Figure 5.

Schematic representation of the apparent disparate destabilization rankings for CNC and GNG bulged duplexes as a function of base identity and flanking residues. The eight heteroduplexes are arranged/ranked according to bulge base identity (A, T, C and G appear from top to bottom) and flanking residues (CC and GG positioned in the left and right columns, respectively). The bulge-induced destabilization energies (ΔΔG in kcal/mol) are expressed relative to the parent dodecamer with the respective heteroduplexes color-coded according to their corresponding category: Red Boxes represent highly destabilized bulges that exhibit non-two-state melting behavior, whereas Blue Boxes comprise moderately destabilizing bulges that undergo ideal two-state dissociation. The magnitude of energetic destabilization (ΔΔG) may be enhanced when a specific bulge base is positioned between Gs (A and C) or within Cs (T and G) as viewed in the horizontal comparisons. Moreover, the trends observed for CNC versus GNG bulges are quite distinct in terms of the overall ΔΔG magnitudes as noted in the vertical comparisons.