ArticleNucleic acids research2010
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
138 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Antisense Versus Antigene in the Computer-Aided Design of Triplex-Forming Oligonucleotides (TFO): Insights from a Dual-Method Review, Combining Bibliometric and Systematic Review.International journal of molecular sciences · 2025Pooled it
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- DNA twist at high alkali ion concentrations: evidence against C-form DNA in solution.Nucleic acids research · 2026Article
- Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation ofJournal of chemical theory and computation · 2025Article
- Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA.The journal of physical chemistry. B · 2025Article
- Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.Nucleic acids research · 2025Article
- Navigating the complexity of p53-DNA binding: implications for cancer therapy.Biophysical reviews · 2024Review
- Molecular stripping underpins derepression of a toxin-antitoxin system.Nature structural & molecular biology · 2024Article
- Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs.Nucleic acids research · 2024Article
- A commentary on the ABC consortium and its impact on the development of mesoscopic models of DNA.Biophysical reviews · 2024Article
- DNA simulation benchmarks revealed with the accumulation of high-resolution structures.Biophysical reviews · 2024Review
- Multiscale simulations of DNA from electrons to nucleosomes: 22 years of the Ascona B-DNA Consortium.Biophysical reviews · 2024Review
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- Bisulfite probing reveals DNA structural intricacies.Nucleic acids research · 2023Article
- Correlated motions in DNA: beyond base-pair step models of DNA flexibility.Nucleic acids research · 2023Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Bubble Relaxation Dynamics in Homopolymer DNA Sequences.Molecules (Basel, Switzerland) · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration.Life (Basel, Switzerland) · 2022Article
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
78 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
Abstract
It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50-100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA.
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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.