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Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules

AuthorsCebrián, Jorge; Castán, Alicia; Martínez-Robles, María Luisa ; Hernandez, Pablo ; Krimer, Dora B. ; Schvartzman, Jorge Bernardo
Issue Date20-Nov-2014
PublisherOxford University Press
CitationNucleic Acids Research, 2014
AbstractWe systematically varied conditions of twodimensional(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.
Description10 p.-7 fig.6 tab. Cebrián, Jorge et al. Este artículo forma parte de tesis doctoral https://digital.csic.es/handle/10261/120925
Publisher version (URL)http://dx.doi.org/10.1093/nar/gku1255
Appears in Collections:(CIB) Artículos
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