title: Active suppressor tRNAs with a double helix between the D- and T-loops.
abstract: One of the most conserved elements of the tRNA structure is the reverse-Hoogsteen base-pair T54--A58 in the T-loop, which plays a major role in the maintenance of the standard L-shape conformation. Here, we present the results of in vivo selection of 51 active suppressor tRNA clones, none of which contains base-pair T54--A58. In 49 clones, we found two regions in the D and T-loops that are complementary to each other. This finding suggests the existence of an inter-loop double helix consisting of three base-pairs, which could have the same role as base-pair T54--A58 in the fixation of the juxtaposition of the two helical domains within the L-shape. From this point of view, the appearance of the inter-loop double helix represents a compensatory effect for the absence of base-pair T54--A58. The results shed new light on the role of different elements of the tRNA structure in the formation of the standard L-shape conformation and on the possibility of synonymous replacements of one arrangement by another in functional RNA molecules.
authors.affiliation: Département de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7.
authors.forename: Natalia
authors.initials: N
authors.lastname: Kotlova
authors.forename: Tetsu M
authors.initials: TM
authors.lastname: Ishii
authors.forename: Ekaterina I
authors.initials: EI
authors.lastname: Zagryadskaya
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Steinberg
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer / Q000737:chemistry* / Q000378:metabolism