Patent Document ID: 9587276
Application ID: 14945256
Patent Flag: 1

Claim One:
1. A method of performing a sequencing by synthesis reaction, the method comprising: a) providing a substrate comprising: i) a first surface and a mask layer disposed over the first surface of the substrate, the mask layer comprising a plurality of apertures that pass through the mask layer, wherein the apertures are configured to spatially confine an individual, optically resolvable complex; ii) at least a first optical waveguide disposed beneath but sufficiently proximal to the plurality of apertures that when excitation radiation is passed through the first optical waveguide, an evanescent field emanating from the first optical waveguide reaches into the apertures; b) immobilizing an individual polymerase/template/primer complex within one of the apertures sufficiently proximal to the first optical waveguide to be illuminated by the evanescent field; c) passing excitation light through the first optical waveguide, thereby generating the evanescent field; d) exposing the polymerase/template/primer complex to a set of labeled nucleotides or nucleotide analogs under conditions that promote nascent strand synthesis; and e) detecting emissions from said one of the apertures, wherein said emissions are emitted from the labeled nucleotides or nucleotide analogs during said nascent strand synthesis, and are indicative of a sequence being synthesized, thereby performing a sequencing by synthesis reaction.