DNA-binding assay.

The affinity of peptide P307 for DNA was investigated by electrophoretic mobility shift assay (27). P307 was mixed with 50 ng of random DNA (1-kb amplicon of Bdellovibrio genomic DNA) at different peptide/DNA ratios (0:1 to 15:1) in a binding buffer (5 mM Tris-HCl [pH 8.0], 10 mM EDTA, 5% glycerol, 20 mM KCl, 50 μg/ml bovine serum albumin). As a positive control, a peptide from Bdellovibrio bacteriovorus that was previously found in our laboratory to have DNA-binding capacity (amino acid sequence MASKTKKTEYIRERKKATSGKKRKAANRTKGTTKSAKTLFKD) was used (unpublished results). After incubation for 1 h at 22 to 25°C, the peptide and DNA mixture was analyzed by agarose gel electrophoresis (27).