Recognition of chemically damaged DNA by the gene 32 protein from bacteriophage T4.

We have used fluorescence spectroscopy to investigate the binding of gene 32 protein from bacteriophage T4 to DNA which has been chemically modified with carcinogens or antitumor drugs. This protein exhibits a high specificity for single-stranded nucleic acids and binds more efficiently to DNA modified either with cis-diaminodichloroplatinum(II) or with aminofluorene derivatives than to native DNA. This increased affinity is related to the formation of locally unpaired regions which are strong binding sites for the single-strand binding protein.

[Recognition and cleavage of apurinic sites in DNA by the tripeptide lysyl-tryptophyl-lysine].

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.

Specific recognition of apurinic sites in DNA by a tryptophan-containing peptide.

We have used fluorescence spectroscopy to study the binding of lysyltryptophyl-alpha-lysine (Lys-Trp-Lys) to DNA modified by dimethyl sulfate before and after depurination and strand breakage. Quenching of tryptophan fluorescence increased upon association of the peptide with modified DNA as compared with native DNA. We have demonstrated that this quenching is related to a preferential stacking of the indole ring with nucleic acid bases in damaged regions.