FIG. 1.

Postulated stem-loop diagram of the 5′ untranslated region of HIV-1_Hxb2 and HIV-1_Lai genomic RNA (3, 4, 6, 19). The cleavage site within the 5′ major splice donor is marked by an arrow within the SD hairpin. The AUG initiation codon of the gag gene is highlighted and somewhat arbitrarily presented as hydrogen bonded in the interest of a compact figure. The PBS and the GCGCGC²⁶² palindrome are also highlighted. Focusing on the L sequence, the model can be considered proven regarding SL3 and the klh (5, 17, 20). It is rather inconclusive regarding stem-loop B and the PBS hairpin; for example, there is little evidence for the formation of stem-loop B in transcripts starting near the physiological 5′ end (1, 6, 8). A different model of the L sequence is shown in the insert (23). Note that stem-loop B and the klh can be theoretically formed from the sequence of any HIV-1 or simian immunodeficiency virus (strain cpz) (SIV_cpz) subtype (10, 13). In contrast, stem I is not found in subtype O and in SIV_cpz, stem-loop A is not found in subtypes D and O, the SD hairpin is not found in subtype N, and SL3 is not found in most SIV_cpz (10), indicating that these four separate folds are extensively but not as absolutely preserved as the stem-loop B and klh folds.