ArticleJournal of chemical theory and computation2012
Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Actively Induced Supercoiling Can Slow Down Plasmid Solutions by Trapping the Threading Entanglements.ACS nano · 2026Article
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.The Journal of chemical physics · 2024Article
- 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
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles.The journal of physical chemistry. B · 2021Article
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops.Biophysical reviews · 2016Article
- DSSR: an integrated software tool for dissecting the spatial structure of RNA.Nucleic acids research · 2015Article
- DNA topology confers sequence specificity to nonspecific architectural proteins.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- What controls DNA looping?International journal of molecular sciences · 2014Article
- Article
- Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations.Biochemical Society transactions · 2013Review
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides.
Identifiers
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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.