ArticlePloS one2013
The effect of a G:T mispair on the dynamics of DNA.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Influence of DNA Mispairing and Abasic Sites on Duplex Dynamics: A Temperature-Jump Infrared Spectroscopy Study.The journal of physical chemistry letters · 2026Article
- Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate.Journal of the American Chemical Society · 2024Article
- Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets.Journal of molecular modeling · 2023Article
- Mismatch discrimination and sequence bias during end-joining by DNA ligases.Nucleic acids research · 2022Article
- Energy Landscapes for Base-Flipping in a Model DNA Duplex.The journal of physical chemistry. B · 2022Article
- Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms.Molecules (Basel, Switzerland) · 2021Article
- Tandem Substitutions in Somatic Hypermutation.Frontiers in immunology · 2021Article
- Importance of base-pair opening for mismatch recognition.Nucleic acids research · 2020Article
- Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases.Scientific reports · 2020Article
- Mismatch Recognition byInternational journal of molecular sciences · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination.Biophysical journal · 2018Article
- Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process.Nucleic acids research · 2018Article
- Lesion search and recognition by thymine DNA glycosylase revealed by single molecule imaging.Nucleic acids research · 2015Article
- Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine.International journal of molecular sciences · 2014Article
- Dynamics of spontaneous flipping of a mismatched base in DNA duplex.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Distortions in the DNA sequence such as damages or mispairs are specifically recognized and processed by DNA repair enzymes. A particular challenge for the enzymatic specificity is the recognition of a wrongly-placed native nucleotide such as thymine in T:G mispairs. An important step of substrate binding which is observed in many repair proteins is the flipping of the target base out of the DNA helix into the enzyme's active site. In this work we investigate how much the intrinsic dynamics of mispaired DNA is changed compared to canonical DNA. Our molecular dynamics simulations of DNA with and without T:G mispairs show significant differences in the conformation of paired and mispaired DNA. The wobble pair T:G shows local distortions such as twist, shear and stretch which deviate from canonical B form values. Moreover, the T:G mispair is found to be kinetically less stable, exhibiting two states with respect to base opening: a closed state comparable to the canonical base pairs, and a more open state, indicating a proneness for base flip. In addition, we observe that the thymine base in a T:G mispair is significantly more probable to be flipped than thymine in a T:A pair or cytosine in a C:G pair. Such local deformations and in particular the existence of a second, more-open state can be speculated to help the target-site recognition by repair enzymes.
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