DNA sequence-specific recognition of peptides incorporating the HPRK and polyamide motifs

Abstract Three peptide amides, HPRK(Py) 4 HPRK-NH 2 (PyH-12), HPRK(Py) 3 HPRK-NH 2 (PyH-11) and HPRK(Py) 2 HPRK-NH 2 (PyH-10), incorporating two HPRK motifs and various 4-amino-1-methylpyrrole-2-carboxylic acid residues (Py) were synthesized by solid-phase peptide methodology. The binding of these three peptides to a 5′- 32 P-labeled 158-mer DNA duplex (Watson fragment) and to a 5′- 32 P-labeled 135-mer DNA duplex (complementary Crick fragment) was investigated by quantitative DNase I footprinting. On the 158-mer Watson strand, the most distinctive DNase I blockages seen with all three peptides occur around positions 105–112 and 76–79, corresponding to the sequences 5′-GAGAAAAT-3′ and 5′-CGGT-3′, respectively. However, on the complementary Crick strand, only PyH-12 strongly discriminates the 5′-TTT-3′ site around positions 108–110 whereas both PyH-11 and PyH-10 have moderate binding around positions 102–112 comprising the sequence 5′-ATTTTCTCCTT-3′. Possible bidentate and single interactions of the side-chain functions and α-amino protons of the peptides with DNA bases are discussed.