ArticleNucleic acids research2008
Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 39 citations in OpenAlex.
- 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
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.Biophysical journal · 2022Article
- 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
- Bending of DNA duplexes with mutation motifs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Analysis of structural flexibility of damaged DNA using thiol-tethered oligonucleotide duplexes.PloS one · 2015Article
- Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine.International journal of molecular sciences · 2014Article
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- DNA bending propensity in the presence of base mismatches: implications for DNA repair.The journal of physical chemistry. B · 2013Article
- The effect of a G:T mispair on the dynamics of DNA.PloS one · 2013Article
- Sequence-specific recognition of cancer drug-DNA adducts by HMGB1a repair protein.Biophysical journal · 2012Article
- The crystal structure of non-modified and bipyridine-modified PNA duplexes.Chemistry (Weinheim an der Bergstrasse, Germany) · 2010Article
- A measure of bending in nucleic acids structures applied to A-tract DNA.Nucleic acids research · 2010Article
- Local and global effects of strong DNA bending induced during molecular dynamics simulations.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA-bending flexibility is central for its many biological functions. A new bending restraining method for use in molecular mechanics calculations and molecular dynamics simulations was developed. It is based on an average screw rotation axis definition for DNA segments and allows inducing continuous and smooth bending deformations of a DNA oligonucleotide. In addition to controlling the magnitude of induced bending it is also possible to control the bending direction so that the calculation of a complete (2-dimensional) directional DNA-bending map is now possible. The method was applied to several DNA oligonucleotides including A(adenine)-tract containing sequences known to form stable bent structures and to DNA containing mismatches or an abasic site. In case of G:A and C:C mismatches a greater variety of conformations bent in various directions compared to regular B-DNA was found. For comparison, a molecular dynamics implementation of the approach was also applied to calculate the free energy change associated with bending of A-tract containing DNA, including deformations significantly beyond the optimal curvature. Good agreement with available experimental data was obtained offering an atomic level explanation for stable bending of A-tract containing DNA molecules. The DNA-bending persistence length estimated from the explicit solvent simulations is also in good agreement with experiment whereas the adiabatic mapping calculations with a GB solvent model predict a bending rigidity roughly two times larger.
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