ArticlePLoS computational biology2015
Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation ofJournal of chemical theory and computation · 2025Article
- C-B-A Test of DNA Force Fields.ACS omega · 2023Article
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
- Slow motions in A·T rich DNA sequence.Scientific reports · 2020Article
- A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level.Nucleic acids research · 2020Article
- The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.Nucleic acids research · 2019Article
- Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond.Nucleic acids research · 2019Article
- How methyl-sugar interactions determine DNA structure and flexibility.Nucleic acids research · 2019Article
- Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies.Journal of molecular modeling · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ↔ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition.
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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.