Substrates, systems and methods for analyzing materials
First Claim
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1. An analytical device, comprising:
- a substrate comprising a first surface and at least a first optical waveguide disposed upon the first surface;
an optically resolvable molecular complex immobilized within a confined region and sufficiently proximal to the first surface to be illuminated by an evanescent field emanating from the optical waveguide when light is passed through said optical waveguide; and
at least a first excitation radiation source optically coupled to the substrate to provide the evanescent field by passing excitation light into the optical waveguide.
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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.
174 Citations
25 Claims
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1. An analytical device, comprising:
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a substrate comprising a first surface and at least a first optical waveguide disposed upon the first surface; an optically resolvable molecular complex immobilized within a confined region and sufficiently proximal to the first surface to be illuminated by an evanescent field emanating from the optical waveguide when light is passed through said optical waveguide; and at least a first excitation radiation source optically coupled to the substrate to provide the evanescent field by passing excitation light into the optical waveguide. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method of detecting a signal from an analyte, comprising:
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providing a substrate comprising a) a first surface; b) at least a first optical waveguide proximal to the first surface; c) a plurality of optically resolvable molecular complexes immobilized within confined regions and sufficiently proximal to the first optical waveguide to be illuminated by an evanescent field emanating from the first optical waveguide when light is passed through said optical waveguide; exposing the first surface to an analyte comprising a fluorescent or fluorogenic moiety that emits a signal in response to the evanescent field; directing light through the first optical waveguide such that the evanescent field from the waveguide illuminates the optically resolvable molecular complexes; and upon interaction of the analyte with one of the optically resolvable molecular complexes, detecting a signal from the analyte. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19)
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20. A method of determining a nucleotide sequence of a template nucleic acid, the method comprising:
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providing a substrate comprising a first surface and at least a first optical waveguide proximal to the first surface of the substrate; immobilizing an optically resolvable polymerase enzyme in a confined region sufficiently proximal to the first optical waveguide to be illuminated by an evanescent field emanating from the first optical waveguide, wherein the polymerase enzyme is further bound to the template nucleic acid, which is further bound to a primer; directing light through the first optical waveguide such that the evanescent field from the waveguide illuminates the confined region; incorporating a plurality of nucleotides into a nascent strand complementary to the template nucleic acid using template-directed synthesis catalyzed by the polymerase enzyme, wherein for each of the nucleotides incorporated into the nascent strand, an identity of a base comprised therein is determined by detecting a signal produced by said each of the nucleotides when exposed to the evanescent field, thereby determining a nucleotide sequence of the nascent strand; and determining a complementary nucleotide sequence that is complementary to the nucleotide sequence of the nascent strand, wherein the complementary nucleotide sequence is the nucleotide sequence of the template nucleic acid. - View Dependent Claims (21, 22, 23, 24, 25)
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Specification