ArticleBiophysical journal2018
Effect of Methylation on Local Mechanics and Hydration Structure of DNA.
Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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.
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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
22 citing papers in PubMed, 48 citations in OpenAlex.
- 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
- Fundamentals of DNA methylation in development.Pediatric research · 2025Review
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.The journal of physical chemistry. B · 2024Article
- Solvation free energy in governing equations for DNA hybridization, protein-ligand binding, and protein folding.FEBS open bio · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- 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
- Article
- Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding.Journal of chemical theory and computation · 2023Article
- Polymer models reveal how chromatin modification can modulate force at the kinetochore.Molecular biology of the cell · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation.Nucleic acids research · 2021Article
- Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer.Journal of molecular modeling · 2021Article
- Single-molecule micromanipulation studies of methylated DNA.Biophysical journal · 2021Article
- Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains.Journal of molecular modeling · 2020Article
- A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.Biochemistry · 2020Article
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
- Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA.The journal of physical chemistry. B · 2020Article
- 5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex.The journal of physical chemistry. B · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.
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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.