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EP-4735958-A1 - PHOTORESIST PATTERNING IN MULTI-DEPTH NANOWELLS

EP4735958A1EP 4735958 A1EP4735958 A1EP 4735958A1EP-4735958-A1

Abstract

Embodiments of the present disclosure relate to patterned substrates with functionalized surface such as flow cells, as well as methods of fabricating the patterned substrate. In particular, patterned substrates of the present disclosure may be prepared using two or more imprint resin layers, one of which acts as a photomask for the photoresist during substate patterning, without the need of any metallic photomask. Embodiments of the patterned substrate may be used for simultaneous paired-end sequencing methods.

Inventors

  • WRIGHT, DANIEL
  • SZEMJONOV, Alexandra
  • GEORGE, Wayne N.
  • PATEL-BURROWS, Francesca

Assignees

  • Illumina, Inc.

Dates

Publication Date
20260506
Application Date
20240625

Claims (20)

  1. WHAT IS CLAIMED IS: 1. A patterned substrate, comprising: a base support; and an imprint layer comprising a first resin layer positioned over the base support, the first resin layer configured to allow passage of light; a second resin layer positioned over the first resin layer, the second resin layer configured as a photomask for blocking passage of light; a plurality of multi-level depressions, each multi-level depression comprising a deep well having a first inner well surface and a first surrounding surface, and a shallow well having a second inner well surface and a second surrounding surface, wherein the deep well and the shallow well are defined by a step portion, each of the first inner well surface and the second inner well surface is parallel to the base support, the first inner well surface resides within the first resin layer, and the second inner well surface resides within the second resin layer.
  2. 2. A patterned substrate, comprising: a base support; and an imprint layer comprising a first resin layer positioned over the base support, the first resin layer configured to allow passage of light; a second resin layer positioned over the first resin layer, the second resin layer configured as a photomask to block passage of light; a third resin layer positioned over the second resin layer, the third resin layer configured to allow passage of light; a plurality of multi-level depressions, each depression comprising a deep well having a first inner well surface and a first surrounding surface, and a shallow well having a second inner well surface and a second surrounding surface, wherein the deep well and the shallow well are defined by a step portion, each of the first inner well surface and the second inner well surface is parallel to the base support, the first surface resides within the first resin layer, and the second inner well surface resides within either the second resin layer or third resin layer.
  3. 3. The patterned substrate of claim 2, wherein the second inner well surface resides within the second resin layer.
  4. 4. The patterned substrate of claim 2 or 3, wherein the first resin layer and the third resin layer comprise the same material.
  5. 5. The patterned substrate of any one of claims 1 to 4, wherein the patterned substrate is configured for exposing a photoresist positioned within the deep well of the depression over the first inner well surface to a light passing through the base support and the first resin layer.
  6. 6. The patterned substrate of any one of claims 1 to 5, wherein the first resin layer is configured to allow passage of UV light, and wherein the second resin layer is a photomask for UV light.
  7. 7. The patterned substrate of any one of claims 1 to 6, wherein the patterned substrate does not include a metallic photomask.
  8. 8. The patterned substrate of any one of claims 1 to 7, wherein the second resin layer is dry etchable.
  9. 9. The patterned substrate of any one of claims 1 to 7, wherein the second resin layer is wet etchable.
  10. 10. The patterned substrate of any one of claims 1 to 7, wherein the second resin layer is both wet etchable and dry etchable.
  11. 11. The patterned substrate of any one of claims 1 to 10, wherein the first resin layer is not wet etchable.
  12. 12. The patterned substrate of any one of claims 1 to 11, wherein the first resin layer is dry etchable.
  13. 13. The patterned substrate of any one of claims 1 to 12, wherein the second resin layer comprises an epoxy resin and one or more light-absorbing agents.
  14. 14. The patterned substrate of claim 13, wherein the epoxy resin comprises at least one of 3,4-epoxycyclohexylmethyl 3,4-epoxycyclohexanecarboxylate (ECHC), trimethylolpropane triglycidyl ether (TTE), BIS(4-methylphenyl)iodonium hexafluorophosphate (IPF), tris (4-((4- acetylphenyl)thio)phenyl)-sulfonium tetrakis(perfluoro-phenyl) borate (PAG290), or diphenyl (2,4,6-trimethylbenzoyl)phosphine oxide (DPBAPO).
  15. 15. The patterned substrate of any one of claims 1 to 12, wherein the second resin layer comprises an acrylate resin and one or more light-absorbing agents.
  16. 16. The patterned substrate of claim 15, wherein the acrylate resin comprises at least one of pentaerythritol triacrylate (PE3A) or diphenyl (2,4,6-trimethylbenzoyl)phosphine oxide (DPBAPO).
  17. 17. The patterned substrate of any one of claims 1 to 16, wherein the second resin layer further comprises at least one leveling agent.
  18. 18. The patterned substrate of claim 17, wherein the leveling agent is selected from the group consisting of BYK-350 (BYK-Chemie GmbH), BYK-394 (BYK-Chemie GmbH), BYK- 354 (BYK-Chemie GmbH), BYK-392 (BYK-Chemie GmbH), BYK-352 (BYK-Chemie GmbH), BYK-356 (BYK-Chemie GmbH), and BYK-359 (BYK-Chemie GmbH), and combinations thereof.
  19. 19. The patterned substrate of any one of claims 13 to 18, wherein one or more light- absorbing agents in the second resin layer comprises one or more UV-absorbing agents.
  20. 20. The patterned substrate of claim 19, wherein the UV-absorbing agents are selected from the group consisting of ZnO nanoparticles, TiO 2 nanoparticles, ZrO 2 nanoparticles, Zn- conjugated acrylate, Ti-conjugated acrylate, Zr-conjugated acrylate, Zn-conjugated epoxy, Ti- conjugated epoxy, Zr-conjugated epoxy, carbon black, photoinitiator (PI), photoacid generator (PAG), quencher dye, poly(pyrrole), poly(thiophene), poly(phenylene), dithiomaleimide and dibromomaleimide, avobenzone, bisoctrizole, meradimate, dioxybenzone, oxybenzone, drometrizole, 4-methacryloxy-2-hydroxybenzophenone, 2,2-dihydroxy, 4- methoxybenzophenone, methyl-2-cyan-3-(4-hydroxyphenyl)acrylate, (E)-ethyl 2-(3-ethoxy-4- hydroxybenzylidene)-3- oxobutanoate, ethyl- 2-cyano-3-(4- hydroxy-3- methoxy phenyl)acrylate, and dimethyl 2-(4-hydroxybenzylidene)malonate, and combinations thereof.

