Orthogonal assembly of nanoparticle building blocks on dip-pen nanolithographically generated templates of DNA.

Nanoscale construction work with DNA: Dip-pen nanolithography (DPN) is used to generate nanostructures which can be subsequently functionalized with oligonucleotides a' and b' and used to assemble, in an orthogonal manner, gold nanoparticles (a, b in scheme) functionalized with sequences complementary to the DPN-generated structures.

Scanometric DNA array detection with nanoparticle probes.

A method for analyzing combinatorial DNA arrays using oligonucleotide-modified gold nanoparticle probes and a conventional flatbed scanner is described here. 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. In addition, when coupled with a signal amplification method based on nanoparticle-promoted reduction of silver(I), the sensitivity of this scanometric array detection system exceeds that of the analogous fluorophore system by two orders of magnitude.