Influence of β-Alanine on Hairpin Polyamide Orientation in the DNA Minor Groove

Abstract

Antiparallel polyamides containing 1H-pyrrole, 1H-imidazole, and 3-hydroxy-1H-pyrrole amino acids display a preference for minor-groove binding oriented N-C with respect to the 5′-3′ direction of the DNA helix. We find that replacement of a central Py/Py pair with a β/β pair within a ten-ring hairpin relaxes the orientation preference and, for some DNA sequences, causes the polyamide to prefer the opposite C-N orientation. Substitution of the achiral γ-aminobutanoic acid (γ) with either (R)(or S)-2-(acetylamino)-4-aminobutanoic acid moderates the orientation preference of the 2-β-2-hairpin.

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