Description

ILLINC.788WO/IP-2806-PCT PATENT PHOTORESIST PATTERNING IN MULTI-DEPTH NANOWELLS REFERENCE TO SEQUENCE LISTING [0001] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as an electronic file entitled Sequence_Listing_ILLINC788WO.xml, created June 7, 2024, which is 9.8 KB in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety. BACKGROUND Field [0002] The present application relates to the fields of nanopatterning processes and substrates comprising microscale or nanoscale patterned surfaces. Description of the Related Art [0003] Flow cells are devices that allow fluid flow through channels or wells within a substrate. Patterned flow cells that are useful in nucleic acid analysis methods include discrete wells having an active surface within inert interstitial regions. Flow cells fabricated through nanoimprint lithography (NIL) consist of a patterned crosslinked resin material on a glass substrate. Patterning is achieved by depositing a NIL resin containing polymerizable multifunctional monomers onto a glass substrate to create a thin film. A working stamp (WS) is pressed onto the resin surface and the NIL resin material deforms to fill the WS pattern. While the WS is still in contact with the surface, polymerization of the resin is initiated by exposure to light or heat, and the resin is cured. After the resin is sufficiently crosslinked such that it is no longer able to flow, the working stamp is peeled away from the surface, leaving behind an imprinted resin surface. The resulting nanostructured surface is then functionalized via multiple chemistry steps (e.g., salinization, hydrogel deposition, DNA oligo grafting) to support sequencing. In some approaches involving use of a photoresist, a metallic photomask is used so that the photoresist can be selectively patterned. [0004] To ensure that DNA sequencing is spatially restricted into nanowells pre- defined by the working stamp pattern, the nanopatterned surfaces can be polished prior to the grafting of the DNA oligos. [0005] Some available platforms for sequencing nucleic acids utilize a sequencing-by- synthesis approach (SBS). With this approach, nascent strands are synthesized, and the incorporation of labeled nucleotides to the growing strands are detected optically and/or electronically. Because template strands direct synthesis of the nascent strands, the sequence of the template DNAs may be determined from the sequential incorporated nucleotides that were added to the growing strand during SBS. In some examples, paired-end sequencing may be used, where forward strands are sequenced (read 1) and removed, and then reverse strands are constructed and sequenced (read 2). Simultaneous paired-end reading (SPEAR) methods have been reported in U.S. Publication No. 2021/0024991 which is incorporated by reference in its entirety. The SPEAR method can simultaneously sequence the forward (read 1) and reverse (read 2) DNA strands, thus reducing sequencing time in half. The spatial separation of read 1 and read 2 pads is generally required in complicated multiple nanopatterning steps involving several layers of materials, some of which act as temporary sacrificial masks. Such a nanopatterning process may include one or more etch steps, for example to prepare the surface of the NIL resin for addition of a photoresist or to remove an aluminum layer prior to addition of a hydrogel layer. [0006] As such, there remains a demand to develop new cost-effective processes to simplify the substrate patterning processes. Provided herein are new process of manufacturing patterned substrate. SUMMARY [0007] One aspect of the present disclosure relates to a patterned substrate, comprising: a base support; and an imprint layer comprising a first resin layer positioned over the base support, the first resin layer configured to allow passage of light; a second resin layer positioned over the first resin layer, the second resin layer configured as a photomask for blocking passage of light; a plurality of multi-level depressions, each multi-level depression comprising a deep well having a first inner well surface and a first surrounding surface, and a shallow well having a second inner well surface and a second surrounding surface, wherein the deep well and the shallow well are defined by a step portion, each of the first inner well surface and the second inner well surface is parallel to the base support, the first inner well surface resides within the first resin layer, and the second inner well surface resides within the second resin layer. [0008] Another aspect of the present disclosure relates to a patterned substrate, comprising: a base support; and an imprint layer comprising a first resin layer positioned over the base support, the first resin layer configured to allow passage of light; a second resin layer positioned over the firs