# US 2017/0322156 A1 · Arrays of integrated analytical devices and methods for production

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- Number: US 2017/0322156 A1
- Document ID: US20170322156A1
- Status: Published application
- Kind: A1
- Application number: 15/600,668
- Filed: 2017-05-19
- Published: 2017-11-09
- Earliest claimed: 2012-06-17
- Assignees: Pacific Biosciences of California, Inc.
- Applicants: Pacific Biosciences of California, Inc.
- Inventors: Ravi SAXENA; Michael Tzu RU; Takashi Whitney ORIMOTO; Annette GROT; Mathieu FOQUET; Hou-Pu CHOU
- Web page: https://patentgrep.com/patent/US20170322156A1

## CPC

- G02B 6/12004: {Combinations of two or more optical elements}
- B29D 11/0073: {Optical laminates}
- B29D 17/007: {Forming the relief pattern on a support larger than the record}
- C12Q 1/6869: Methods for sequencing
- G01N 21/6454: {using an integrated detector array}
- G01N 21/648: {using evanescent coupling or surface plasmon coupling for the excitation of fluorescence}
- G02B 5/189: {Structurally combined with optical elements not having diffractive power}
- G02B 6/02123: {characterised by the method of manufacture of the grating (photolithography G03F7/0005)}
- G02B 6/12002: {Three-dimensional structures}
- G02B 6/124: Geodesic lenses or integrated gratings
- G02B 6/136: by etching
- B29L 2011/005: {Fresnel lenses}
- B29L 2011/0066: {Optical filters}
- B29L 2011/0075: {Light guides, optical cables}
- G01N 2021/6467: {Axial flow and illumination}
- G01N 2021/6471: {Special filters, filter wheel}
- G01N 2021/6478: {Special lenses}
- G01N 2021/7713: {in core}
- G01N 2201/0873: Using optically integrated constructions
- G02B 2006/12038: {Glass (SiO2 based materials)}
- G02B 2006/12109: {Filter}
- G02B: OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
- B29D: PRODUCING PARTICULAR ARTICLES FROM PLASTICS OR FROM SUBSTANCES IN A PLASTIC STATE (making granules B29B9/00; making preforms B29B11/00)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- B29L: INDEXING SCHEME ASSOCIATED WITH SUBCLASS B29C, RELATING TO PARTICULAR ARTICLES

## Abstract

Arrays of integrated analytical devices and their methods for production are provided. The arrays are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

## Claims

### Claim at position 1

1-51. (canceled)

### Claim 52

An analytical system for the simultaneous measurement of multiple reactions comprising:
an array of integrated analytical devices; and
an excitation light source;
wherein the array of integrated analytical devices comprises:
a substrate layer;
a filter module layer disposed on the substrate layer;
a collection module layer disposed on or with the filter module layer, wherein the collection module layer comprises a Fresnel lens structure configured to split a light beam into a plurality of light beams;
a waveguide module layer disposed on the collection module layer; and
a zero-mode waveguide module layer disposed on the waveguide module layer;
wherein the zero-mode waveguide module layer comprises a plurality of nanometer-scale apertures penetrating into the waveguide module layer.

### Claim 53 (depends on 52)

The analytical system of claim 52, wherein the substrate layer is a detector layer.

### Claim 54 (depends on 52)

The analytical system of claim 52, wherein the substrate layer is a CMOS wafer.

### Claim 55 (depends on 52)

The analytical system of claim 52, wherein the filter module layer comprises a dielectric filter.

### Claim 56 (depends on 52)

The analytical system of claim 52, wherein the filter module layer comprises an absorptive filter.

### Claim 57 (depends on 53)

The analytical system of claim 53, wherein the detector layer comprises a color-separation layer.

### Claim 58 (depends on 52)

The analytical system of claim 52, wherein the plurality of nanometer-scale apertures is formed by etching, and the etching is stopped using an endpoint signal.

### Claim 59 (depends on 52)

The analytical system of claim 52, wherein the waveguide module layer comprises an upper cladding of waveguide cladding material disposed on a waveguide core material, and at least one nanometer-scale aperture fully penetrates the upper cladding of waveguide cladding material into the waveguide core material.

### Claim 60 (depends on 59)

The analytical system of claim 59, wherein the at least one nanometer-scale aperture is partially backfilled.

### Claim 61 (depends on 60)

The analytical system of claim 60, wherein the at least one nanometer-scale aperture is partially backfilled using atomic layer deposition or low pressure chemical vapor deposition.

### Claim 62 (depends on 59)

The analytical system of claim 59, wherein the upper cladding of waveguide cladding material is SiO2.

### Claim 63 (depends on 59)

The analytical system of claim 59, wherein the waveguide core material is Si3N4.

### Claim 64 (depends on 59)

The analytical system of claim 59, further comprising an etch hardmask disposed between the waveguide core material and the upper cladding of waveguide cladding material.

### Claim 65 (depends on 52)

The analytical system of claim 52, wherein at least one nanometer-scale aperture comprises a fluid sample comprising a fluorescent species.

### Claim 66 (depends on 65)

The analytical system of claim 65, wherein the fluorescent species is a fluorescently labeled nucleotide analog.

### Claim 67 (depends on 52)

The analytical system of claim 52, wherein the plurality of nanometer-scale apertures comprise at least 100 nanometer-scale apertures.

### Claim 68 (depends on 52)

The analytical system of claim 52, wherein the plurality of nanometer-scale apertures have a density of at least 1000 apertures per cm2.

### Claim 69 (depends on 52)

The array of claim 52, wherein the Fresnel lens structure is a diffractive Fresnel lens structure.

### Claim 70 (depends on 52)

The analytical system of claim 52, wherein the Fresnel lens structure is a refractive Fresnel lens structure.

### Claim 71 (depends on 52)

The analytical system of claim 52, wherein the Fresnel lens structure combines refractive and diffractive features.

### Claim 72 (depends on 52)

The analytical system of claim 52, wherein the Fresnel lens structure is a phase Fresnel zone plate.

### Claim 73 (depends on 72)

The analytical system of claim 72, wherein the Fresnel lens structure is at least a two-phase Fresnel zone plate.

### Claim 74 (depends on 72)

The analytical system of claim 72, wherein the Fresnel lens structure is at least a four-phase Fresnel zone plate.

### Claim 75 (depends on 52)

The analytical system of claim 52, wherein the excitation light source is coupled to the array of integrated analytical devices through an optical coupler integrated in the array.

### Claim 76 (depends on 52)

The analytical system of claim 52, wherein the array of integrated analytical devices further includes an alignment feature.