Silicon nanowire-based molecular beacons for high-sensitivity and sequence-specific DNA multiplexed analysis

Nanomaterial-based molecular beacons (nanoMBs) have been extensively explored due to unique merits of nanostructures, including gold nanoparticle (AuNP)-, carbon nanotube (CNT)-, and graphene-based nanoMBs. Those nanoMBs are well-studied; however, they possess relatively poor salt stability or low specificity, limiting their wide applications. Here, we present a novel kind of multicolor silicon-based nanoMBs by using AuNP-decorated silicon nanowires as high-performance quenchers. Significantly, the nanoMBs feature robust stability in high-concentration (0.1 M) salt solution and wide-ranging temperature (10-80 °C), high quenching efficiency (>90%) for various fluorophores (e.g., FAM, Cy5, and ROX), and large surfaces for simultaneous assembly of different DNA strands. We further show that silicon-based nanoMBs are highly effective for sensitive and specific multidetection of DNA targets. The unprecedented advantages of silicon-based multicolor nanoMBs would bring new opportunities for challenging bioapplications, such as allele discrimination, early cancer diagnosis, and molecular engineering, etc. © 2012 American Chemical Society.