title: NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA.
abstract: Pseudoknot formation folds the 3' ends of many plant viral genomic RNAs into structures that resemble transfer RNA in global folding and in their reactivity to transfer RNA-specific proteins. The solution structure of the pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy. The molecule is stabilized by the hairpin formed by the 5' end of the RNA, and by the intricate interactions related to the loops of the pseudoknot. Loop 1 spans the major groove of the helix with only two of its four nucleotides. Loop 2, which crosses the minor groove, interacts closely with its opposing helix, in particular through hydrogen bonds with a highly conserved adenine. The structure resulting from this interaction between the minor groove and single-stranded RNA at helical junctions displays internal mobility, which may be a general feature of RNA pseudoknots that regulates their interaction with proteins or other RNA molecules.
authors.affiliation: Nijmegen SON Research Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld, 6525 ED Nijmegen, The Netherlands.
authors.forename: M H
authors.initials: MH
authors.lastname: Kolk
authors.forename: M
authors.initials: M
authors.lastname: van der Graaf
authors.forename: S S
authors.initials: SS
authors.lastname: Wijmenga
authors.forename: C W
authors.initials: CW
authors.lastname: Pleij
authors.forename: H A
authors.initials: HA
authors.lastname: Heus
authors.forename: C W
authors.initials: CW
authors.lastname: Hilbers
mesh_terms: D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D004047:Diethyl Pyrocarbonate / Q000737:chemistry; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry*; D017806:Tymovirus / Q000235:genetics
chemical_list: D012330:RNA, Double-Stranded; D012367:RNA, Viral; D012343:RNA, Transfer; D000604:Amino Acyl-tRNA Synthetases; D004047:Diethyl Pyrocarbonate