SECONDARY STRUCTURE MODEL OF THE MASON-PFIZER MONKEY VIRUS 5' LEADER SEQUENCE - IDENTIFICATION OF A STRUCTURAL MOTIF COMMON TO A VARIETY OFRETROVIRUSES

A stable secondary structure model is presented for the region 3' of t he primer-binding site to 130 bases into the gag sequence of the proto type type D retrovirus Mason-Pfizer monkey virus. Using biochemical pr obing of RNA from this region in association with free energy minimiza tion, we have identified a stem-loop structure in the region, which fr om other studies has been shown to be important for genomic RNA encaps idation. The structure involves a highly stable stem of five G-C pairs terminating in a heptaloop. Comparison of the Mason-Pfizer monkey vir us structure with one predicted for squirrel monkey retrovirus demonst rates an identical stem and a common ACC motif in the loop. Free energ y studies of the secondary structure of the 5' regions of eight other retroviruses predict stem loops which have similar GAYC motifs. We bel ieve this may represent a common structural and sequence motif which a mong other functions may be involved in genomic RNA packaging in these viruses.