title: A new structural motif in the left terminal domain of large viroids identified by covariation analysis.
abstract: Sequence alignment of non-hammerhead viroids (Pospiviroidae) reveals that they can be divided into large and small viroids. Covariation analysis of these groups provides evidence for a rod-like secondary structure, but also for two proposed suboptimal structures, namely hairpin I and a bifurcation in the left terminus of large viroids. The strongest covariation within the branched T1 domain of all large Pospiviroidae indicates a new tertiary interaction, resulting in a double-pseudoknot within the (+) strand or an additional hairpin in the (-) strand. The structural element is expected to play a role in the viroid's life cycle.
authors.affiliation: Institut für Anorganische und Analytische Chemie, Justus-Liebig-Universität Giessen, Schuberstrasse 60, D-35392 Giessen, Germany. gast@gesim.de
authors.forename: Frank-Ulrich
authors.initials: FU
authors.lastname: Gast
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry*; D000079962:RNA, Circular; D012367:RNA, Viral / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D014772:Viroids / Q000737:chemistry* / Q000145:classification
chemical_list: D000079962:RNA, Circular; D012367:RNA, Viral; D012313:RNA