Figure 2.

RNA Secondary Structure Predictions of Designed 3′ Exon Replacement HIV Binding Domains

RNA secondary structures of 3′ exon replacement cassettes containing HIV binding domains were predicted using Mfold and RNAfold web servers. MFE RNA secondary structures of HIV binding domain regions predicted in Mfold are shown (left column). RNAfold secondary structure predictions showing MFE (middle column) and centroid folds are shown (right column). RNA secondary structures of HIV binding domains with only a small region of the backbone plasmid are shown for clarity. Predicted free energies for the complete fold (binding domain and backbone cassette) are shown as ΔG.