ArticleThe journal of physical chemistry. B2013
DNA bending propensity in the presence of base mismatches: implications for DNA repair.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 55 citations in OpenAlex.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- Searching for sequence features that control DNA cyclizability.PNAS nexus · 2026Article
- LysR-type regulator LrhA promotes CRISPR-Cas immunity in Escherichia coli.Nucleic acids research · 2026Article
- An Insight into Cancer Cells and Disease Progression Through the Lens of Mathematical Modeling.Current issues in molecular biology · 2025Review
- A high-throughput single-molecule platform to study DNA supercoiling effect on protein-DNA interactions.Nucleic acids research · 2025Article
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- Re-pairing DNA: binding of a ruthenium phi complex to a double mismatch.Chemical science · 2024Article
- Molecular dynamics of mismatch detection-How MutS uses indirect readout to find errors in DNA.Biophysical journal · 2023Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Noncanonical DNA structures are drivers of genome evolution.Trends in genetics : TIG · 2023Review
- "Flexible hinge" dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy.Journal of biological physics · 2022Article
- Molecular Mechanisms Associated with Clustered Lesion-Induced Impairment of 8-oxoG Recognition by the Human Glycosylase OGG1.Molecules (Basel, Switzerland) · 2021Article
- Importance of base-pair opening for mismatch recognition.Nucleic acids research · 2020Article
- Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.Nucleic acids research · 2020Article
- Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases.Scientific reports · 2020Article
- Investigating the pathogenic SNPs in BLM helicase and their biological consequences by computational approach.Scientific reports · 2020Article
- Mismatch Recognition byInternational journal of molecular sciences · 2019Article
- Bending of DNA duplexes with mutation motifs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking.Physical review letters · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
DNA bending is believed to facilitate the initial recognition of the mismatched base for repair. The repair efficiencies are dependent on both the mismatch type and neighboring nucleotide sequence. We have studied bending of several DNA duplexes containing canonical matches: A:T and G:C; various mismatches: A:A, A:C, G:A, G:G, G:T, C:C, C:T, and T:T; and a bis-abasic site: X:X. Free-energy profiles were generated for DNA bending using umbrella sampling. The highest energetic cost associated with DNA bending is observed for canonical matches while bending free energies are lower in the presence of mismatches, with the lowest value for the abasic site. In all of the sequences, DNA duplexes bend toward the major groove with widening of the minor groove. For homoduplexes, DNA bending is observed to occur via smooth deformations, whereas for heteroduplexes, kinks are observed at the mismatch site during strong bending. In general, pyrimidine:pyrimidine mismatches are the most destabilizing, while purine:purine mismatches lead to intermediate destabilization, and purine:pyrimidine mismatches are the least destabilizing. The ease of bending is partially correlated with the binding affinity of MutS to the mismatch pairs and subsequent repair efficiencies, indicating that intrinsic DNA bending propensities are a key factor of mismatch recognition.
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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.