Three-dimensional folding of an RNA hairpin required for packaging HIV-1 1 1 Edited by I. Tinoco

Three-dimensional folding of an RNA hairpin required for packaging HIV-1 1 1 Edited by I. Tinoco An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Molecular Biology Elsevier

Three-dimensional folding of an RNA hairpin required for packaging HIV-1 1 1 Edited by I. Tinoco

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Publisher
Academic Press
Copyright
Copyright © 1998 Academic Press
ISSN
0022-2836
D.O.I.
10.1006/jmbi.1998.2046
Publisher site
See Article on Publisher Site

Abstract

An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors.

Journal

Journal of Molecular BiologyElsevier

Published: Oct 2, 1998

References

  • Relaxation matrix analysis of 2D NMR data
    Borgias, B.A.; Gochin, M.; Kerwood, D.J.; James, T.L.
  • First glimpses at structure-function relationships of the nucleocapside protein of retroviruses
    Darlix, J.-L.; Lapadat-Tapolsky, M.; de Rocquigny, H.; Roques, B.P.
  • Ring current effects in the NMR of nucleic acids
    Giessner-Prettre, C.; Pullman, B.; Borer, P.N.; Kan, L.S.; Ts’o, P.O.P.
  • Evidence that a kissing loop structure facilitates genomic RNA dimerisation in HIV-1
    Haddrick, M.; Lear, A.L.; Cann, A.J.; Heaphy, S.
  • Improved predictions of secondary structures for RNA
    Jaeger, J.A.; Turner, D.H.; Zuker, M.
  • Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein
    South, T.L.; Summers, M.F.

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