title: RNA motifs that determine specificity between a viral replicase and its promoter.
abstract: The 3' end of brome mosaic virus RNA contains a tRNA-like sequence that directs its RNA synthesis. A stem loop structure in this sequence, stem loop C (SLC), was investigated using NMR, and correlated with its ability to direct RNA synthesis by its replicase. SLC consists of two discrete domains, a flexible stem with an internal loop and a rigid stem containing a 5'-AUA-3' triloop. Efficient RNA synthesis requires the sequence on only one side of the flexible stem and a specific compact conformation of the triloop. A high resolution structure of the triloop places the 5' adenine out in solution, and the 3' adenine within the triloop, held tightly through stacking and unusual hydrogen bonds. This high resolution structure of an RNA promoter from a (+)-strand RNA virus provides new insights into how the RNA-dependent RNA polymerase binds to the RNA to initiate synthesis.
authors.affiliation: Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720-1460, USA.
authors.forename: C H
authors.initials: CH
authors.lastname: Kim
authors.forename: C C
authors.initials: CC
authors.lastname: Kao
authors.forename: I
authors.initials: I
authors.lastname: Tinoco
mesh_terms: D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D017795:Bromovirus / Q000201:enzymology / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012367:RNA, Viral / Q000096:biosynthesis* / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase / Q000378:metabolism*; D012996:Solutions; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D012367:RNA, Viral; D012996:Solutions; D012324:RNA-Dependent RNA Polymerase