Gel mobility shift assays for rna binding viral rnai suppressors

Tibor Csorba, József Burgyán

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)


The host-virus interaction is a continuous coevolutionary race involving both host defence strategies and virus escape mechanisms. RNA silencing is one of the main processes employed by eukaryotic organisms to fight viruses. However, viruses encode suppressor proteins to counteract this antiviral mechanism. Virtually all plant viruses encode at least one suppressor. In spite of being highly diverse at the protein level, a large group of these proteins inhibit RNA silencing very similarly, by sequestration of double-stranded RNA or small-interfering RNA molecules, the central players of the pathway. The RNA binding capacity of virus suppressor proteins can be studied by the electrophoretic mobility shift assay method. Also known as gel retardation assay, gel mobility assay, gel shift assay or band shift assay, EMSA is an in vitro technique used to characterize protein:DNA or protein:RNA interactions. The method had been developed based on the observation that protein: nucleic acid complexes migrate slower through a non-denaturing polyacrylamide gel than the free nucleic acid fragments. Here, we provide a detailed protocol for the analysis of crucifer-infecting Tobacco mosaic tobamovirus (cr-TMV) silencing suppressor protein p122 RNA binding capacity.

Original languageEnglish
Title of host publicationAntiviral RNAi
Subtitle of host publicationConcepts, Methods, and Applications
EditorsRonald Rij
Number of pages8
Publication statusPublished - Dec 1 2011

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Antiviral silencing
  • Band shift assay
  • Electro mobility shift assay
  • RNA binding
  • Viral suppressor proteins
  • cr-TMV p122
  • siRNA

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Csorba, T., & Burgyán, J. (2011). Gel mobility shift assays for rna binding viral rnai suppressors. In R. Rij (Ed.), Antiviral RNAi: Concepts, Methods, and Applications (pp. 245-252). (Methods in Molecular Biology; Vol. 721).