A Ribose Sugar Conformational Switch in the LTR-Retrotransposon Ty3 Polypurine Tract-Containing RNA/DNA Hybrid

Published

November 30, 2005

Author(s)

Hye Y. Yi-Brunozzi, D M. Brabazon, Daniela Lener, Stuart F. LeGrice, John Marino

Abstract

To probe structural features of a polypurine-tract (PPT) that mediate its specific recognition and processing, a model 20bp RNA/DNA duplex, which includes the full PPT sequence of the saccharomyces cerevisiae LTR-retrotransposon Ty3, has been investigated using high-resolution NMR spectroscopy. While homonuclear NOESY and DQF-COSY analysis 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 switch shows a dramatic alteration in the backbone trajectory of the RNA/DNA duplex upstream of the scissile phosphate bond, which misaligns the presentation of phosphate and hydroxyl groups relative to critical amino acid residues within the RNase H active site. The +1 sugar pucker switch may therefore represent an intrinsic structural feature of the Ty3 PPT structure which contributes to the fidelity of RNase H cleavage.

Citation

Journal of the American Chemical Society

Volume

127

Issue

No. 47

Pub Type

Journals

Keywords

high-resolution, NMR, polypurine tract, retrotransposon, RNA/DNA hybird, Ty3

Citation

Yi-Brunozzi, H. , Brabazon, D. , Lener, D. , LeGrice, S. and Marino, J. (2005), A Ribose Sugar Conformational Switch in the LTR-Retrotransposon Ty3 Polypurine Tract-Containing RNA/DNA Hybrid, Journal of the American Chemical Society (Accessed October 11, 2025)