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.
Three-dimensional folding of an RNA hairpin required for packaging HIV-1.,Pappalardo L, Kerwood DJ, Pelczer I, Borer PN J Mol Biol. 1998 Oct 2;282(4):801-18. PMID:9743628[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
↑ Pappalardo L, Kerwood DJ, Pelczer I, Borer PN. Three-dimensional folding of an RNA hairpin required for packaging HIV-1. J Mol Biol. 1998 Oct 2;282(4):801-18. PMID:9743628 doi:http://dx.doi.org/S0022-2836(98)92046-0
