Figure 2.

Binding fraction for polyamides composed of two different types of rings. (a) For polyamides composed of a ring that recognizes adenine and a ring that recognizes thymine, target sequences composed of only AT bp may be recognized with a binding fraction close to one for rings with strong base specificity. A given level of binding may be obtained with an adenine-specific ring and a thymine-specific ring of identical specificity (point marked “A”) or with a placeholder and an adenine-specific ring of twice that strength (“B”). (b) For polyamides composed of a ring that recognizes adenine and a ring that recognizes guanine, binding to a sequence with 4-AT and 1-GC bp, the maximal binding fraction is 0.5. To achieve this fraction, the polyamide must be designed from a strong adenine-specific ring and a weaker guanine-specific ring (“A”). If the guanine-specific ring is replaced by a placeholder, the maximal binding fraction drops to 0.25 (“B”). If the guanine-specific ring is stronger than the adenine-specific ring, the binding fraction drops to close to zero (“C”).