Recognition of the Minor Groove of DNA by Hairpin Polyamides Containing α-Substituted-β-Amino Acids

Incorporation of the flexible amino acid β-alanine (β) into hairpin polyamides composed of N -methylpyrrole (Py) and N -methylimidazole (Im) amino acids is required for binding to DNA sequences longer than seven base pairs with high affinity and sequence selectivity. Pairing the α-substituted-β-amino acids ( S )-isoserine ( S Is), ( R )-isoserine ( R Is), β-aminoalanine (Aa), and α-fluoro-β-alanine (Fb) side-by-side with β in hairpin polyamides alters DNA binding affinity and selectivity relative to the parent polyamide containing a β/β pairing. Quantitative DNase I footprinting titration studies on a restriction fragment containing the sequences 5‘-TGC N GTA-3‘ ( N = A, T, G, and C) show that the polyamide ImPy S IsImPy-γ-PyPyβImPy-β-Dp ( S Is/β pairing) binds to N = T ( K a = 4.5 × 10 9 M - 1 ) in preference to N = A ( K a = 6.2 × 10 8 M - 1 ). This result stands in contrast to the essentially degenerate binding of the parent ImPyβImPy-γ-PyPyβImPy-β-Dp (β/β pairing) to N = T and N = A, and to the slight preference of ImPyβImPy-γ-PyPy S IsImPy-β-Dp (β/ S Is pairing) to N = A over N = T. Additionally, this study reveals that incorporation of R Is, Aa, and Fb into polyamides significantly reduces binding affinity. Therefore, DNA binding in the minor groove is sensitive to the stereochemistry, steric bulk, and electronics of the substituent at the α-position of β-amino acids in hairpin polyamides containing β/β pairs.