The development of a nanoparticle based detection methodology for DNA microarray applications is described. Originally reported by Mirkin and co-workers, the technology utilizes gold nanoparticles derivatized with thiol-modified oligonucleotides that are designed to bind complementary DNA targets. A glass surface with arrays of immobilized DNA capture sequences is used to capture DNA targets, which are then detected via hybridization to the gold nanoparticle probes. For maximum signal strength a layer of silver is deposited onto the gold nanoparticles, providing for highly sensitive and specific detection of target sequences using low cost optical detection systems. The relative optical detection limits for silver amplified gold nanoparticle probes and Cy3 based fluorescence have been tested. Furthermore, we report progress towards the direct detection of non-amplified genomic DNA from infectious agents and single nucleotide polymorphisms (SNP) in human genomic DNA based on nanoparticle technology.
The possibility of using microarray technology for mechanistic understanding of drug toxicity has opened up a new research field in Toxicology. In an attempt to build knowledge in the field, we have designed a 1C-gene array composed of 85 known human genes with toxicological interests and 15 control genes. HepG2 cells were treated with ethanol and two anticancer drugs, mitomycin C and doxorubicin. RNA were isolated and labeled by fluorescent dyes, then hybridized to the 1C-gene array. Our results showed that a number of cytochrome P450 genes, such as CYP4F2/3, CYP3A3, CYP24, and CYP51, were consistently responsive to the toxicant treatment. However, different genes response to different toxicants. For example, CYP24 and CYP51 were up regulated by the ethanol treatment but remained unresponsive to the other two drugs. The anticancer drugs, but not ethanol differentially regulated several other genes including CYP3A3, TNFRSF6 and CHES1, implying that the two drugs might function through a similar mechanism, which differs from that of ethanol. The reproducibility of our results suggests that microarray- based expression analysis may offer a rapid and efficient means of assessing drug toxicity.