The rapidly decreasing costs of DNA sequencing have made the genomic sequences from thousands of pathogens broadly accessible. The utilization of this new knowledge in clinical practice, however, critically depends on the availability of new analytical tools and techniques that could quickly and efficiently detect the presence of specific genomic variants of pathogens. Some recent examples include the outbreak of H1N1 (Swine flu) and HIV-AIDS. Current approaches rely on costly and time-consuming Polymerase Chain Reaction (PCR), to achieve the specificity and quantity required by standard means of detection. Here I propose to develop a radically low-cost, single-molecule, genotyping method based on nanopore sensing of Peptide Nucleic Acids (PNA) markers. This method is designed to yield an extremely low cost, single-molecule detection of viral infections.
Nanopores are emerging single-molecule sensors, where an electrophoretic force threads DNA or RNA biopolymers, into a nanoscale aperture made in a thin film. The threading process uncoils the biopolymers, as they move from one side of the film to the other. Molecules entering the nanopore occlude some of the free ions in the solution from the pore volume, thus permitting real-time electrical detection of the local cross-section of the biopolymer. We propose to develop this method to permit the rapid detection of sequence-specific PNA markers, known to invade double-stranded DNA and form bulges at the points of invasion. We recently showed that PNAs can be detected using tiny solid-state nanopores. To transform this discovery into a robust analytical tool, extensive studies are now required to critically improve the nanopore fabrication, the signal over noise of the measurements, and the biomolecular strategies for efficient PNA invasion. Our studies will ultimately enable the development of low-cost, portable, and high-throughput devices for a broad range of genome based molecular diagnostics.
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