ArticleNucleic acids research2013
Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 71 citations in OpenAlex.
- The role of cytosine modification symmetry in mammalian epigenome regulation.Chemical science · 2026Review
- Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.Nucleic acids research · 2024Article
- DNA methylation induces subtle mechanical alteration but significant chiral selectivity.Chemical communications (Cambridge, England) · 2023Article
- A High-Throughput Method Based on Microculture Technology for Screening of High-Yield Strains of Tylosin-ProducingJournal of microbiology and biotechnology · 2023Article
- DNA Glycosylases Define the Outcome of Endogenous Base Modifications.International journal of molecular sciences · 2023Review
- DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons.Communications biology · 2022Article
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1.Nucleic acids research · 2022Article
- Cytosine base modifications regulate DNA duplex stability and metabolism.Nucleic acids research · 2021Article
- Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation.Nucleic acids research · 2021Article
- Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes.International journal of molecular sciences · 2021Article
- The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs.Nucleic acids research · 2021Article
- bZIP Dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun Prefer to Bind to Some Double-Stranded DNA Sequences Containing 5-Formylcytosine and 5-Carboxylcytosine.Biochemistry · 2020Article
- Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA.The journal of physical chemistry. B · 2020Article
- Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine.Chemical science · 2019Article
- The road to aryl CHanion binding was paved with good intentions: fundamental studies, host design, and historical perspectives in CH hydrogen bonding.Chemical communications (Cambridge, England) · 2019Article
- Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Article
- Selective recognition ofPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Effect of Methylation on Local Mechanics and Hydration Structure of DNA.Biophysical journal · 2018Article
- 5-Formylcytosine does not change the global structure of DNA.Nature structural & molecular biology · 2017Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
5-Hydroxymethylcytosine (5-hmC) was recently identified as a relatively frequent base in eukaryotic genomes. Its physiological function is still unclear, but it is supposed to serve as an intermediate in DNA de novo demethylation. Using X-ray diffraction, we solved five structures of four variants of the d(CGCGAATTCGCG) dodecamer, containing either 5-hmC or 5-methylcytosine (5-mC) at position 3 or at position 9. The observed resolutions were between 1.42 and 1.99 Å. Cytosine modification in all cases influences neither the whole B-DNA double helix structure nor the modified base pair geometry. The additional hydroxyl group of 5-hmC with rotational freedom along the C5-C5A bond is preferentially oriented in the 3' direction. A comparison of thermodynamic properties of the dodecamers shows no effect of 5-mC modification and a sequence-dependent only slight destabilizing effect of 5-hmC modification. Also taking into account the results of a previous functional study [Münzel et al. (2011) (Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Chem. Eur. J., 17, 13782-13788)], we conclude that the 5 position of cytosine is an ideal place to encode epigenetic information. Like this, neither the helical structure nor the thermodynamics are changed, and polymerases cannot distinguish 5-hmC and 5-mC from unmodified cytosine, all these effects are making the former ones non-mutagenic.
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