Fabrication of optical confinements

• US 20060062531A1
• Filed: 09/16/2005
• Published: 03/23/2006
• Est. Priority Date: 09/17/2004
• Status: Abandoned Application

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Turner, Stephen, Korlach, Jonas
• Application Number:
  US11/229,376
• Publication Number:
  US 20060062531A1
• Time in Patent Office: Days
• US Class Current: 385/123
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0896 Nanoscaled
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 20/00 Nanooptics, e.g. quantum optics or photonic crystals
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2521/543 Immobilised enzyme(s)
• CPC Class Codes: C12Q 2561/113 Real time assay
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G02B 6/13 Integrated optical circuits characterised by the manufacturing method
• CPC Class Codes: Y10T 436/10 Composition for standardization, calibration, simulation, stabilization, preparation or preservation; processes of use in preparation for chemical testing

Abstract

The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.

Claims

1. A method of fabricating an optical confinement that comprises a cladding surrounding a core, comprising:

(a) providing a substrate coated with a layer of photoresist;

(b) patterning said layer of photoresist to define boundaries of said core;

(c) removing said layer of photoresist surrounding said defined boundaries so that a sufficient amount of photoresist remains to occupy said core;

(d) depositing a layer of cladding material over said remaining photoresist and said substrate;

(e) removing at least a portion of said cladding material deposited over said remaining photoresist; and

(f) removing said photoresist of step (e) to form said core surrounded by said cladding of said optical confinement.

2. The method of claim 1, wherein said photoresist is negative and said patterning step employs a positive pattern.

3. The method of claim 1, wherein said photoresist is positive and said patterning step employs a negative pattern.

4. The method of claim 1, wherein said removing step is effected by a technique selected from the group consisting of etching, mechanical polishing, ion milling, and solvent dissolution.

5. The method of claim 1, wherein said layer of cladding material is deposited by vapor deposition.

6. The method of claim 1, wherein said cladding is made of metal.

7. The method of claim 1, wherein said cladding is made of semiconductor.

8. The method of claim 1, wherein said cladding is made of alloy.

9. The method of claim 8, wherein said alloy is aluminum alloy.

10. The method of claim 9, wherein said aluminum alloy contains more than 0.0001% dopant.

11. The method of claim 9, wherein said aluminum alloy contains more than 0.005% dopant.

12. The method of claim 9, wherein said aluminum alloy contains more than 0.1% dopant.

13. The method of claim 8, wherein said alloy comprises an element constituting at least 90% of said metal cladding by weight.

14. The method of claim 1, wherein said cladding is coated with a coating material.

15. The method of claim 1, wherein said core is cylindrical.

16. The method of claim 1, wherein said core is non-cylindrical in shape.

17. The method of claim 1, wherein said optical confinement precludes propagation of a majority of incident light having a wavelength greater than a cutoff wavelength through said core.

18. The method of claim 1, wherein said optical confinement precludes propagation of more than 90% of an incident light beam having a wavelength greater than a cutoff wavelength through said core.

19. The method of claim 1, wherein said optical confinement precludes propagation of more than 99% of an incident light beam having a wavelength greater than a cutoff wavelength through said core.

20. The method of claim 1, wherein said substrate is transparent.

21. The method of claim 1, wherein said substrate is glass.

22. An optical confinement fabricated by said method of claim 1.

23. An array of optical confinements fabricated by said method of claim 1.

24. The array of claim 23 having a density on a substrate exceeding 4×

10⁴ confinements per mm².

25. The array of claim 23 having a density on a substrate exceeding 10⁵ confinements per mm².

26. The array of claim 23 having a density on a substrate exceeding 10⁶ confinements per mm².

27. The array of claim 23, wherein the optical confinements hold a biological reagent and permit resolution of individual molecules present in said biological reagent.

28. The array of claim 23 having a fill fraction greater than 0.0001.

29. The array of claim 23 having a fill fraction greater than 0.001.

30. The array of claim 23 having a fill fraction greater than 0.01.

31. The array of claim 23 having a fill fraction greater than 0.1.

32. The array of claim 23 having a fill fraction ranging from about 0.0001 to about 0.1.