Sequence selective recognition of double-stranded RNA using triple helix-forming peptide nucleic acids

Methods Mol Biol. 2014:1050:83-94. doi: 10.1007/978-1-62703-553-8_7.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Calorimetry
  • Chromatography, High Pressure Liquid
  • Nucleic Acid Conformation*
  • Oligonucleotide Probes / chemistry
  • Peptide Nucleic Acids / chemistry*
  • Peptide Nucleic Acids / metabolism*
  • RNA, Double-Stranded / genetics*
  • RNA, Double-Stranded / metabolism*
  • Substrate Specificity

Substances

  • Oligonucleotide Probes
  • Peptide Nucleic Acids
  • RNA, Double-Stranded