Scanometric DNA Array Detection with Nanoparticle Probes*
This chapter describes a method for analyzing combinatorial DNA arrays using oligonucleotide-modified gold nanoparticle probes and a conventional flatbed scanner. Labeling oligonucleotide targets with nanoparticle rather than fluorophore probes substantially alters the melting profiles of the targets from an array substrate. This difference permits the discrimination of an oligonucleotide sequence from targets with single-nucleotide mismatches with a selectivity that is over three times that observed for fluorophore-labeled targets. The chapter reports that the use of single-nanoparticle probes in recognizing DNA segments immobilized on a chip affords substantially sharper and higher temperature melting profiles than those obtained with analogous, conventional fluorophore-based systems. This observation, combined with the development of a quantitative signal amplification method based on nanoparticle-promoted reduction of silver and the use of a conventional flatbed scanner as a reader, allowed development of a new “scanometric” chip-based detection system for DNA that has single mismatch selectivity and a sensitivity that is 100 times greater than that of analogous fluorescence-based assays.