Microarray with hydrophobic barriers

• US 7,498,176 B2
• Filed: 09/29/2003
• Issued: 03/03/2009
• Est. Priority Date: 09/27/2002
• Status: Expired due to Fees

• Current Assignee: Roche NimbleGen, Inc. (Roche Holding AG)
• Original Assignee: Roche NimbleGen, Inc. (Roche Holding AG)
• Inventors: Stengele, Klaus-Peter, Green, Roland, McCormick, Mark, Barrett, Gary
• Primary Examiner(s): Warden; Jill
• Assistant Examiner(s): Handy; Dwayne K
• Application Number:
  US10/673,760
• Publication Number:
  US 20040110211A1
• Time in Patent Office: 1,982 Days
• Field of Search: 422/61, 422/68.1, 422/99, 422/101, 422/100, 436/94, 436/174, 436/180, 435/6
• US Class Current: 436/180
• 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 method for preparing a microarray having a hydrophobic barrier defining a plurality of subarrays on the microarray, the microarray constructed by a light-directed maskless array synthesizer instrument, the method comprising the steps of:

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

b) synthesizing the probe sets selected in step a) on a microarray slide to provide the plurality of subarrays using the light-directed maskless array synthesizer instrument;

c) depositing between each of the subarrays synthesized in step b) a hydrophobic group-bearing phosphoramidite to provide a hydrophobic barrier which surrounds each subarray, wherein the deposit of the hydrophobic barrier is made by using the same light-directed maskless array synthesizer instrument used in step b); and

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

2. The method of claim 1 wherein hydrophobic barrier is synthesized using a hydrophobic group-bearing phosphoramidite.

3. The method of claim 2 wherein the phosphoramidite is a trityl protected phosphoramidite.

4. A method for preparing a microarray having a hydrophobic barrier defining a plurality of subarrays on the microarray, wherein a substrate containing the microarray is held in the identical position by a light-directed maskless array synthesizer instrument throughout the method, the method comprising the steps of:

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

b) synthesizing the probe sets selected in step a) on a microarray slide using the light-directed maskless array synthesizer instrument to provide the plurality of subarrays; and

c) depositing between each of the subarrays synthesized in step b) a hydrophobic group-bearing phosphoramidite to provide a hydrophobic barrier which surrounds each subarray, wherein the deposit of the hydrophobic barrier is made by using the same light-directed maskless array synthesizer instrument used to synthesize the probe sets of step b), and wherein the substrate containing the microarray is held in the identical position by the instrument throughout each step of the method.

5. The method of claim 4 wherein hydrophobic barrier is synthesized using a hydrophobic group-bearing phosphoramidite.

6. The method of claim 5 wherein the is a trityl protected phosphoramidite.