US-20260125753-A1 - PROTECTIVE SURFACE COATINGS FOR FLOW CELLS

US20260125753A1US 20260125753 A1US20260125753 A1US 20260125753A1US-20260125753-A1

Abstract

An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.

Inventors

Sean M. Ramirez
Maxwell Zimmerley
Julia Morrison
Gianluca Andrea Artioli
KRYSTAL SLY
Hayden Black
Lewis J. Kraft
Hong Xie
Wei Wei
Ryan Sanford
Brian D. Mather
Edwin Li
Sojeong Moon
Innsu Daniel Kim
Alexandre Richez
Ludovic Vincent
Xavier von Hatten
Hai Quang Tran

Assignees

ILLUMINA, INC.
ILLUMINA CAMBRIDGE LIMITED
ILLUMINA SINGAPORE PTE. LTD.

Dates

Publication Date: 20260507
Application Date: 20251231

Claims (20)

1 .- 8 . (canceled)
9 . A method, comprising: providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer.
10 . The method of claim 9 , wherein the substrate is a non-patterned substrate, and wherein the method further comprises bonding a lid to a bonding region of the non-patterned substrate, wherein the lid and the non-patterned substrate at least partially define a flow channel including the exposed surface.
11 . The method of claim 10 , wherein the modifying of the exposed surface, the reacting of the first chemical group with the first reactive group, the grafting of the primer, and the forming of the water-soluble protective coating involve respective flow through processes.
12 . The method of claim 9 , wherein: the substrate is a non-patterned substrate; the modifying of the exposed surface comprises plasma ashing; and after the modifying of the exposed surface, the method further comprises bonding a lid to a bonding region of the non-patterned substrate, wherein the lid and the non-patterned substrate at least partially define a flow channel including some of the exposed surface.
13 . The method of claim 9 , wherein: the substrate is a patterned substrate comprising depressions separated by interstitial regions; the modifying of the exposed surface involves attaching a silane or a silane derivative comprising the first chemical group to the exposed surface to form silanized depressions and silanized interstitial regions; the reacting forms the functionalized polymer coating layer in the silanized depressions and on the silanized interstitial regions; and prior to the grafting of the primer, the method further comprises removing the functionalized polymer coating layer from the silanized interstitial regions.
14 . The method of claim 13 , wherein: the grafting attaches the primer to the functionalized polymer coating layer in the silanized depressions, thereby forming functionalized depressions; and the forming yields the water-soluble protective coating on the functionalized depressions and at least some of the interstitial regions.
15 . The method of claim 13 , wherein after the removing of the functionalized polymer coating layer, the method further comprises bonding a lid to a bonding region of the patterned substrate, wherein the lid and the patterned substrate at least partially define a flow channel including the silanized depressions having the functionalized polymer coating layer thereon.
16 . The method of claim 15 , wherein the grafting of the primer and the forming of the water-soluble protective coating involve respective flow through processes.
17 . The method of claim 9 , wherein after the functionalized polymer coating layer is formed and before the grafting of the primer and the forming of the water-soluble protective coating, the method further comprises: patterning an initial water-soluble protective coating on the functionalized polymer coating layer such that a bonding region of the substrate remains exposed; bonding a lid to the bonding region of the substrate to form a flow channel that is in selective fluid communication with the initial water-soluble protective coating; and removing the initial water-soluble protective coating.
18 . The method of claim 9 , wherein the forming of the water-soluble protective coating involves applying an aqueous solution including up to about 15%, or about 1 to 15%, or about 1 to 10%, or about 1 to 5%, or about 2 to 5%, or about 4 to 8%, or about 5 to 7.5% (mass to volume), of a water-soluble material.
19 . The method of claim 18 , wherein a percentage of the water-soluble material in the aqueous solution is adjusted based on a primer density of the primer.
20 . The method of claim 9 , wherein the water-soluble protective coating comprises; a non-cationic synthetic polymer; a natural polysaccharide or a derivative thereof; a natural protein or a derivative thereof; a water-soluble salt; or a small molecule compound selected from the group consisting of a water-soluble surfactant, a sugar, an antioxidant, a chelator, a buffer, a glycol, glycerol, and a cyclodextrin; or a combination thereof.
