title: Sequence selective recognition of double-stranded RNA using triple helix-forming peptide nucleic acids.
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.
authors.affiliation: Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Zengeya
authors.forename: Pankaj
authors.initials: P
authors.lastname: Gupta
authors.forename: Eriks
authors.initials: E
authors.lastname: Rozners
mesh_terms: D001483:Base Sequence; D002151:Calorimetry; D002851:Chromatography, High Pressure Liquid; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes / Q000737:chemistry; D020135:Peptide Nucleic Acids / Q000737:chemistry* / Q000378:metabolism*; D012330:RNA, Double-Stranded / Q000235:genetics* / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D015345:Oligonucleotide Probes; D020135:Peptide Nucleic Acids; D012330:RNA, Double-Stranded