Microfluidic sequencing by hybridization with quantum-dot barcode labels

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Goal of the proposed project is i) to use droplet-based microfluidics to generate a library of micro-sized, fluorescent labels and ii) to use these labels to encode a library of DNA strands that can then be used for sequencing by hybridization in a microfluidic chip. A set of different fluorescent quantum dots will be encapsulated into polymeric microbeads produced in a microfluidic device. With a number of different distinguishable intensity levels and emission wavelengths, a large number of unique labels can be generated. These barcode-like labels will be used for DNA sequencing by hybridization, to encode a large library of DNA oligomer probe strands. The DNA probe strand its barcode label are contained in the same droplet of a water-in-oil emulsion and merged with a second droplet containing the template. The hybridization event and the identity of the probe strand via its barcode label can be read out by fluorescence detection. Microfluidic sequencing based on droplets is a new approach expected to allow for high parallelization and minimal reagent volumes, resulting in high speed and cost efficiency.