title: Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron.
abstract: The J4/5 loop of the group I intron in the mouse-derived fungal pathogen Pneumocystis carinii is the docking site for the first step of the RNA-catalyzed self-splicing reaction and thus is a model of a potential drug target. This purine-rich asymmetric internal loop, 5'GGAAG/3'UAGU, is also thermodynamically more stable than other internal loops with two GU closing pairs and three nucleotides opposite two nucleotides. The results from optical melting, nuclear magnetic resonance spectroscopy, and functional group substitution experiments suggest that the GU closing pairs form and that sheared GA pairs form in the internal loop. The NMR spectra show evidence of conformational dynamics, and several GA pairings are possible. Thus, this dynamic loop presents several possible structures for potential binding of drugs that target group I self-splicing introns. The results also contribute to understanding the structural and dynamic basis for the function and thermodynamic stability of this loop.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Schroeder
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Fountain
authors.forename: Scott D
authors.initials: SD
authors.lastname: Kennedy
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Lukavsky
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Puglisi
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Krugh
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives* / Q000737:chemistry; D000818:Animals; D001483:Base Sequence; D007288:Inosine / Q000737:chemistry; D007438:Introns; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D009843:Oligoribonucleotides / Q000138:chemical synthesis; D045363:Pneumocystis carinii / Q000737:chemistry*; D011522:Protons; D016337:RNA, Catalytic / Q000737:chemistry*; D012331:RNA, Fungal / Q000737:chemistry*; D013816:Thermodynamics; D013873:Thionucleotides / Q000737:chemistry
chemical_list: C116167:GIR1 ribozyme; D009692:Nucleic Acid Heteroduplexes; D009843:Oligoribonucleotides; D011522:Protons; D016337:RNA, Catalytic; D012331:RNA, Fungal; D013873:Thionucleotides; C043837:7-deazaadenine; D007288:Inosine; D000225:Adenine