Two 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. Although agreement on the stem/loop organization outside the high-affinity site 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 enough HIV material is present to allow the formation of an extended central stem structure (I/I'). Here we address the contribution of the original and alternative structures to function in RRE constructs with short 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 stabilizes 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.