2 SECONDARY STRUCTURES FOR THE RRE OF HIV-1

The RRE, the target sequence for the Rev protein of HIV-1, is a highly structured RNA sequence characterized by multiple stem loops. Althoug h agreement on the stem/loop organization outside the high-affinity si te was reached some time ago by several laboratories, recent work has suggested an alternative structure in which sequences from two of the stem/loops (IV and V) pair to form one long stem/loop (IV/V) when enou gh HIV material is present to allow the formation of an extended centr al stem structure (I/I'). Here we address the contribution of the orig inal and alternative structures to function in RRE constructs with sho rt and extended I'I' regions. We confirm that extended I/I' structures improve RRE function and may stabilize the overall structure. However , we find no evidence that an extended I/I' structure preferentially s tabilizes either alternative structure with respect to the other. The two alternative structures are approximately functionally equivalent, and both are probably present in an in vivo population of RREs.