Nucleotide sequence and predicted conformation (3, 4, 9, 36, 39) of the DEN2NGC 3′-SL. Nucleotides are numbered in reverse order, starting at the 3′ terminus of the dengue virus genome. The nucleotide sequence of the DEN1WP 3′-SL was identical to that of DEN2NGC, except as indicated for nt 63, 64, and 87, where nucleotides present in the DEN1WP 3′-SL are shown in parentheses adjacent to the replaced nucleotides in the DEN2NGC 3′-SL. The hatched rectangle enclosing nt A-7 and U-73 indicates that this base pair is deleted in DEN1mutF and DEN2mutF cDNAs and the respective genomic RNAs. Likewise, nucleotides U-3 and C-74, shown in bold italic type, are substituted, as indicated by arrows, in DEN1mutF and DEN2mutF genomes. The asterisk indicates a spontaneous substitution mutation to A that occurred at U-12 in DEN1mutFRev genomic RNA. The plus sign indicates the presence of the remaining ∼10.4 kb of the DEN1WP or DEN2NGC genome upstream from the 3′-SL in mutant genomes. All nucleotide sequence data were obtained as previously described by direct nucleotide sequencing of a PCR product derived from the 5′-3′ junction of circularized viral RNA (39) (see Materials and Methods).