Light-mediated polymerase chain reaction amplification and product detection system and methods of use

A polymerase chain reaction (PCR) amplification and detection apparatus, comprising:

• a) an assembly subsystem comprising:
• i) a plurality of vessels in the form of a continuous polymer strip, each such vessel having a volume of 0.2 to 20 μl and a vessel diameter of 0.5 to 4 mm;
• ii) said plurality of vessels each comprising an aqueous oil matrix, each aqueous oil matrix comprising:
• 1) an aqueous reaction mix comprising a polynucleotide sample and reagents, the reagents comprising a first reagent capable of excitation by a fluorescence excitation light having a first spectral wavelength when the first reagent hybridizes to the polynucleotide sample;
• and
• 2) one or two non-miscible oils selected from the group consisting of an encapsulation oil, a carrier oil, and both an encapsulation oil and a carrier oil;
• wherein components of the aqueous reaction mix do not mix with the one or two non-miscible oils;
• b) a plurality of heating positions, temperature monitoring positions, and PCR product detection positions defining a plurality of alternating first vessels stations and second vessels stations where the plurality of vessels may be stationed, and wherein each of the first vessels stations comprises a heating position, and each of the second vessels stations comprises a PCR product detection position;
• c) a reaction-by-reaction, light-driven photonic heating subsystem comprising a plurality of electromagnetic radiation sources, wherein, when the plurality of vessels are in the heating position, each vessel is in optical communication with an electromagnetic radiation source, and the electromagnetic radiation source emits electromagnetic radiation to that vessel;
• d) a reaction-by-reaction temperature monitoring subsystem comprising a plurality of thermal detection devices, wherein each vessel corresponds to a thermal detection device the thermal detection device is configured to provide a measuring signal dependent on the temperature of the aqueous oil matrix contained in the vessel;
• e) a microcontroller temperature feedback and light source control subsystem communicatively connected to both the photonic heating subsystem and the temperature monitoring subsystem, wherein the microcontroller temperature feedback and light source control subsystem is configured to regulate an energy input required for controlling an output and a duration of an electromagnetic energy emitted by each electromagnetic radiation source through a cycle of reaction temperatures;
• f) a fluorescence detection subsystem comprising:
• i) one or more fluorescence excitation light sources;
• ii) one or more fluorescence emission light sensing devices;
• iii) a plurality of first optical members in optical communication with the one or more fluorescence excitation light sources, wherein, when the vessels are in the PCR detection positions, each first optical member is configured to provide an optical path for fluorescence excitation light having the first spectral wavelength from the one or more fluorescence excitation light sources to one of said vessels containing the aqueous oil matrix, and wherein each first optical member is further configured to provide an optical path for fluorescence emission light from the aqueous reaction mix to the one or more fluorescence emission light sensing devices;
• and
• iv) an active or passive cooling mechanism at the PCR product detection positions whereby each of the vessels in the PCR product detection positions are cooled;
• and
• g) a mechanical and electronic control system communicatively connected to a moveable belt and to the assembly subsystem, wherein the mechanical and electronic control system causes the assembly subsystem to assemble the aqueous oil matrices in the plurality of vessels, and wherein the mechanical and electronic control system causes the moveable belt to move the plurality of vessels with the aqueous oil matrix in a step-by-step movement through the assembly subsystem in order to align the plurality of vessels with the aqueous oil matrix with the plurality of alternating first vessels stations and second vessels stations.