Three-dimensional folding of an RNA hairpin required for packaging HIV-1.


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.

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@article{Pappalardo1998ThreedimensionalFO, title={Three-dimensional folding of an RNA hairpin required for packaging HIV-1.}, author={Luciano Libero Pappalardo and Deborah J Kerwood and Istvan Pelczer and Philip N. Borer}, journal={Journal of molecular biology}, year={1998}, volume={282 4}, pages={801-18} }