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Nucleic Acids Research, 2001, Vol. 29, No. 13 e67
© 2001 Oxford University Press

Novel display of knotted DNA molecules by two-dimensional gel electrophoresis

Sonia Trigueros, Javier Arsuaga1, Maria E. Vazquez1, De Witt Sumners1 and Joaquim Roca* Institut de Biologia Molecular de Barcelona, CSIC, Jordi Girona 18–26, 08034 Barcelona, Spain and 1Mathematics Department, Florida State University, FL, USA

We describe a two-dimensional agarose gel electrophoresis procedure that improves the resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA knots migrate according to their compactness. The second gel dimension is run at high voltage, and DNA knots migrate according to other physical parameters such as shape and flexibility. In comparison with one-dimensional gel electrophoresis, this procedure segregates the knotted DNA molecules from other unknotted forms of DNA, and partially resolves populations of knots that have the same number of crossings. The two-dimensional display may allow quantitative and qualitative characterization of different types of DNA knots simply by gel velocity.

* To whom correspondence should be addressed. Tel: +343 400 6178; Fax: +343 204 5904; Email: jrbbmc{at}cid.csic.es Present address: Javier Arsuaga and Maria E. Vazquez, Department of Mathematics and Department of Molecular and Cellular Biology, University of California Berkeley, CA, USA


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