Specific nicking of DNA at apurinic sites by peptides containing aromatic residues

Tripeptides containing aromatic residues between basic ones, such as Lys-Trp-Lys and Lys-Tyr-Lys can nick supercoiled or relaxed DNAs containing apurinic/apyrimidinic sites (AP-sites). The nicking, which is ionic strength-dependent, occurs at AP-sites, since native PM2 DNA is not hydrolyzed. The nicking activity of the tripeptides at AP-sites occurs in total darkness. An activation energy of 21 +/- 2 kcal . mol-1 has been calculated for the incision of PM2 DNA by Lys-Trp-Lys. Tripeptides without aromatic residues, such as Lys-Ala-Lys-O-Methyl and Lys-Lys-Lys, can nick apurinic DNA, although with a much lower efficiency. Relaxed depurinated PM2 DNA is a poor substrate for the tripeptide, indicating that single-stranded regions are better recognition sites. The nicking of the DNA backbone probably occurs by beta elimination, since reduced AP-sites do not act as substrate. The termini generated are 3'-hydroxyl and 5'-phosphoryl.