System, method, and product for generating patterned illumination

• US 7,803,609 B2
• Filed: 07/13/2007
• Issued: 09/28/2010
• Est. Priority Date: 07/21/2006
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Kaplan, Peter S.
• Primary Examiner(s): Lam; Ann Y
• Application Number:
  US11/777,914
• Publication Number:
  US 20080020938A1
• Time in Patent Office: 1,173 Days
• Field of Search: None
• US Class Current: 435/288.7
• CPC Class Codes: C40B 60/12 for screening libraries
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6456 Spatial resolved fluorescence measurements; Imaging

Abstract

An embodiment of a method for generating an interference pattern at a probe array is described that comprises directing light at a first waveguide and second waveguide, wherein the first and second waveguides are positioned adjacent to each other and the output from the first and second waveguides produce an interference pattern; and directing the interference pattern at the probe array.

Claims

1. A method for generating an interference pattern at a probe array, comprising:

directing light at a first waveguide and second waveguide, wherein the first and second waveguides are positioned adjacent to each other and the output from the first and second waveguides produce an interference pattern; and

directing the interference pattern at the probe array.

2. The method according to claim 1 wherein the probe array has a biopolymer affixed to the surface of a support selected from the group consisting of nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, inverted nucleotides, peptide nucleic acids, and Meta-DNA.

3. The method according to claim 2 wherein the probe array is a nucleic acid or protein probe array.

4. The method according to claim 1 further comprising imaging the probe array using a detector.

5. The method according to claim 4, wherein the detector comprises a charge coupled device (CCD), an electron multiplying charge coupled device (EM CCD), an electron bombardment charge coupled device (EBCCD), a complementary metal oxide semiconductor (CMOS), an avalanche photosensor (APS), or a photomultiplier tube (PMT).

6. The method according to claim 1 further comprising processing the detected image using a computer system.

7. The method according to claim 1 wherein the waveguides are optical fibers or rectangular waveguides.

8. A method for generating an interference pattern to interrogate a surface of a support comprising:

directing light at a first waveguide;

directing light at a second waveguide,

wherein the first and second waveguides are positioned in an operative relationship so as to produce an interference pattern; and

directing the interference pattern at a surface of a support; and

detecting signals from the surface of the support.

9. The method according to claim 8, wherein the probe array has a biopolymer affixed to the surface of a support selected from the group consisting of nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, inverted nucleotides, peptide nucleic acids, and Meta-DNA.

10. The method according to claim 9, wherein the detecting step comprises using a detector comprising a charge coupled device (CCD), an electron multiplying charge coupled device (EM CCD), an electron bombardment charge coupled device (EBCCD), a complementary metal oxide semiconductor (CMOS), an avalanche photosensor (APS), or a photomultiplier tube (PMT).

11. The method according to claim 8 wherein the waveguides are optical fibers or rectangular waveguides.

20. The method according to claim 8 wherein the probe array is a nucleic acid or protein probe array.

12. A system to image the surface of a support comprising:

a source of excitation light;

a first waveguide capable of receiving light from the excitation light and transmitting the light out an exit port;

a second waveguide capable of receiving light from an excitation light and producing an interference pattern when proximately positioned near the first waveguide, the second waveguide is capable of transmitting the light out an exit port;

a support having a probe array on a surface of a support facing the exit ports of the first and second waveguides;

a detector capable of receiving reflected signals from the surface of the support; and

a processor for analyzing the detected signals.

13. The method according to claim 12 wherein the probe array has a biopolymer affixed to the surface of a support selected from the group consisting of nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, inverted nucleotides, peptide nucleic acids, and Meta-DNA.

14. The method according to claim 12 wherein the probe array is a nucleic acid or protein probe array.

15. The method according to claim 12, wherein the detector is used to image the probe array.

16. The system according to claim 15, wherein the detector comprises a charge coupled device (CCD), an electron multiplying charge coupled device (EM CCD), an electron bombardment charge coupled device (EBCCD), a complementary metal oxide semiconductor (CMOS), an avalanche photosensor (APS), or a photomultiplier tube (PMT).

17. The method according to claim 12 further comprising a computer system to process the detected image. -

18. The method according to claim 12 wherein the waveguides are optical fibers or rectangular waveguides.

19. The method according to claim 12 further comprising:

a dispersion cone in an operative relationship with the exit port of the first waveguide for dispersing the exit light from the first waveguide; and

a dispersion cone in an operative relationship with the exit port of the second waveguide for dispersing the exit light from the first waveguide.