ArticleNucleic acids research2015
Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules.
Article in Nucleic acids research, 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.
- Surface-Capped Protein Nanoparticles for Nonviral Gene Delivery.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Electrophoretic Mobility Assay to Separate Supercoiled, Catenated, and Knotted DNA Molecules.Bio-protocol · 2024Article
- DNA-Topology Simplification by Topoisomerases.Molecules (Basel, Switzerland) · 2021Review
- Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.Nucleic acids research · 2019Review
- Quantitative disclosure of DNA knot chirality by high-resolution 2D-gel electrophoresis.Nucleic acids research · 2019Article
- Investigating DNA supercoiling in eukaryotic genomes.Briefings in functional genomics · 2017Review
- Review
- Numerical investigation of molecular nano-array in potential-energy profile for a single dsDNA.The European physical journal. E, Soft matter · 2016Article
- Topological patterns in two-dimensional gel electrophoresis of DNA knots.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Direct Evidence for the Formation of Precatenanes during DNA Replication.The Journal of biological chemistry · 2015Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We systematically varied conditions of two-dimensional (2D) agarose gel electrophoresis to optimize separation of DNA topoisomers that differ either by the extent of knotting, the extent of catenation or the extent of supercoiling. To this aim we compared electrophoretic behavior of three different families of DNA topoisomers: (i) supercoiled DNA molecules, where supercoiling covered the range extending from covalently closed relaxed up to naturally supercoiled DNA molecules; (ii) postreplicative catenanes with catenation number increasing from 1 to ∼15, where both catenated rings were nicked; (iii) knotted but nicked DNA molecules with a naturally arising spectrum of knots. For better comparison, we studied topoisomer families where each member had the same total molecular mass. For knotted and supercoiled molecules, we analyzed dimeric plasmids whereas catenanes were composed of monomeric forms of the same plasmid. We observed that catenated, knotted and supercoiled families of topoisomers showed different reactions to changes of agarose concentration and voltage during electrophoresis. These differences permitted us to optimize conditions for their separation and shed light on physical characteristics of these different types of DNA topoisomers during electrophoresis.
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