Patent ID: 8867038

Claim:
A method for sequencing a plurality of template nucleic acid molecules comprising: adding a sequencing reaction mixture comprising reagents for carrying out polymerase dependent nucleic acid synthesis, including fluorescently labeled nucleotides, to the fluidic layer of an optode array chip; wherein the optode array chip comprises a two dimensional array of optode elements, each optode element comprising: a nanoscale aperture within an aperture layer, the aperture forming a fluid receiving nanoscale well for receiving a fluid including sequencing reagents; above the aperture layer a fluidic layer in fluidic contact with the nanoscale well; below the aperture layer a waveguide layer that provides illumination to the nanoscale well, the waveguide layer comprising an array of channel waveguides, each channel waveguide extending across a plurality of optode elements; below the waveguide layer a transmission layer that transmits light emitted from the fluorescent species in the nanoscale well to a detector layer; and below the transmission layer the detector layer comprising a detector which receives and detects the emitted light from the nanoscale well and transmitted through the transmission layer; wherein a plurality of the nanoscale wells have within them a single polymerase-template complex comprising a polymerase enzyme and a template nucleic acid; providing illumination to waveguides on the chip to illuminate optode array elements; detecting fluorescent light emitted from the nanoscale wells using the detectors in the detector layer; transmitting electrical signals from the detectors off of the chip through electrical contacts on the chip, and processing the signals from the detectors in order to sequence a plurality of template nucleic acid molecules.