MicroRNAs (miRNAs) are an emerging class of diagnostic markers that can signify the presence of disease and be used to predict its course.[1, 2] Indeed, miRNAs are now known to be involved in tumor metastasis,[3] stem-cell differentiation and renewal,[4] and viral replication.[5] The analysis of the intracellular levels of miRNAs is challenging, however, because their short lengths, low abundances, and high levels of sequence similarity present obstacles in the use of conventional analytical methods. Hybridization-based approaches (eg microarray analyses) are attractive for microRNA profiling because of the potential for extensive multiplexing and the discrimination of closely related sequences; however, such methodology requires large quantities (micrograms) of starting material.[6–8] The lack of sensitivity of existing arraybased methods is related to the type of readout used: typically fluorescence signals emitted from an RNA-conjugated fluorophore. Very low levels of signal derived from low-abundance sequences are extremely difficult to detect without sophisticated optics. Impressive progress in this area has been made with the development of novel methods for the ultrasensitive detection of miRNA hybridization on array surfaces;[9, 10] however, the methods available involve many steps and have not yet been validated with biological samples. We describe herein a new approach to ultrasensitive, direct, hybridization-based microRNA profiling using a multiplexed electronic chip and electrocatalytic readout. The very high sensitivity of this method enables the direct analysis of small samples (nanograms of total RNA) within 30 minutes. The power of this method is demonstrated by the identification of specific microRNA sequences that are overexpressed in human head and neck cancer cells relative to normal epithelial cells.

We endeavored to develop a new method for microRNA profiling that would feature the convenience of array-based analysis, but would augment the power of such multiplexing with the exceptional sensitivity required to assay small biological samples for low-abundance microRNAs. We pursued an approach based on electronic readout and prepared a multiplexed chip that featured an electrode pattern generated by photolithography (Figure1a). The chip was made by depositing a pattern of gold on the surface of a silicon wafer to provide a multiplexed set of leads and external contacts. A layer of SiO2 was deposited on top of the gold to passivate the metal; then, in the final fabrication step, apertures of 500 nm in diameter were opened at the end of each lead to expose gold. To generate protruding microelectrodes, palladium was electrodeposited in the apertures (Figure 1b). The electrodeposition step can be engineered to produce highly nanostructured microelectrodes (NMEs; Figure1b). Previous studies have indicated that nanostructured sensing elements