Studies of the interaction of platinum drugs with DNA using oligonucleotide microarrays

A novel method for the study of the interaction of the platinum drug cis-diamminedichloroplatinum(II) (cis-DDP or cisplatin) with 50-mer oligonucleotides that were printed in high throughput microarray format is introduced. Our aim has been to identify sequence level differences in the interaction of various drug candidates that may serve to enable rational targeting of drugs to specific genes. A microarray of 26 control genes commonly used in oligonucleotide, Affymetrix and c-DNA microarray platforms were microcontact spotted as amine-terminated 50-mer oligonucleotides onto glycidoxypropyltimethoxy silane (CPMS)-modified glass slides. The generalized study format involved hybridization of probes with 10 fluorescently labeled complements as target followed by confocal imaging to reveal original spot intensities. Microarrays were then incubated at 37°C with hydrolysed cisplatin while in hybridization cassettes, washed in buffer and then scanned again to reveal secondary intensities. We have investigated the influence of cisplatin to stabilize the relative fluorescence intensity via intrastrand crosslinking by studying the impact of varying drug:probe-DNA mole ratio (0:1 (blank), 1:1, 25:1 and 50:1) and annealing temperatures (36, 46, or 56°C) on retained intensity. ANOVA revealed that 4 of the 10 genes demonstrated (p < 0.0001) the expected result of increased signal retention with decreased temperature and increased drug concentration.