SpringerProtocols: Abstract: Analysis of DNA Topoisomers, Knots, and Catenanes by Agarose Gel Electrophoresis

2. Analysis of DNA Topoisomers, Knots, and Catenanes by Agarose Gel Electrophoresis

By: Stephen D. Levene¹

Abstract

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Agarose gel electrophoresis is by far the most widely used method for characterizing the topological state of DNA molecules. Although this technique has been used for more than 30 years, the physical mechanism underlying the resolution of topological states remains poorly understood. However, electrophoretic methods remain the most robust and precise techniques for determining the local unwinding of DNA induced by the binding of proteins and small-molecule ligands, analyzing conformational transitions in duplex DNA, measuring changes in helical repeat that accompany shifts in environmental conditions, and characterizing knotting and linking in duplex DNA.

Affiliation(s): (1) Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Dallas, TX, USA

Book Title: DNA Topoisomerases: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 582 | Pub. Date: Sep-22-2009 | Page Range: 11-25 | DOI: 10.1007/978-1-60761-340-4_2

Subject: Genetics/Genomics

Key Words: Topoisomers - electrophoresis - catenanes - linking number - DNA knots

References

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