Microarray with hydrophobic barriers

• US 20040110211A1
• Filed: 09/29/2003
• Published: 06/10/2004
• Est. Priority Date: 09/27/2002
• Status: Active Grant

• Current Assignee: Roche NimbleGen, Inc. (Roche Holding AG)
• Original Assignee: Roche NimbleGen, Inc. (Roche Holding AG)
• Inventors: Green, Roland, McCormick, Mark, Barrett, Gary, Stengele, Klaus-Peter
• Granted Patent: US 7,498,176 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/00439 using micromirror arrays
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2300/165 Specific details about hydrophobic, oleophobic surfaces
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: B01L 3/5088 confining liquids at a location by surface tension, e.g. virtual wells on plates, wires B01L3/50857 takes precedence
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: Y02P 20/55 : Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

The present invention is a microarray having a plurality of subarrays with a hydrophobic barrier that defines each subarray of the microarray, and a method for preparing such a microarray. The hydrophobic barrier is prepared using a microarray synthesis instrument, where NPPOC photoprotected and other hydrophobic group-bearing phosphoramidites are coupled to the microarray using light from a digital micromirror to direct formation of the hydrophobic barrier. The method utilizes hydrophobicity, a well-established property, of conventional phosphoramidite protecting groups for an entirely new application, the synthesis of hydrophobic barriers on microarrays.

Claims

1. A microarray comprising a substrate on which are arranged a plurality of subarrays, wherein each subarray on the microarray is surrounded by a hydrophobic barrier, which separates each subarray from an adjacent subarray and wherein the hydrophobic barrier inhibits fluid communication between each subarray of the microarray.

2. The microarray of claim 1 wherein the hydrophobic barrier comprises of a hydrophobic group-bearing phosphoramidite.

3. The microarray of claim 2 wherein the hydrophobic group-bearing phosphoramidite is a trityl protected phosphoramidite.

4. The method of claim 1 wherein the hydrophobic barrier is flexibly deployable within the array and can be placed with great precision immediately adjacent to and surrounding the subarray areas.

5. A method for preparing a microarray having a hydrophobic barrier defining a plurality of subarrays on the microarray, the method comprising the steps of:

a) selecting at least one probe set comprising probes of interest;

b) synthesizing the probe sets on a microarray slide to provide the plurality of subarrays;

c) depositing between each of the subarrays a hydrophobic group-bearing phosphoramidite to provide a hydrophobic barrier which surrounds each subarray; and

d) inhibiting fluid communication between each of the subarrays on the microarray.

6. The method of claim 5 wherein hydrophobic barrier is synthesized using a hydrophobic group-bearing phosphoramidite.

7. The method of claim 6 wherein the phosphoramidite is a trityl protected phosphoramidite.

8. The method of claim 5 wherein the hydrophobic barrier is flexibly deployable within the array and can be placed with great precision immediately adjacent to and surrounding the subarray areas.