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Tryptophan-containing peptides, such as Lys-Trp-Lys, Lys-Trp-Gly-Lys and Lys-Gly-Trp-Lys, bind with high affinity to apurinic sites in DNA. The association constant for binding of Lys-Trp-Lys to an apurinic site is two orders of magnitude higher than that for binding to a native site. This is due to a very efficient stacking of tryptophan with the bases on both sides of the vacant apurinic site. When the complexes were incubated at 37 or 45 degrees C a cleavage of the phosphodiester bond was observed. Using pBR 322 DNA containing apurinic sites, conversion of the superhelical to the relaxed circular form was observed as a result of single-strand breakage. The peptide Lys-Gly-Lys had no effect and Lys-Trp-Lys did not induce any cleavage in pBR 322 DNA which did not contain any apurinic site. Therefore, a simple tripeptide, Lys-Trp-Lys, exhibits both the specificity of recognition and the activity of an endonuclease for apurinic sites in DNA.
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