21 . The method of claim 20 , wherein the water-soluble protective coating comprises: (a) the non-cationic synthetic polymer comprising polyacrylamide, poly(acrylic acid), polyacrylate, poly(methacrylic acid), poly(vinyl pyrrolidone), poly(vinyl alcohol), poly (methacrylamide), a poly(N-alkyl acrylamide), a poly(N-dialkyl acrylamide), poly(N-(2-hydroxypropyl)methacrylamide), poly(divinyl ether-maleic anhydride), a poly(phosphate), a poly(2-alkyl-2-oxazoline), poly(hydroxyethyl methacrylate), poly(2-hydroxyethyl acrylate), polyethylene glycol, a polyether, poly(sulfobetaine methacrylate), poly(vinyl ether-maleic acid), a hydroxyl functional polymer, a non-natural polypeptide, or a silicone, or a combination thereof; (b) the natural polysaccharide or derivative thereof comprising starch, carboxymethylcellulose, xanthan gum, pectin, dextran, carrageenan, guar gum, cellulose, hydroxypropylmethyl cellulose (HPMC), hydroxypropyl cellulose (HPC), hydroxyethyl cellulose (HEC), methyl cellulose, carboxymethylhydroxyethyl cellulose (CMHEC), hyaluronic acid, starch phosphate, hydroxypropyl starch, hydroxyethyl starch, agarose, agar, or alginate, or a combination thereof; (c) the natural protein or derivative thereof comprising casein or albumin; (d) the water-soluble salt comprising sodium chloride, sodium bromide, sodium sulfate, sodium phosphate, sodium carbonate, sodium acetate, sodium citrate, potassium chloride, potassium bromide, potassium sulfate, potassium phosphate, potassium carbonate, potassium acetate, or potassium citrate, or saline sodium citrate, or a combination thereof; (e) the buffer comprising an aqueous solution of saline sodium citrate, tris(hydroxymethyl)aminomethane (Tris) optionally with ethylenediaminetetraacetic acid, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 3-[[1,3-dihydroxy-2-(hydroxymethyl) propan-2-yl]amino]-2-hydroxypropane-1-sulfonic acid (TAPSO), N-(2-hydroxy-1,1-bis(hydroxymethyl)ethyl)glycine (tricine), 3-(N-morpholino) propanesulfonic acid (MOPS), or 3-(N,N-bis([2-hydroxyethyl]amino)-2-hydroxypropanesulfonic acid (DIPSO); (f) the water-soluble surfactant comprising an anionic or nonionic surfactant, or comprising sodium dodecyl sulfate, an alkyl ethoxylate, an ethoxylated oil, a fat, or a sulfosuccinate; or (g) the sugar, the antioxidant, the glycol, glycerol, or the cyclodextrin; (h) the chelator comprising ethylenediaminetetraacetic acid sodium salt, tris(3-hydroxypropyltriazolylmethyl)amine, (tris(2-carboxyethyl) phosphine), or bathophenanthrolinedisulfonic acid disodium salt; or (i) a combination thereof.
22 . The method of claim 20 , wherein the water-soluble protective coating comprises a polyvinyl alcohol/polyethylene glycol graft copolymer, sucrose, dextran, a polyacrylamide, a glycol, tris(hydroxymethyl)aminomethane or a salt thereof, ethylenediaminetetraacetic acid or a salt thereof, (tris(2-carboxyethyl) phosphine), tris(3-hydroxypropyltriazolylmethyl)amine or a salt thereof, bathophenanthrolinedisulfonic acid disodium salt, a hydroxyl functional polymer, glycerol, or saline sodium citrate, or a mixture thereof.
23 . The method of claim 20 , wherein the water-soluble protective coating comprises a polyvinyl alcohol/polyethylene glycol graft copolymer, sucrose, or a mixture thereof.
24 . The method of claim 9 , wherein the functionalized polymer coating layer is poly(N-(5-azidoacetamidylpentyl) acrylamide-co-acrylamide (PAZAM).
25 . (canceled)
26 . The method of claim 9 , wherein the first chemical group is optionally substituted alkenyl, optionally substituted cycloalkenyl, optionally substituted norbornenyl, optionally substituted cyclooctynyl, optionally substituted bicyclononynyl, optionally substituted alkynyl, azido, optionally substituted tetrazinyl, hydrazonyl, optionally substituted tetrazolyl, formyl, or hydroxyl.
