ArticleThe journal of physical chemistry. B2016
Transitions of Double-Stranded DNA Between the A- and B-Forms.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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.
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Who cites it
19 citing papers in PubMed, 51 citations in OpenAlex.
- MACRO-MOLECULAR CROWDING FAVORS WRITHE IN UNWOUND DNA.bioRxiv : the preprint server for biology · 2026Article
- Ultra-Short DNA Fragments Undergo A-to-B Conformational Transitions Revealed by FTIR Spectroscopy.International journal of molecular sciences · 2026Article
- Discovering, Integrating, and Reinterpreting the Molecular Logic of Life: From Classical Theories of Heredity to an Extended Functional Perspective on the Central Dogma.Life (Basel, Switzerland) · 2026Review
- DNA Noncovalent Interactions of Dinuclear ηChemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.Nucleic acids research · 2025Article
- Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes.Journal of chemical theory and computation · 2024Article
- Special Issue "Bioinformatics of Unusual DNA and RNA Structures".International journal of molecular sciences · 2024Article
- The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides.International journal of molecular sciences · 2022Article
- Article
- DNA binding by polycomb-group proteins: searching for the link to CpG islands.Nucleic acids research · 2022Review
- Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.The journal of physical chemistry. B · 2021Article
- Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer.ACS omega · 2020Article
- DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging.Biophysical journal · 2019Article
- Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].Living journal of computational molecular science · 2019Article
- Comparison of the Binding Geometry of Free-Base and Hexacoordinated Cationic Porphyrins to A- and B-Form DNA.ACS omega · 2018Article
- Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes.Frontiers in microbiology · 2018Review
- Review
- Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations.Nucleic acids research · 2017Article
- Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.Biophysical journal · 2017Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
The structure of double-stranded DNA (dsDNA) is sensitive to solvent conditions. In solution, B-DNA is the favored conformation under physiological conditions, while A-DNA is the form found under low water activity. The A-form is induced locally in some protein-DNA complexes, and repeated transitions between the B- and A-forms have been proposed to generate the forces used to drive dsDNA into viral capsids during genome packaging. Here, we report analyses on previous molecular dynamics (MD) simulations on B-DNA, along with new MD simulations on the transition from A-DNA to B-DNA in solution. We introduce the A-B Index (ABI), a new metric along the A-B continuum, to quantify our results. When A-DNA is placed in an equilibrated solution at physiological ionic strength, there is no energy barrier to the transition to the B-form, which begins within about 1 ns. The transition is essentially complete within 5 ns, although occasionally a stretch of a few base pairs will remain A-like for up to ∼10 ns. A comparison of four sequences with a range of predicted A-phobicities shows that more A-phobic sequences make the transition more rapidly than less A-phobic sequences. Simulations on dsDNA with a region of roughly one turn locked in the A-form allow us to characterize the A/B junction, which has an average bend angle of 20-30°. Fluctuations in this angle occur with characteristic times of about 10 ns.
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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.