title: Using triple-helix-forming Peptide nucleic acids for sequence-selective recognition of double-stranded RNA.
abstract: Non-coding RNAs play important roles in regulation of gene expression. Specific recognition and inhibition of these biologically important RNAs that form complex double-helical structures will be highly useful for fundamental studies in biology and practical applications in medicine. This protocol describes a strategy developed in our laboratory for sequence-selective recognition of double-stranded RNA (dsRNA) using triple-helix-forming peptide nucleic acids (PNAs) that bind in the major grove of the RNA helix. The strategy developed uses chemically modified nucleobases, such as 2-aminopyridine (M), which enables strong triple-helical binding under physiologically relevant conditions, and 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E), which enable recognition of isolated pyrimidines in the purine-rich strand of the RNA duplex. Detailed protocols for preparation of modified PNA monomers, solid-phase synthesis, HPLC purification of PNA oligomers, and measuring dsRNA binding affinity using isothermal titration calorimetry are included.
authors.affiliation: Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York.
authors.forename: Dziyana
authors.initials: D
authors.lastname: Hnedzko
authors.forename: Samwel K
authors.initials: SK
authors.lastname: Cheruiyot
authors.forename: Eriks
authors.initials: E
authors.lastname: Rozners
mesh_terms: D020135:Peptide Nucleic Acids / Q000138:chemical synthesis* / Q000737:chemistry*; D012330:RNA, Double-Stranded / Q000737:chemistry*
chemical_list: D020135:Peptide Nucleic Acids; D012330:RNA, Double-Stranded
keywords: PNA; double-stranded RNA; isothermal titration calorimetry; peptide nucleic acids; triple helix