title: Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus.
abstract: The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenomic RNA synthesis. Short synthetic oligoribonucleotide mimics of the RNA-1 TABS and the RNA-2 TA form a weak 1:1 bimolecular complex in vitro with a K(a) of 5.3 x 10(4) M(-1). K(a) determination for a series of RNA-1 and RNA-2 mimic variants indicated optimum stability is obtained with seven-base complementarity. Thermal denaturation and NMR show that the RNA-1 TABS 8mers are weakly ordered in solution while RNA-2 TA oligomers form the predicted hairpin. NMR diffusion studies confirmed RNA-1 and RNA-2 oligomer complex formation in vitro. MC-Sym generated structural models suggest that the bimolecular complex is composed of two stacked helices, one being the stem of the RNA-2 TA hairpin and the other formed by the intermolecular base pairing between RNA-1 and RNA-2. The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function.
authors.affiliation: Department of Plant Pathology, Box 7616, North Carolina State University, Raleigh, NC 27695, USA.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Guenther
authors.forename: Tim L
authors.initials: TL
authors.lastname: Sit
authors.forename: Hanna S
authors.initials: HS
authors.lastname: Gracz
authors.forename: Michael A
authors.initials: MA
authors.lastname: Dolan
authors.forename: Hannah L
authors.initials: HL
authors.lastname: Townsend
authors.forename: Guihua
authors.initials: G
authors.lastname: Liu
authors.forename: Winnell H
authors.initials: WH
authors.lastname: Newman
authors.forename: Paul F
authors.initials: PF
authors.lastname: Agris
authors.forename: Steven A
authors.initials: SA
authors.lastname: Lommel
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003198:Computer Simulation; D015967:Gene Expression Regulation, Viral; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid; D019183:Tombusviridae / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D046911:Macromolecular Substances; D012367:RNA, Viral; D038621:Regulatory Sequences, Ribonucleic Acid