Elucidation of a conserved RNA stem-loop structure in the packaging signal of human immunodeficiency virus type 1

A region of human immunodeficiency virus type 1 (HIV-1) genomic RNA known to interact with the viral nucleocapsid protein is one of the crucial components for retroviral genomic RNA packaging. We have investigated the secondary structure for this RNA packaging signal of HIV-1 using RNA mapping techniques and extensive computer analyses. Our results suggest that the RNA sequence containing the packaging signal conforms to a stable stem-loop structure and that a portion of this structure is conserved among twenty independent HIV-1 isolates. The heterogeneity of the RNA packaging sequence was not correlated with the amino acid sequence variability of the viral nucleocapsid protein. These findings have critical implication in understanding the viral maturation process.