pair opening/closing dynamics of DNA triplex structures.The FEBS journal · 2026Article
- Self-assembled xK1 rosette nanotube as a nanocarrier for chemotherapeutic drug molecules: a molecular dynamics study.RSC advances · 2025Article
- Cyclic GMP-AMP synthase recognizes the physical features of DNA.Acta pharmacologica Sinica · 2025Review
- Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.Nucleic acids research · 2024Article
- DNA damage twists base choreography.Nature chemical biology · 2023Article
- Shedding light on the base-pair opening dynamics of nucleic acids in living human cells.Nature communications · 2022Article
- A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix.RNA (New York, N.Y.) · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Roles of physical exercise in neurodegeneration: reversal of epigenetic clock.Translational neurodegeneration · 2021Review
- Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE iminoMagnetic resonance (Gottingen, Germany) · 2021Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of DNA is known to affect the binding of proteins to methylated DNA. Here, we have carried out a semi-quantitative analysis of the dynamics of double-stranded DNA (dsDNA) containing various epigenetic modifications by combining data from imino 1H exchange and imino 1H R1ρ relaxation dispersion NMR experiments in a complementary way. Using this approach, we characterized the base-opening (kopen) and base-closing (kclose) rates, facilitating a comparison of the base-opening and -closing process of dsDNA containing cytosine in different states of epigenetic modification. A particularly striking result is the increase in the kopen rate of hemi-methylated dsDNA 5mC/C relative to unmodified or fully methylated dsDNA, indicating that the Watson-Crick base pairs undergo selective destabilization in 5mC/C. Collectively, our findings imply that the epigenetic modulation of cytosine dynamics in dsDNA mediates destabilization of the GC Watson-Crick base pair to allow base-flipping in living cells.
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