27 . The method of claim 9 , wherein the first chemical group is covalently linked to the exposed surface of the substrate through a silane linker.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application is a division of U.S. application Ser. No. 18/195,321, filed May 9, 2023, which itself is a division of U.S. application Ser. No. 15/969,562, filed May 2, 2018 (now U.S. Pat. No. 11,667,969), which itself claims the benefit of U.S. Provisional Application No. 62/504,977, filed May 11, 2017, each of which is incorporated by reference in its entirety. BACKGROUND Biological arrays are among a wide range of tools used to detect and analyze molecules, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). In these applications, the arrays are engineered to include probes for nucleotide sequences present in genes of humans and other organisms. In certain applications, for example, individual DNA and RNA probes may be attached at small locations in a geometric grid (or randomly) on an array support. A test sample, e.g., from a known person or organism, may be exposed to the grid, such that complementary fragments hybridize to the probes at the individual sites in the array. The array can then be examined by scanning specific frequencies of light over the sites to identify which fragments are present in the sample, by fluorescence of the sites at which the fragments hybridized. Biological arrays may be used for genetic sequencing. In general, genetic sequencing involves determining the order of nucleotides or nucleic acids in a length of genetic material, such as a fragment of DNA or RNA. Increasingly longer sequences of bases are being analyzed, and the resulting sequence information may be used in various bioinformatics methods to logically fit fragments together so as to reliably determine the sequence of extensive lengths of genetic material from which the fragments were derived. Automated, computer-based examination of characteristic fragments have been developed, and have been used in genome mapping, identification of genes and their function, evaluation of risks of certain conditions and disease states, and so forth. Beyond these applications, biological arrays may be used for the detection and evaluation of a wide range of molecules, families of molecules, genetic expression levels, single nucleotide polymorphisms, and genotyping. SUMMARY In one aspect a flow cell comprises: a substrate, a lid bonded to a bonding region of the substrate wherein the lid and the substrate at least partially define a flow channel, and surface chemistry positioned on the substrate and in the flow channel. A water-soluble protective coating covers the surface chemistry on the substrate. In one aspect a flow cell comprises: a substrate comprising an exposed surface; a functionalized polymer coating layer covalently bound to the exposed surface of the substrate through a chemical group on the exposed surface; a primer grafted to the functionalized polymer coating layer; and a water-soluble protective coating on the primer and the functionalized polymer coating layer. In some examples, the flow cell further comprises a lid bonded to a bonded region of the substrate, wherein the lid and the substrate at least partially define a flow channel. In some aspects of the flow cells described herein, the functionalized polymer coating layer is covalently bound to the exposed surface due to reaction of a chemical group on the exposed surface with a first reactive group of the functionalized polymer coating layer. In some examples, the primer is grafted to the functionalized polymer coating layer due to reaction of the primer with a second reactive group of the functionalized polymer coating layer. An example of a flow cell disclosed herein includes a patterned substrate. The patterned substrate includes depressions separated by interstitial regions, and surface chemistry positioned in the depressions. In some examples, a lid is bonded to a bonding region of the patterned substrate, wherein the lid at least partially defines a flow channel that is in selective communication with the depressions. A water-soluble protective coating covers the surface chemistry in the depressions. In some examples, the chemical group on the exposed surface is attached to the substrate in the depressions. Another example of a flow cell disclosed herein includes a non-patterned substrate. In some examples, a lid is bonded to a bonding region of the non-patterned substrate, wherein the lid and the non-patterned substrate at least partially define a flow channel including the exposed surface. Surface chemistry is positioned on the non-patterned substrate and in the flow channel. A water-soluble protective coating covers the surface chemistry. In some examples, the chemical group on the exposed surface is attached to the non-patterned substrate. In another aspect, a method of using a flow cell as described herein comprises: inserting the flow cell into a sequencing instrument; and removing the water-soluble protective coating by exposing the water-soluble protective coating to water (optionally in th