Search for low-molecular-weight compounds that specifically bind UV-damaged DNA

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DNA duplexes (20-bp long) containing the (6-4) photoproduct or the cyclobutane pyrimidine dimer (CPD) at the target sequence for distamycin A, AATh AATT, were prepared, and distamycin binding was analyzed by CD spectroscopy. Induced CD signals at the long wavelength region, which showed the distamycin binding, were detected for the duplex containing the (6-4) photoproduct. Only a small induction was observed for the CPD-containing duplex. Careful titration experiments were carried out using 14-bp duplexes at a high salt concentration to avoid nonspecific binding, and the curve fitting analysis revealed a reduced affinity and a stoichiometry of 2.50 for the photoproduct-containing DNA. The induced CD difference spectra obtained for the complexes with the normal target DNA and the damaged DNA were identical with those reported previously for the 1:1 and 2:1 complexes, respectively. The 2:1 binding was observed even at low drug concentrations, and this result indicated that distamycin A always shows the 2:1 binding mode for the (6-4) photoproduct-containing DNA. In order to compare the binding of distamycin A with that of the human UV-damaged DNA-binding protein, which recognizes DNA containing the (6-4) photoproduct in human cells, the recognition spectrum of distamycin A was obtained, and the spectrum was almost the same as that obtained previously for the protein. From these results, it is concluded that distamycin A is a good lead compound to obtain molecules that specifically bind the UV-damaged DNA. Toward the development of the artificial repair system of the UV-damaged DNA, we analyzed the alkali degradation reaction of the (6-4) photoproduct and found that the first step was hydrolysis of the N3-C4 bond of the 5' component.