Method and apparatus for rapid nucleic acid analysis

A microfluidic device comprising:

• a substrate;
• a first inlet disposed in the substrate and coupled to first and second channels terminating on opposing sides of a junction;
• second and third inlets disposed in the substrate, the second and third inlets being coupled to respective channels terminating at an upstream side of the junction;
• and
• a mixing channel coupled a downstream side of the junction, the mixing channel comprising a channel having a sawtooth configuration.

A method of detecting the presence of a target nucleic acid sequence in a sample comprising:

• providing a microfluidic device having a mixing channel coupled to an output of a droplet generation region, the droplet generation region being coupled to first and second channels adapted to contain an oil phase and first and second reactant inlets, wherein one of the first and second reactant inlets is coupled to a sample and the other of the first and second reactant inlets is coupled to a source of molecular beacon material;
• flowing the first and second reactants and the oil phase into the droplet generation region so as to generate a plurality of droplets in the generation zone;
• and
• monitoring the fluorescence level of the droplets in at least a portion of the mixing channel, wherein the fluorescence level is indicative of the presence of the target nucleic acid sequence in the sample.

A method of monitoring the binding kinetics of an analyte and a molecular beacon comprising:

• providing a microfluidic device having a mixing channel coupled to an output of a droplet generation region, the droplet generation region being coupled to first and second channels adapted to contain an oil phase and first and second reactant inlets, wherein one of the first and second reactant inlets is coupled to a source of analyte and the other of the first and second reactant inlets is coupled to a source of molecular beacon material;
• flowing the first and second reactants and the oil phase into the droplet generation region so as to generate a plurality of droplets in the generation zone;
• and
• monitoring the fluorescence level of the droplets in at least a portion of the mixing channel, wherein the fluorescence level at a given point in the mixing channel is indicative of the binding kinetics between the analyte and the molecular beacon.