Binding of a tryptophan-containing peptide (lysyltryptophyllysine) to deoxyribonucleic acid modified by 2-(N-acetoxyacetylamino)fluorene.

The binding of the tripeptide Lys-Trp-Lys to DNA modified by reaction with the chemical carcinogen 2-(N-acetoxyacetylamino)fluorene (AAAF) has been investigated by fluorescence spectroscopy. A quenching of tryptophan fluorescence was observed which increased when the degree of base substitution by AAAF increased. Similar results were obtained with the 7-iodo derivative of AAAF (AAAIF). Two hypotheses are discussed which could account for the experimental results: (1) stacking interactions of the tryptophyl residue of the peptide with nucleic acid bases in locally unpaired regions in the vicinity of modified bases; (2) energy transfer from the tryptophyl residue of the peptide to acetylaminofluorene bound to guanine bases without direct interaction of this residue with nucleic acid bases (outside binding). The results obtained with denatured DNA in the absence and the presence of chemical modifications by AAAF or AAAIF allow us to conclude that energy transfer contributes to fluorescence quenching in the case of AAIF but not in that of AAF. Stacking interactions are therefore responsible for fluorescence quenching of Lys-Trp-Lys when bound to AAF-modified DNA. In the case of DNA-AAIF, fluorescence quenching is due both to energy transfer and to stacking of the tryptophan ring with bases inside the helix. These results are discussed in relation to what is already known in terms of local structure and with respect to the role that could be played by aromatic residues of proteins in the recognition of chemically damaged DNA.