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Analysis of branched nucleic acid structure using comparative gel electrophoresis

Published online by Cambridge University Press:  29 August 2008

David M. J. Lilley
David M. J. Lilley*
Affiliation:
Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, Dundee, UK
*
*Professor D. M. J. Lilley, Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, MSI/WTB Complex, Dundee DD1 5EH, UK. Tel.: +44 1382 384 243; Fax: +44 1382 385 893; Email: d.m.j.lilley@dundee.ac.uk
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Abstract

Electrophoresis in polyacrylamide gels provides a simple yet powerful means of analyzing the relative disposition of helical arms in branched nucleic acids. The electrophoretic mobility of DNA or RNA with a central discontinuity is determined by the angle subtended between the arms radiating from the branchpoint. In a multi-helical branchpoint, comparative gel electrophoresis can provide a relative measure of all the inter-helical angles and thus the shape and symmetry of the molecule. Using the long–short arm approach, the electrophoretic mobility of all the species with two helical arms that are longer than all others is compared. This can be done as a function of conditions, allowing the analysis of ion-dependent folding of branched DNA and RNA species. Notable successes for the technique include the four-way (Holliday) junction in DNA and helical junctions in functionally significant RNA species such as ribozymes. Many of these structures have subsequently been proved correct by crystallography or other methods, up to 10 years later in the case of the Holliday junction. Just as important, the technique has not failed to date. Comparative gel electrophoresis can provide a window on both fast and slow conformational equilibria such as conformer exchange in four-way DNA junctions. But perhaps the biggest test of the approach has been to deduce the structures of complexes of four-way DNA junctions with proteins. Two recent crystallographic structures show that the global structures were correctly deduced by electrophoresis, proving the worth of the method even in these rather complex systems. Comparative gel electrophoresis is a robust method for the analysis of branched nucleic acids and their complexes.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 41 , Issue 1 , February 2008 , pp. 1 - 39
Copyright
Copyright © 2008 Cambridge University Press

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