Substrates, systems and methods for analyzing materials
First Claim
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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.
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Abstract
Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.
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20 Claims
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1. A method of performing a sequencing by synthesis reaction, the method comprising:
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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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method for analyzing an analyte, comprising:
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a) providing a substrate comprising; i) a first surface; ii) a mask layer disposed over the first surface, the mask layer comprising a plurality of apertures that pass through the mask layer; and iii) at least a first optical waveguide disposed beneath but sufficiently proximal to at least a first aperture in 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 at least the first aperture; b) disposing an optically resolvable individual analyte within said first aperture, wherein the analyte is disposed sufficiently proximal to the first optical waveguide to be illuminated by the evanescent field; c) directing light into the first optical waveguide, thereby generating the evanescent field and, in doing so, illuminating the analyte; and d) detecting an optical signal from the analyte disposed within said first aperture, thereby analyzing the analyte. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19, 20)
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Specification