title: Structural characterization of the 69 nucleotide potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis.
abstract: The 69 nucleotide left-terminal domain (T(L)) of the potato spindle tuber RNA viroid (PSTVd) constitutes one of its five structural elements. Due to a twofold complementary sequence repeat, two possible conformations are proposed for the T(L) secondary structure; an elongated-rod and a bifurcated form. In the present study, two T(L) mutants were designed that remove the symmetry of the sequence repeats and ensure that either the bifurcated or the elongated-rod conformation is thermodynamically favored. Imino 1H and 15N resonances were assigned for both mutants and the native T(L) domain based on 1H-1H NOESY and heteronuclear 1H-15N HSQC high-resolution NMR spectra. The NMR secondary structure analysis of all constructs establishes unambiguously the elongated-rod form as the secondary structure of the native T(L) domain. Temperature-gradient gel electrophoresis and UV melting experiments corroborate these results. A combined secondary structure and sequence analysis of T(L) domains of other Pospiviroidae family members indicates that the elongated-rod form is thermodynamically favored for the vast majority of these viroids.
authors.affiliation: Institut für Physikalische Biologie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany. dingley@biochem.ac.uk
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Dingley
authors.forename: Gerhard
authors.initials: G
authors.lastname: Steger
authors.forename: Bernd
authors.initials: B
authors.lastname: Esters
authors.forename: Detlev
authors.initials: D
authors.lastname: Riesner
authors.forename: Stephan
authors.initials: S
authors.lastname: Grzesiek
mesh_terms: D001483:Base Sequence; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010942:Plant Viruses / Q000737:chemistry* / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D011198:Solanum tuberosum / Q000382:microbiology / Q000502:physiology; D013816:Thermodynamics; D014772:Viroids / Q000737:chemistry* / Q000235:genetics
chemical_list: D012367:RNA, Viral