Extended hairpin polyamide motif for sequence-specific recognition in the minor groove of DNA

Background: Three-ring polyamides containing N-methylimidazole and N-methylpyrrole amino acids bind sequence;specifically to double-helical DNA by forming side-by-side complexes in the minor groove, Simple pairing rules relate the amino-acid sequence of a pyrrole-imidazole polyamide to its expected DNA target site, and polyamides that target a wide variety of DNA sequences have been synthesized, We have shown previously that two three-ring subunits could be linked together by an aliphatic amino acid, increasing the binding affinity of the polyamide and, in some cases, increasing the length of the target sequence. We set out to determine whether different types of linkers could be used in a single molecule to generate a nine-ring polyamide molecule that would bind to specific DNA sequences. Results: A nine-ring pyrrole-imidazole polyamide, containing two different amino acid linkers, beta-alanine and gamma-aminobutyric acid, has been synthesized and shown to specifically bind a designated nine-base-pair target site at subnanomolar concentration in a novel extended hairpin conformation. Conclusions: The amino acids gamma-aminobutyric acid and beta-alanine optimally link three-ring pyrrole-imidazole subunits in 'hairpin' and 'extended' conformations, respectively, Both aliphatic amino acids can be combined to generate a nine-ring polyamide that specifically recognizes a nine-base-pair target site with very high affinity.