Peptides which bind in the minor groove of DNA as antiparallel side-by-side dimers can be linked head-to-tail afford a new class of hairpin oligopeptides with enhanced sequence specificity for DNA. Four hexapeptides were wherein the terminal amine and carboxyl groups of tris(N-methylpyrrolecarboxamide) (P3) and -methylimidazole-2-carboxamide-netropsin (2-ImN), respectively, have been connected with glycine (Gly), β-alanine (βAla), 4-aminobutyric acid (GABA), and 5-aminovaleric acid (Ava) amino acids. The hexapeptide 2-ImN-GABA-P3 5'-TGTTA-3' sites with a binding affinity of 7.6 X 10^7 M^(-1) (10 mM Tris·HCl, 10 mM KCl, 10 mM MgCl_2, 5 mM CaCl_2 at pH 7.0 and 22 °C). The general and efficient synthetic methodology-for preparation of head-to-tail peptides should allow the design of a new class of hairpin peptides for specific recognition of many different in the minor groove of DNA.
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Mrksich et al. (1994) studied this question.