title: Triplex-forming PNA modified with unnatural nucleobases: the role of protonation entropy in RNA binding.
abstract: Peptide nucleic acid (PNA) modified with unnatural nucleobases enables the formation of a highly stable triplex with a double-stranded RNA at physiological pH. In this communication, we evaluated kinetics and thermodynamics of PNA/RNA triplex formation as a function of both pH and temperature. Protonation entropy was found to be the major factor responsible for the destabilization of the triplex and for the progressive decrease in the association rate at more basic pHs.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan. sugimoto@konan-u.ac.jp.
authors.forename: Tamaki
authors.initials: T
authors.lastname: Endoh
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan. sugimoto@konan-u.ac.jp.
authors.forename: Chiara
authors.initials: C
authors.lastname: Annoni
authors.affiliation: Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA.
authors.forename: Dziyana
authors.initials: D
authors.lastname: Hnedzko
authors.affiliation: Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA.
authors.forename: Eriks
authors.initials: E
authors.lastname: Rozners
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan. sugimoto@konan-u.ac.jp and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D019277:Entropy; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D009690:Nucleic Acid Conformation; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D020135:Peptide Nucleic Acids; D012330:RNA, Double-Stranded