ArticlePloS one2012
The role of methylation in the intrinsic dynamics of B- and Z-DNA.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
41 citing papers in PubMed, 74 citations in OpenAlex.
- CRISPR technologies for detecting DNA and RNA methylation: Mechanisms, platforms, and translational opportunities.Bioengineering & translational medicine · 2026Review
- Biomolecular and cellular chirality: Novel diagnostic perspectives for diseases.APL bioengineering · 2026Review
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- Formation and biological implications of Z-DNA.Trends in genetics : TIG · 2026Review
- Discovering, Integrating, and Reinterpreting the Molecular Logic of Life: From Classical Theories of Heredity to an Extended Functional Perspective on the Central Dogma.Life (Basel, Switzerland) · 2026Review
- Assessment of the effectiveness of serum-infrared spectroscopy in conjunction with multivariate analysis methods for atherosclerosis diagnosis.Scientific reports · 2026Article
- Global identification and functional characterization of Z-DNA in rice.Plant biotechnology journal · 2025Article
- Structural features of DNA and their potential contribution to blind mole rat (Nannospalax xanthodon) longevity.Biogerontology · 2025Article
- Extracellular G-quadruplexes and Z-DNA protect biofilms from DNase I, and G-quadruplexes form a DNAzyme with peroxidase activity.Nucleic acids research · 2024Article
- Evaluation of Controlled Ovarian Stimulation Protocols in Patients with Normal and Low Ovarian Reserve: Analyses of miRNAs and Selected Target Genes Involved in the Proliferation of Human Cumulus Cells and Oocyte Quality.International journal of molecular sciences · 2022Article
- Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint.Nucleic acids research · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- Article
- Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence.BMC chemistry · 2021Article
- DNA Studies: Latest Spectroscopic and Structural Approaches.Micromachines · 2021Review
- Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides.International journal of molecular sciences · 2021Review
- Article
- The Binding of Monoclonal and Polyclonal Anti-Z-DNA Antibodies to DNA of Various Species Origin.International journal of molecular sciences · 2021Article
- Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer.Journal of molecular modeling · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Methylation of cytosine at the 5-carbon position (5 mC) is observed in both prokaryotes and eukaryotes. In humans, DNA methylation at CpG sites plays an important role in gene regulation and has been implicated in development, gene silencing, and cancer. In addition, the CpG dinucleotide is a known hot spot for pathologic mutations genome-wide. CpG tracts may adopt left-handed Z-DNA conformations, which have also been implicated in gene regulation and genomic instability. Methylation facilitates this B-Z transition but the underlying mechanism remains unclear. Herein, four structural models of the dinucleotide d(GC)(5) repeat sequence in B-, methylated B-, Z-, and methylated Z-DNA forms were constructed and an aggregate 100 nanoseconds of molecular dynamics simulations in explicit solvent under physiological conditions was performed for each model. Both unmethylated and methylated B-DNA were found to be more flexible than Z-DNA. However, methylation significantly destabilized the BII, relative to the BI, state through the Gp5mC steps. In addition, methylation decreased the free energy difference between B- and Z-DNA. Comparisons of α/γ backbone torsional angles showed that torsional states changed marginally upon methylation for B-DNA, and Z-DNA. Methylation-induced conformational changes and lower energy differences may contribute to the transition to Z-DNA by methylated, over unmethylated, B-DNA and may be a contributing factor to biological function.
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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.