SUBSTRATES, SYSTEMS AND METHODS FOR ANALYZING MATERIALS
First Claim
Patent Images
1. An analytical device, comprising:
- a substrate comprising a first surface and an array of optical waveguide cores proximal to the first surface;
a plurality of optically resolvable molecular complexes, each of which is immobilized sufficiently proximal to the first surface to be illuminated by an evanescent field emanating from at least one of the optical waveguide cores when light is passed through said array; and
at least a first excitation radiation source optically coupled to the array to provide the evanescent field by passing excitation light into the array.
0 Assignments
0 Petitions
Accused Products
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.
-
Citations
64 Claims
-
1. An analytical device, comprising:
-
a substrate comprising a first surface and an array of optical waveguide cores proximal to the first surface; a plurality of optically resolvable molecular complexes, each of which is immobilized sufficiently proximal to the first surface to be illuminated by an evanescent field emanating from at least one of the optical waveguide cores when light is passed through said array; and at least a first excitation radiation source optically coupled to the array to provide the evanescent field by passing excitation light into the array. - View Dependent Claims (2, 3, 4, 5, 6, 11, 12, 13, 14, 18, 19, 21, 22, 23, 24)
-
-
7-9. -9. (canceled)
-
15-17. -17. (canceled)
-
20. (canceled)
-
25. A method of detecting a signal from an analyte, comprising:
-
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 individual enzymes immobilized upon the first surface sufficiently proximal to the first optical waveguide to be illuminated by an evanescent field emanating from the first 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 individual enzymes; and upon interaction of the analyte with one of the individual enzymes, detecting a signal from the analyte. - View Dependent Claims (26, 27, 28, 29, 30, 33, 35, 36, 37, 40, 41)
-
-
31-32. -32. (canceled)
-
34. (canceled)
-
38-39. -39. (canceled)
-
42-43. -43. (canceled)
-
44. A system for analyzing an analyte, comprising:
-
a substrate comprising a first surface and a plurality of optical waveguide cores disposed within the first surface, wherein the plurality of optical waveguide cores is optically coupled to an originating waveguide core; at least a first light source optically coupled to the originating waveguide core of the plurality to direct light into the originating waveguide core, which directs the light into the plurality of optical waveguide cores; an ordered array of reaction regions, each of which is disposed within one of the apertures sufficiently proximal to the first surface and external to the first optical waveguide core to be within an evanescent field emanating from the first optical waveguide core when light from the light source is passed through the first optical waveguide core; a mask layer disposed over a first portion of the first surface, but not over a second portion of the first surface, wherein the second portion of the first surface comprises the ordered array of reaction regions, wherein each of the reaction regions is disposed beneath one of a plurality of apertures disposed through the mask layer; and an optical detection system positioned to receive and detect optical signals from the ordered array of reaction regions.
-
-
45-57. -57. (canceled)
-
58. A method of determining a nucleotide sequence of a template nucleic acid, the method comprising:
-
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 reaction volume on the first surface 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 reaction volume; 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 (61, 63)
-
-
59-60. -60. (canceled)
-
62. (canceled)
-
64-65. -65. (canceled)
Specification