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. 2007 Aug 7;35(15):5253–5261. doi: 10.1093/nar/gkm564

Figure 6.

Figure 6.

RNA structure probing of the gag–U3R interaction. (A) 5′ radiolabeled gag and U3R transcripts were either incubated alone or with the other non-radiolabeled U3R transcript as indicated (left panel). The same experiments were performed with 3′ radiolabeled transcripts (right panel). Subsequently, the transcripts were treated with lead acetate (5 mM) for different time periods (0, 2.5, 5 and 10 min). The lane denoted OH− indicates the hydrolysis ladder upon alkali treatment. The polyA, TAR and U3 sequences are indicated by black lines. The numbered stretches are discussed in the text and correlate with specific domains in panel B. (B) RNA base-pairing model of the gag–U3R interaction based on RNA structure probing. Gag 619–696 nt and U3R 9109–9229 nt (LAI coordinates) are shown. Blue arrows indicate nucleotides that are cleaved by lead ions and thus likely to be single stranded. Red circles indicate nucleotides that are cleaved by lead ions in monomeric RNA, but become protected upon gag–U3R complex formation. Blue circles indicate nucleotides that become more exposed upon gag–U3R interaction.