Probing RNA Translocases with DNA

  • Kimberly A. Reynolds
  • Veronica M. Raney
  • Kevin D. RaneyEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1259)


For some helicases, it is possible to investigate RNA translocase activity on DNA substrates because the enzyme acts on both substrates. Potassium permanganate (KMnO4) footprinting is a method used to chemically probe the conformation of DNA as well as the binding of proteins. Combining footprinting methods with rapid mixing methods that utilize a chemical quench-flow instrument can enable tracking of the translocase with nucleotide resolution.

Key words

RNA translocase Nonstructural protein 3 (NS3) Permanganate footprinting Fast footprinting 


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Kimberly A. Reynolds
    • 1
  • Veronica M. Raney
    • 1
  • Kevin D. Raney
    • 1
    Email author
  1. 1.Department of Biochemistry and Molecular BiologyUniversity of Arkansas for Medical SciencesLittle RockUSA

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