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. 2011 Jul;17(7):1307–1320. doi: 10.1261/rna.2564311

FIGURE 3.

FIGURE 3.

Summary of the base-pairing interactions involving the C-box and G-box found in the predicted optimal RNA structures from the co-randomized viral selection. (A) The most stable secondary structure predicted by Mfold for nucleotides 1–557 of the wild-type HIV-2 genomic RNA. (B,C) When analyzed similarly, the 34 viral sequences from the evolved co-randomized library (Table 4) grouped into two CGI conformations, the branched CGI (B) and the extended CGI (C). Each potential base-pairing interaction of the randomized nucleotides is shown. Each ratio indicates the number of times this base-pairing is found in the most stable CGI-containing structure for each of the 34 viral sequences. (Double arrows) A level of flexibility exists with regard to the base-pairing partner for the randomized nucleotide. Depending on the identity of the randomized nucleotide, the base-pairing partner in the designated region may shift by one or two positions.