Nanowire-based biosensor for short DNA using fluorescent silver nanoclusters

Sensitive detection of short nucleic acids is used to identify viral and bacterial diseases, detect biomarkers of cancer, as well as in gene expression studies. Currently available techniques such as PCR, electrochemical detection and SPR are typically costly and often require amplification of the DNA. Additionally, the PCR methods that involve enzymatic elongation of primers are often not optimal for short nucleic acids as a short target limits the size and specificity of the primers. Here, we demonstrate a sensing system for picomolar detection of short single-stranded DNA by fluorescence without any need for amplification, thermal cycling and expensive reagents. The platform harnesses the capability of waveguiding semiconductor nanowires to substantially enhance the signal of surface-bound fluorescent molecules. Employing molecular beacons based on DNA-templated silver nanoclusters that exhibit a larger signal in the presence of the target DNA, we improve the limit of detection by five orders of magnitude compared to flat substrates and demonstrate detection of HIV-1 DNA. The signal indicates single-molecule sensitivity of detection. Our sensor is easily adaptable for other short DNA and potentially can be mass-produced. The method requires only a small volume of analyte sample and a microscope for the detection of fluorescence on nanowires.