ArticleNucleic acids research2009
Local and global effects of strong DNA bending induced during molecular dynamics simulations.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Inferring DNA Kinkability from Biased MD Simulations.Journal of chemical theory and computation · 2026Article
- 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
- Structural Characterization of the Interaction of Hypoxia Inducible Factor-1 with Its Hypoxia Responsive Element at the -964G > A Variation Site of theInternational journal of molecular sciences · 2021Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.Nature communications · 2021Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- 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
- Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment.Frontiers in physics · 2019Article
- Bending of DNA duplexes with mutation motifs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Strong deformations of DNA: Effect on the persistence length.The European physical journal. E, Soft matter · 2018Article
- Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins.Scientific reports · 2018Article
- Article
- Conformational rearrangement of 1,2-d(GG) intrastrand cis-diammineplatinum crosslinked DNA is driven by counter-ion penetration within the minor groove of the modified site.Journal of molecular modeling · 2017Article
- Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.Nucleic acids research · 2016Article
- DNA minicircles clarify the specific role of DNA structure on retroviral integration.Nucleic acids research · 2016Article
- Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.Nucleic acids research · 2016Article
- Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.Structure (London, England : 1993) · 2016Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA bending plays an important role in many biological processes, but its molecular and energetic details as a function of base sequence remain to be fully understood. Using a recently developed restraint, we have studied the controlled bending of four different B-DNA oligomers using molecular dynamics simulations. Umbrella sampling with the AMBER program and the recent parmbsc0 force field yield free energy curves for bending. Bending 15-base pair oligomers by 90 degrees requires roughly 5 kcal mol(-1), while reaching 150 degrees requires of the order of 12 kcal mol(-1). Moderate bending occurs mainly through coupled base pair step rolls. Strong bending generally leads to local kinks. The kinks we observe all involve two consecutive base pair steps, with disruption of the central base pair (termed Type II kinks in earlier work). A detailed analysis of each oligomer shows that the free energy of bending only varies quadratically with the bending angle for moderate bending. Beyond this point, in agreement with recent experiments, the variation becomes linear. An harmonic analysis of each base step yields force constants that not only vary with sequence, but also with the degree of bending. Both these observations suggest that DNA is mechanically more complex than simple elastic rod models would imply.
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