Overall , the SHAPE data support our original model ( Figure 1A ) ; this is particularly the case for SLs 1 - 4 . The loops of these four regions contain the most highly reactive , exposed nucleotides . The remainder of the most highly reactive nucleotides are situated in bulges , internal loops , single - stranded regions linking SLs and the closing pairs of helices , with the exception of G 90 , U101 and A320 . The tip of SL5 contains mainly unreactive nucleotides , possibly indicating kissing - loop interactions involved in dimer initiation . Nucleotides that were predicted to be base - paired in SL1 were unreactive to 1M7 , with the exception of A131 . As the A residue 3 0 of this was predicted to be bulged , and is unreactive , it is likely that the bulge forms consistently at A131 and not at A132 ( shown in Figure 2 ) . Predicted base - paired nucleotides in SL2 are relatively unreactive , except for closing pairs and G - U pairs . The exceptions are nucleotides U244 - G246 , which are highly reactive ; this may indicate that the internal loop 3 0 of this is larger and includes these nucleotides . Structural predictions using the RNA structure programme ( 44 ) and 1M7 reactivities as pseudo free - energy constraints suggest that this is the case in the alternative structure ( shown in Figure 2 ) . Minimal free energy predictions suggested that the SL2 structure is maintained independently of adjacent sequences . To validate this hypothesis and search for LRIs that the single - stranded regions of SL2 may form with other areas of the packaging signal , we transcribed SL2 RNA independently , examined its 1M7 reactivity , and compared the data with SL2 in the context of the 511 - nt RNA ( Figure 1B ) . Nucleotide reactivities are broadly similar across SL2 , whether analysed alone or in the context of the extended 5 0 and 3 0 structure , suggesting that SL2 forms independently of 5 0 and 3 0 sub - domains , i.e. independent of LRIs . Subtle differences in nucleotide reactivity were noted between the structures shown in Figure 1A and B , which may reflect minor experimental variation .