Microarray fabrication system and method

• US 9,670,535 B2
• Filed: 02/28/2014
• Issued: 06/06/2017
• Est. Priority Date: 10/28/2011
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Bowen, M. Shane, Vijayan, Kandaswamy, Venkatesan, Bala Murali, Gunderson, Kevin L., Lin, Shengrong, Rogert Bacigalupo, Maria Candelaria, Wu, Yir-Shyuan, Tsay, James, Beierle, John M., Berti, Lorenzo, Park, Sang Ryul
• Primary Examiner(s): Zhang, Kaijiang
• Application Number:
  US14/194,143
• Publication Number:
  US 20140200158A1
• Time in Patent Office: 1,194 Days
• Field of Search: None
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00788 Three-dimensional assemblies, i.e. the reactor comprising a form other than a stack of plates
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/18 using a particular method of attachment to the solid support

Abstract

A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.

Claims

1. A method for preparing a biological microarray, comprising:

activating regions on a substrate to form a pattern of activated regions;

contacting the substrate with monomers of a self-assembling monomer solution;

polymerizing the monomers to form polymer base pads comprising a poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM) polymer only on the activated regions, wherein the polymer base pads are coupled to a molecule binding substance.

2. The method of claim 1, wherein the activated regions are silane pads.

3. The method of claim 1, wherein the activated regions are formed by one or more of photolithography, etching, or masking.

4. The method of claim 1, wherein the polymer extends from the substrate as one or more polymer brushes.

5. The method of claim 1, wherein the polymer is covalently attached to the substrate.

6. The method of claim 1, wherein the molecule binding substance comprises a primer.

7. The method of claim 1, comprising grafting the molecule binding substance to the polymer base pads before the polymerizing is complete.

8. The method of claim 1, comprising grafting the molecule binding substance to the polymer base pads after the polymerizing is complete.

9. The method of claim 1, wherein the activated regions comprise reactive silane.

10. The method of claim 1, wherein activating regions on the substrate comprises contacting the substrate with 3-Triethoxysilylpropylamine (APTES).

11. The method of claim 1, wherein the polymer is a polymer having the formula: