# US 2020/0399684 A1 · Patterned flow-cells useful for nucleic acid analysis

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- Number: US 2020/0399684 A1
- Document ID: US20200399684A1
- Status: Published application
- Kind: A1
- Application number: 17/010,675
- Filed: 2020-09-02
- Published: 2020-12-24
- Earliest claimed: 2011-06-09
- Assignees: Illumina, Inc.
- Applicants: Illumina, Inc.
- Inventors: Shengrong LIN; Yir-Shyuan WU; Kevin GUNDERSON; John A. MOON
- Web page: https://patentgrep.com/patent/US20200399684A1

## CPC

- C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence)
- C12Q 1/6837: using probe arrays or probe chips (C12Q1/6874 takes precedence)
- G01N 27/447: using electrophoresis
- 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)

## Abstract

Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.

## Claims

### Claim 1

A method of making an analyte array, comprising
(a) providing a surface comprising mask regions and transparent regions, the mask regions having a composition that blocks transmittance of radiation in a first part of the electromagnetic spectrum and transparent regions having a composition that transmits radiation in the first part of the electromagnetic spectrum, wherein a continuous gel layer coats the surface across the mask regions and the transparent regions;
(b) contacting the continuous gel layer with a fluid comprising a population of different analytes under conditions wherein analytes from the population become attached to the gel layer and wherein a first subpopulation of the analytes attach to portions of the gel layer that coat the mask regions and a second subpopulation of the analytes attach to portions of the gel layer that coat the transparent regions; and
(c) irradiating the surface with radiation in the first part of the electromagnetic spectrum, thereby selectively modifying the analytes of one of the subpopulations compared to the analytes of the other subpopulation.

### Claim 2 (depends on 1)

The method of claim 1, further comprising removing the mask regions from the surface under conditions wherein the analytes remain attached to the gel layer on the surface.

### Claim 3 (depends on 1)

The method of claim 1, wherein the selectively modifying comprises selectively removing the analytes of the second population compared to the analytes of the first subpopulation.

### Claim 4 (depends on 3)

The method of claim 3, wherein the removing comprises photo-cleaving the analytes of the second population using radiation in the first part of the electromagnetic radiation spectrum.

### Claim 5 (depends on 4)

The method of claim 4, wherein the analytes of the first subpopulation are masked from the photo-cleaving by the mask regions.

### Claim 6 (depends on 1)

The method of claim 1, wherein the analytes comprise nucleic acids.

### Claim 7 (depends on 6)

The method of claim 6, further comprising amplifying the nucleic acids on the portions of the gel layer that coat the mask regions.

### Claim 8 (depends on 7)

The method of claim 7, further comprising removing the mask regions from the surface under conditions wherein the products of the amplifying of the nucleic acids remain attached to the gel layer.

### Claim 9 (depends on 6)

The method of claim 6, wherein the contacting occurs under conditions wherein a uniform concentration of the nucleic acids contacts the portions of the continuous gel layer that coat the mask regions and the transparent regions.

### Claim 10 (depends on 6)

The method of claim 6, wherein the continuous gel layer comprises a continuous polyacrylamide layer.

### Claim 11 (depends on 6)

The method of claim 6, wherein the nucleic acids that attach to the portions of the gel layer that coat the mask regions have the same sequence.

### Claim 12 (depends on 11)

The method of claim 11, wherein the nucleic acids comprise a pair of primers.

### Claim 13 (depends on 1)

The method of claim 1, wherein the transparent regions comprise glass, plastic or silica.

### Claim 14 (depends on 1)

The method of claim 1, wherein the surface of the mask regions comprise metal, thereby forming metal regions on the surface.

### Claim 15 (depends on 1)

The method of claim 1, wherein the surface is located in a flow-cell.

### Claim 16 (depends on 1)

The method of claim 1, wherein step (c) comprises selectively modifying the analytes of the second subpopulation compared to the analytes of the first subpopulation.

### Claim 17 (depends on 16)

The method of claim 16, wherein the selectively modifying comprises photo-chemically activating the analytes of the second population.

### Claim 18 (depends on 1)

The method of claim 1, wherein step (c) comprises selectively modifying the analytes of the first subpopulation compared to the analytes of the second subpopulation.

### Claim 19

A method of making a nucleic acid array, comprising
(a) providing a surface comprising metal regions and interstitial regions, the interstitial regions having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions;
(b) contacting the continuous gel layer with a fluid comprising analytes; and
(c) selectively modifying the portions of the gel layer that coat the interstitial regions compared to the portions of the gel layer that coat the metal regions,
thereby attaching the analytes to the gel layer, wherein a greater amount of the analytes from the fluid attach to portions of the gel layer that coat the metal regions than the amount of analytes that attach to portions of the gel layer that coat the interstitial regions.

### Claim 20

A method of preparing a surface, comprising
(a) providing a surface comprising metal regions and interstitial regions, the interstitial regions having a composition that differs from the metal regions;
(b) contacting the surface with a fluid comprising a polymerizable material, wherein the fluid coats the surface across the metal regions and the interstitial regions; and
(c) polymerizing the polymerizable material, thereby forming a continuous gel layer that coats the surface across the metal regions and the interstitial regions, wherein portions of the gel layer that coat the metal regions have greater mass than portions of the gel layer that coat the interstitial regions.