EXTENDED HAIRPIN POLYAMIDE MOTIF FOR SEQUENCE-SPECIFIC RECOGNITION INTHE MINOR-GROOVE OF DNA

Background: Three-ring polyamides containing N-methylimidazole and N-m ethylpyrrole amino acids bind sequence;specifically to double-helical DNA by forming side-by-side complexes in the minor groove, Simple pair ing rules relate the amino-acid sequence of a pyrrole-imidazole polyam ide to its expected DNA target site, and polyamides that target a wide variety of DNA sequences have been synthesized, We have shown previou sly that two three-ring subunits could be linked together by an alipha tic amino acid, increasing the binding affinity of the polyamide and, in some cases, increasing the length of the target sequence. We set ou t to determine whether different types of linkers could be used in a s ingle molecule to generate a nine-ring polyamide molecule that would b ind to specific DNA sequences. Results: A nine-ring pyrrole-imidazole polyamide, containing two different amino acid linkers, beta-alanine a nd gamma-aminobutyric acid, has been synthesized and shown to specific ally bind a designated nine-base-pair target site at subnanomolar conc entration in a novel extended hairpin conformation. Conclusions: The a mino acids gamma-aminobutyric acid and beta-alanine optimally link thr ee-ring pyrrole-imidazole subunits in 'hairpin' and 'extended' conform ations, respectively, Both aliphatic amino acids can be combined to ge nerate a nine-ring polyamide that specifically recognizes a nine-base- pair target site with very high affinity.