Sequence-specific DNA recognition by cyclic pyrrole-imidazole cysteine-derived polyamide dimers

Pyrrole-imidazole (PI) polyamides bind to the minor groove of the DNA duplex in a sequence-specific manner and thus have the potential to regulate gene expression. To date, various types of PI polyamides have been designed as sequence-specific DNA binding ligands. One of these, cysteine cyclic PI polyamides containing two β-alanine molecules, were designed to recognize a 7 bp DNA sequence with high binding affinity. In this study, an efficient cyclization reaction between a cysteine and a chloroacetyl residue was used for dimerization in the synthesis of a unit that recognizes symmetrical DNA sequences. To evaluate specific DNA binding properties, dimeric PI polyamide binding was measured by using a surface plasmon resonance (SPR) method. Extending this molecular design, we synthesized a large dimeric PI polyamide that can recognize a 14 bp region in duplex DNA.