Key result
Biochemical probing and free energy minimization identified a highly stable stem-loop structure with a heptaloop and common ACC/GAYC motifs in the 5' leader sequence of Mason-Pfizer monkey virus.
Identifies a common structural and sequence motif in the 5' leader sequence of retroviruses that may be involved in genomic RNA packaging.
A stable secondary structure model is presented for the region 3' of the primer-binding site to 130 bases into the gag sequence of the prototype type D retrovirus Mason-Pfizer monkey virus. Using biochemical probing of RNA from this region in association with free energy minimization, we have identified a stem-loop structure in the region, which from other studies has been shown to be important for genomic RNA encapsidation. The structure involves a highly stable stem of five G-C pairs terminating in a heptaloop. Comparison of the Mason-Pfizer monkey virus structure with one predicted for squirrel monkey retrovirus demonstrates an identical stem and a common ACC motif in the loop. Free energy studies of the secondary structure of the 5' regions of eight other retroviruses predict stem loops which have similar GAYC motifs. We believe this may represent a common structural and sequence motif which among other functions may be involved in genomic RNA packaging in these viruses.
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Harrison et al. (1995) studied Mason-Pfizer monkey virus. Biochemical probing and free energy minimization identified a highly stable stem-loop structure with a heptaloop and common ACC/GAYC motifs in the 5' leader sequence of Mason-Pfizer monkey virus.
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