Sequence Selective Recognition of Double-Stranded RNA Using Triple Helix-Forming Peptide Nucleic Acids

  • Thomas Zengeya
  • Pankaj Gupta
  • Eriks Rozners
Part of the Methods in Molecular Biology book series (MIMB, volume 1050)


Noncoding RNAs are attractive targets for molecular recognition because of the central role they play in gene expression. Since most noncoding RNAs are in a double-helical conformation, recognition of such structures is a formidable problem. Herein, we describe a method for sequence-selective recognition of biologically relevant double-helical RNA (illustrated on ribosomal A-site RNA) using peptide nucleic acids (PNA) that form a triple helix in the major grove of RNA under physiologically relevant conditions. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.

Key words

Double-stranded RNA Peptide nucleic acids (PNA) Triple helix Isothermal titration calorimetry (ITC) 



This work was supported by NIH grant GM071461 and Binghamton University.


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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Thomas Zengeya
    • 1
  • Pankaj Gupta
    • 1
  • Eriks Rozners
    • 1
  1. 1.Department of ChemistryBinghamton University, State University of New YorkBinghamtonUSA

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