title: Recognition of double-stranded RNA by guanidine-modified peptide nucleic acids.
abstract: Double-helical RNA has become an attractive target for molecular recognition because many noncoding RNAs play important roles in the control of gene expression. Recently, we discovered that short peptide nucleic acids (PNA) bind strongly and sequence selectively to a homopurine tract of double-helical RNA via formation of a triple helix. Herein, we tested if the molecular recognition of RNA could be enhanced by α-guanidine modification of PNA. Our study was motivated by the discovery of Ly and co-workers that the guanidine modification greatly enhances the cellular delivery of PNA. Isothermal titration calorimetry showed that the guanidine-modified PNA (GPNA) had reduced affinity and sequence selectivity for triple-helical recognition of RNA. The data suggested that in contrast to unmodified PNA, which formed a 1:1 PNA-RNA triple helix, GPNA preferred a 2:1 GPNA-RNA triplex invasion complex. Nevertheless, promising results were obtained for recognition of biologically relevant double-helical RNA. Consistent with enhanced strand invasion ability, GPNA derived from d-arginine recognized the transactivation response element of HIV-1 with high affinity and sequence selectivity, presumably via Watson-Crick duplex formation. On the other hand, strong and sequence selective triple helices were formed by unmodified and nucelobase-modified PNA and the purine-rich strand of the bacterial A-site. These results suggest that appropriate chemical modifications of PNA may enhance molecular recognition of complex noncoding RNAs.
authors.affiliation: Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Gupta
authors.forename: Oluwatoyosi
authors.initials: O
authors.lastname: Muse
authors.forename: Eriks
authors.initials: E
authors.lastname: Rozners
mesh_terms: D001665:Binding Sites / Q000235:genetics; D002151:Calorimetry; D002942:Circular Dichroism; D024202:Electrophoretic Mobility Shift Assay; D019791:Guanidine / Q000737:chemistry*; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D009687:Nuclear Proteins / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D020135:Peptide Nucleic Acids / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics; D012330:RNA, Double-Stranded / Q000037:antagonists & inhibitors / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D020218:Response Elements / Q000235:genetics; D013816:Thermodynamics; D000099253:Trans-Activation Responsive RNA-Binding Protein
chemical_list: D019791:Guanidine; D009687:Nuclear Proteins; D020135:Peptide Nucleic Acids; D012330:RNA, Double-Stranded; D016601:RNA-Binding Proteins; C071598:TARBP1 protein, human; D000099253:Trans-Activation Responsive RNA-Binding Protein