DC92-B

The sequence selectivity of DNA alkylation by the recently isolated pluramycin antitumour antibiotic DC92-B has been investigated using two methods: a piperidine-induced strand-breaking procedure and a Taq DNA polymerase/linear amplification method. These techniques reveal that guanines are the most reactive sites for alkylation and that the level of adduct formation at these sites is clearly sequence dependent. The highest levels of alkylation occurred at isolated guanines located in 5'-CGT sequences and also at the 5'-G in some 5'-CGG sequences. Isolated guanines in 5'-TGT sequences were also quite reactive. We have also re-examined, in parallel, the sequence selectivity of binding of the structurally-related compound hedamycin: the first known example of a bis(epoxide)-containing, DNA-alkylating pluramycin. Our studies included a more extensive sequence analysis of hedamycin binding than that previously reported and we are able, therefore, to define more precisely the sequence preference. Despite significant differences in the stereochemistry and substitution of their bis(epoxide) sidechains, hedamycin and DC92-B exhibited very similar sequence selectivities in our assays.

The DNA-binding mode of antitumor and antiviral agents has been evaluated by electrochemiluminescence (ECL) of tris(1,10-phenanthroline)-ruthenium complex (Ru(phen)(3)(2+)) in the presence of oxalate ion in pH 7.3 Tris buffer solution. An emission of Ru(phen)(3)(2+) was observed repeatedly with a voltage above 1000mV subjected to a potential sweep from 0 to 1250mV. The addition of lambdaDNA into the solution containing 1 micro M of Ru(phen)(3)(2+) caused the decrease in the ECL intensity, which became half at a DNA concentration of 20 micro M. This is due to the binding of Delta-type of Ru(phen)(3)(2+) with DNA in the major groove of DNA. When the various concentrations of the drug were added to the solution containing 1& micro M Ru(phen)(3)(2+), the ECL intensity was not affected by the concentration of the drug in the absence of DNA. In the presence of DNA (10 micro M), however, two ECL emission patterns were observed when the concentration of the drug was varied. The pattern that the ECL intensity increased with increasing the drug concentration was observed for cisplatin, daunomycin, and DC92-B. This may have resulted from the DNA binding of the drug with a major groove site, where Ru(phen)(3)(2+) should bind. Ru(phen)(3)(2+) nonbinding to DNA might exist in the bulk solution and exhibits ECL emission. The drug exhibiting the drug-concentration-dependent ECL is classified as a drug with a major groove binding character. The addition of drugs, such as mitomycin C and duocarmycin SA, did not cause a change in the ECL intensity even in the presence of DNA. This result indicates that these drugs bind to DNA with minor groove binding. Since similar trends were observed for actinomycin D, distamycin A, doxorubicin, and chromomycin A3; these drugs are also considered as minor groove binding agents. All these results demonstrate that the DNA-binding mode of the drug can be evaluated easily by utilizing the ECL of Ru(phen)(3)(2+), which is used as the sensing probe.

The sequence specificity of the pluramycin antibiotics hedamycin and DC92-B, was established in intact human cells using a linear amplification system. In this system an oligonucleotide primer is extended by Taq DNA polymerase up to a damage site. The products are run on a DNA sequencing gel and the damage can be determined to the exact base pair. The human repetitive alpha RI DNA was used as the target DNA sequence for these experiments. It was found that G residues were the main site of adduct formation, for both hedamycin and DC92-B. The sequences 5'-TGT and 5'-CGT were the most intense sites of DNA damage. A comparison of the DNA damage intensity in intact cells and purified DNA revealed that the sequence position of adduct formation was very similar in the two environments. However, a densitometric comparison of the damage intensity in the two environments revealed significant differences. Two regions were found (120 and 130 bp in length) where the damage intensity was relatively lower in intact cells compared to purified DNA. But at the boundaries of these sequences, there were regions (approx. 50-60 bp long) that were relatively more damaged in intact cells compared to purified DNA. One explanation of this phenomenon is the presence of a protecting nucleosome core on each of the 120/130 bp regions and flanking nucleosome linker regions of 50-60 bp. This postulated sequence phasing of the nucleosomes corresponds almost exactly with the major nucleosome phasing found in African green monkey cells. Also the centromere protein B binding site is found in the border region between the nucleosome core and linker DNA regions. Hedamycin and DC92-B produced nearly identical results in this human cell system.