title: A ribose sugar conformational switch in the LTR-retrotransposon Ty3 polypurine tract-containing RNA/DNA hybrid.
abstract: To probe structural features of a polypurine tract (PPT) that mediate its specific recognition and processing, a model 20 bp RNA/DNA hybrid duplex, which includes the full PPT sequence of the Saccharomyces cerevisiae LTR-retrotransposon Ty3, has been investigated using solution NMR spectroscopy. While homonuclear NOESY and DQF-COSY analyses indicate that this PPT-containing RNA/DNA hybrid adopts an overall A-form-like helical geometry, an unexpected sugar pucker switch has been detected for the ribose at position +1, relative to the cleavage site, on the RNA strand. A model of the conformational changes induced by the A- to B-type sugar pucker switch shows a significant change in the backbone trajectory of the RNA strand, which alters the presentation of backbone phosphate and 2' hydroxyl groups 3' of this residue. This observation implies that part of the mechanism governing RNase H fidelity may be through distortion of the RNA/DNA helix one base ahead of the scissile bond.
authors.affiliation: HIV Drug Resistance Program, NCI-Frederick, Frederick, Maryland 21702, USA.
authors.forename: Hye Young
authors.initials: HY
authors.lastname: Yi-Brunozzi
authors.forename: Danielle M
authors.initials: DM
authors.lastname: Brabazon
authors.forename: Daniela
authors.initials: D
authors.lastname: Lener
authors.forename: Stuart F J
authors.initials: SF
authors.lastname: Le Grice
authors.forename: John P
authors.initials: JP
authors.lastname: Marino
mesh_terms: D002236:Carbohydrate Conformation; D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D011687:Purines / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry*; D018626:Retroelements; D012266:Ribose / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D020079:Terminal Repeat Sequences; D045564:Transposon Resolvases / Q000737:chemistry
chemical_list: D009692:Nucleic Acid Heteroduplexes; D011687:Purines; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins; D012313:RNA; D012266:Ribose; D004247:DNA; D045564:Transposon Resolvases; D012194:RNA-Directed DNA Polymerase; C496084:reverse transcriptase Ty3, S cerevisiae