title: NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.
abstract: The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared with predictions made with the MC-Sym program.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
authors.forename: Yelena V
authors.initials: YV
authors.lastname: Lerman
authors.forename: Scott D
authors.initials: SD
authors.lastname: Kennedy
authors.forename: Neelaabh
authors.initials: N
authors.lastname: Shankar
authors.forename: Marc
authors.initials: M
authors.lastname: Parisien
authors.forename: Francois
authors.initials: F
authors.lastname: Major
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D000225:Adenine / Q000737:chemistry; D020816:Amino Acid Motifs; D020029:Base Pairing; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D054730:Protein Interaction Domains and Motifs; D011685:Purine Nucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D018626:Retroelements; D017423:Sequence Analysis, RNA; D013816:Thermodynamics
chemical_list: D011685:Purine Nucleotides; D018626:Retroelements; D012313:RNA; D000225:Adenine