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Comparative gel electrophoresis analysis of helical junctions in RNA

Comparative gel electrophoresis analysis of helical junctions in RNA

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  • David M. J. Lilley

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Original languageEnglish
Title of host publicationBiophysical, chemical, and functional probes of RNA structure, interactions and folding
Subtitle of host publicationPart B
EditorsDaniel Herschlag
Place of PublicationSan Diego
PublisherAcademic Press
Number of pages15
ISBN (Print)9780123809223
StatePublished - 2009

Publication series

NameMethods in Enzymology
PublisherAcademic Press


Comparative gel electrophoresis provides information on the relative angles subtended between helical arms at a branchpoint in RNA. It is based upon the comparison of electrophoretic mobility in polyacrylamide gels of species containing two long arms, with the remaining one(s) being significantly shorter. Although the method currently lacks a really well-established basis of physical theory, it is very powerful, yet simple to apply. It has had a number of significant successes in RNA, DNA and DNA-protein complexes, and in all cases to date the results have stood the test of time and eventual comparison with crystallographic analysis.



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