Analysis of DNA Knots and Catenanes by Agarose-Gel Electrophoresis

Supercoiling, knotting, and catenation are three common higher-order structures involving coiling of the axis of double-stranded DNA. These forms appear as a result of a number of important biological activities, including topoisomerase action, DNA replication, and genetic recombination (1 -3 ). All of these species have mobilities in agarose gels that are distinct from those of normal open circular and linear DNA molecules of the same size. The electrophoretic properties of linking number topoisomers are dealt with elsewhere in this volume; this chapter focuses on the separation and characterization of mixtures of knotted or catenated forms.