Systems and method for examination of microarrays using scanning electron microscope

• US 20040081985A1
• Filed: 07/08/2003
• Published: 04/29/2004
• Est. Priority Date: 07/12/2002
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Ciccolella, Paul C., Hozbor, Maria A.
• Application Number:
  US10/615,560
• Publication Number:
  US 20040081985A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G01N 23/2251 using incident electron beams, e.g. scanning electron microscopy [SEM]

Abstract

The present invention provides methods to detect biomolecules on a microarray using a scanning electron microscope. In one embodiment of the invention, errors in oligonucleotide synthesis during manufacturing of microarrays are detected by monitoring synthesis of control probes on the chips. In another embodiment, misalignment of features on the chip is determined. In yet another embodiment, the size, shape and edge definition of features on the chip is determined. In further embodiments, methods are provided for analyzing interactions between an oligonucleotide target and an oligonucleotide probe on a microarray and methods for testing conditions in a microarray manufacturing process.

Claims

1. A method of detecting biomolecules on a microarray comprising

synthesizing said biomolecules on a microarray;

scanning said microarray with a scanning electron microscope; and

detecting said biomolecules on said microarray.

2. A method of claim 1 wherein said biomolecules are nucleotides, oligonucleotides or polynucleotides.

3. A method of claim 1 wherein said microarray is synthesized by light directed oligonucleotide synthesis.

4. A method of claim 1 wherein said method is used to detect errors in said synthesizing said biomolecules.

5. A method of claim 1 wherein said method is used to detect misalignment of said plurality of biomolecules on said microarray.

6. A method of claim 5 wherein said misalignment is detected with a resolution of less than about 5 micron.

7. A method of claim 5 wherein said misalignment is detected with a resolution of less than about 1 micron.

8. A method of claim 1 wherein said microarray is coated with a layer of metals.

9. A method analyzing interactions between a biomolecule target and a biomolecule probe on a microarray, comprising

exposing said biomolecule probe on said microarray to a plurality of biomolecule targets under a hybridization condition;

scanning said microarray with a scanning electron microscope; and

detecting said biomolecule targets binding to said biomolecule probe on said microarray.

10. A method of claim 9 wherein said microarray is synthesized by light directed syntheses.

11. A method of claim 9 wherein said biomolecules are nucleotides, oligonucleotides or polynucleotides.

12. A method of claim 9 wherein said biomolecule target is labeled with a heavy atom.

13. A method of claim 12 wherein said heavy atom is a colloidal gold.

14. A method of claim 13 wherein said heavy atom is detected using a backscattered electron detector.

15. A method of testing conditions in a microarray manufacturing process comprising

synthesizing biomolecules on a first microarray using a microarray manufacturing process with a first condition;

inspecting a pattern on said first microarray with a scanning electron microscope;

synthesizing biomolecules on a second micro array using a micro array manufacturing process with a second condition;

inspecting a pattern on said second microarray with a scanning electron microscope;

comparing said patterns on said first microarray and said second microarrays; and

selecting a condition for said microarray manufacturing process.

16. A method of claim 15 wherein said biomolecules are nucleotides, oligonucleotides or polynucleotides.

17. A method of claim 15 wherein said microarray is synthesized by light directed oligonucleotide synthesis.