3-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-famil y structure. However, the GGAG tetraloop appears to be flexible with t he second (G10) and fourth (G12) bases extruded from the normal stacki ng arrangement. The A-base (All) 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, All, a nd G12 are unoccupied in the free RNA structure. The loop should be ea sily adaptable to binding by the HIV-1 nucleocapsid protein or loop re ceptors. (C) 1998 Academic Press.