The synthetic peptide wrwycr binds Holliday junctions and other branched DNA repair intermediates, and interferes in vitro with enzymes that participate in DNA repair. Peptide wrwycr is bactericidal for both Gram- and Gram+ bacteria. Because peptide wrwycr is synergistically lethal with DNA-damaging agents such as UV and mitomycin C, we hypothesized that the peptide traps DNA repair intermediates that arise during the repair of DNA damage. Therefore, we investigated the potential synergy between peptide wrwycr and two distinct topoisomerase II inhibitors: norfloxacin, a fluoroquinolone antibiotic that stabilizes open DNA complexes, and novobiocin, a coumarin that inhibits their ATPase activity. Repair of breaks caused by topoisomerases II requires recombination-dependent DNA repair. Co-treatments with sublethal concentrations of peptide wrwycr and a bacteriostatic concentration of norfloxacin indicated synergy only at high sublethal concentrations of the peptide. Surprisingly, low sublethal concentrations of wrwycr protected cells from the effects of norfloxacin: co-treated cells showed increased cell viability and reduced DNA damage compared to treatment with norfloxacin alone. E. coli lacking tolC lost this "protection", and wrwycr co-treatment with norfloxacin induces the expression of TolC and its regulator MarA. In contrast, wrwycr demonstrated synergistic lethality with novobiocin even at low peptide concentration. We propose that this synergy is due not only to inhibition of DNA damage repair but also to the peptide-mediated increased membrane permeability, thereby permitting novobiocin to be more efficient.