Integrated optics fiber array

• US 20050042651A1
• Filed: 06/24/2004
• Published: 02/24/2005
• Est. Priority Date: 01/08/1999
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Vann, Charles S., Blasband, Andrew J., Geiser, Tim
• Granted Patent: US 7,595,189 B2
• Time in Patent Office: Days
• US Class Current: 506/13
• 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 2219/00326 Movement by rotation
• CPC Class Codes: B01J 2219/0043 for direct application of reagents, e.g. through openings in a shutter
• CPC Class Codes: B01J 2219/00495 Means for heating or cooling the reaction vessels
• CPC Class Codes: B01J 2219/00515 in the shape of strings
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential 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 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00628 Ionic
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00635 by reactive plasma treatment
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00675 : In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00702 : Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01L 3/5023 : with a sample being transported to, and subsequently stored in an absorbent for analysis
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• 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: G01N 2021/6484 : Optical fibres
• 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 21/648 : using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
• CPC Class Codes: G01N 21/7703 : using reagent-clad optical fibres or optical waveguides using measurement of total internal reflection or attenuated total reflection G01N21/552; optical fibres or waveguides per se G02B

Abstract

The device for detecting the binding of two chemical species includes a first plate having a base, multiple optical fibers and a second plate. The base has multiple grooves formed therein. The multiple optical fibers are each disposed within a corresponding one of the multiple grooves. The second plate has multiple channels formed therein. The first plate and the second plate are configured to be placed adjacent to one another such that each the optical fiber is exposed to and traverses the multiple channels.

Claims

1. A device for detecting the binding of two chemical species, comprising:

a first plate comprising;

a base having multiple grooves formed therein; and

multiple optical fibers each disposed within a corresponding one of said multiple grooves; and

a second plate having multiple channels formed therein,

where said first plate and said second plate are configured to be placed adjacent to one another such that each said optical fiber is exposed to and traverses said multiple channels.

2. The device of claim 1, wherein said grooves are substantially parallel to one another.

3. The device of claim 1, wherein said multiple channels are substantially parallel to one another.

4. The device of claim 1, wherein each of said grooves have a cross-section selected from the group consisting of:

a square cross-section, a rectangular cross-section, a semicircular cross section, and a mixture thereof.

5. The device of claim 1, wherein each of said grooves have a substantially square cross-section.

6. The device of claim 1, wherein each of said optical fibers substantially occupies said corresponding one of said multiple grooves.

7. The device of claim 1, wherein said base and said optical fibers have different refractive indices.

8. The device of claim 1, wherein an upper surface of said base and said optical fibers are substantially flush with one another.

9. The device of claim 1, wherein each optical fiber comprises a different chemical species immobilized thereon.

10. The device of claim 1, wherein said optical fibers are substantially parallel to one another.

11. The device of claim 1, wherein said grooves extend across an entire length of said base.

12. The device of claim 1, wherein said channels extend partially across a length of said channel plate.

13. The device of claim 1, wherein said channel plate defines multiple wells, each fluidly coupled to a corresponding channel of said multiple channels.

14. The device of claim 1, wherein said base is opaque.

15. The device of claim 1, wherein said base is reflective.

16. A method for making a device for detecting the binding of two chemical species, said method comprising:

immobilizing each of a plurality of known chemical species on a separate optical fiber of multiple optical fibers each disposed within a corresponding one of multiple grooves formed in a first plate; and

placing a second plate having multiple channels formed therein adjacent to said first plate such that each said optical fiber is exposed to and traverses said multiple channels.

17. A method for using a device for detecting the binding of two chemical species, said method comprising:

placing a second plate having multiple channels formed therein adjacent to a first plate having a plurality of immobilized chemical species each immobilized on a separate optical fiber of multiple optical fibers each disposed within a corresponding one of multiple grooves formed in the first plate, such that each said optical fiber is exposed to and traverses said multiple channels; and

depositing each of a plurality of mobile chemical species into a separate one of said channels;

contacting said mobile chemical species with said immobilized chemical species; and

detecting whether binding occurs between at least one of said mobile chemical species and at least one of said immobilized chemical species.

18. A portable detector for detecting the binding of two chemical species, the portable detector comprising:

a support configured to receive a fiber array, wherein said fiber array comprises multiple optical fibers;

a light source configured to direct light at an end of each of the multiple optical fibers; and

a detector configured to detect light emitted from at least one of the multiple optical fibers caused by binding of two chemical species.

19. The detector of claim 18, further comprising a housing configured to receive said fiber array therein, wherein said support is disposed within said housing and said light source and detector are coupled to said housing.

20. The detector of claim 18, wherein the fiber array comprises a support having multiple channels therein, wherein the multiple optical fibers are disposed on the support across the channels, where each of the multiple optical fibers has an immobilized chemical species thereon.

21. The detector of claim 18, further comprising a power source coupled to said housing.

22. The detector of claim 18, wherein said power source is a battery.

23. The detector of claim 18, wherein said power source is a fuel-cell.

24. The detector of claim 18, further comprising a computing device coupled to said housing and electrically coupled to said detector for controlling said binding detection.

25. The detector of claim 24, wherein said computing device is further configured to receive commands for performing a binding assay, controlling the binding assay, and displaying results of the binding assay.

26. The detector of claim 18, further comprising a thermal cycler coupled to said housing for thermally cycling the fiber array.

27. The detector of claim 18, further comprising an agitator for agitating the fiber array.

28. The detector of claim 18, further comprising optical elements disposed between said light source and the multiple optical fibers.

29. The detector of claim 18, further comprising optical elements disposed between the multiple optical fibers and said detector.

30. The detector of claim 18, further comprising a computer within said housing for controlling said binding detection.

31. The detector of claim 18, further comprising at least one motion device coupled to said housing for moving said detector relative to the fiber array.

32. The detector of claim 18, further comprising at least one motion device coupled to said housing for moving said light source relative to the fiber array.

33. A portable detector, configured to be carried by hand, for detecting the binding of two chemical species, the portable detector comprising:

a fiber array comprising;

a plate having multiple channels therein;

multiple optical fibers disposed on said plate across the channels,

where each of the multiple optical fibers has an immobilized chemical species thereon;

a housing configured to receive said fiber array therein;

a light source coupled to said housing, wherein said light source is configured to direct light at an end of each of said multiple optical fibers; and

a detector coupled to said housing, wherein said detector is configured to detect light emitted from at least one of said multiple optical fibers caused by binding of two chemical species.

34. The detector of claim 33, further comprising optical elements disposed between said light source and said multiple optical fibers, and optical elements disposed between said multiple optical fibers and said detector.

35. A device for contacting at least two chemical species, comprising:

a plate comprising a channel capable of receiving a mobile chemical species; and

a fiber having an immobilized chemical species disposed along a portion of said fiber, wherein said fiber is disposed on said plate across a width of said channel such that said portion of said fiber is exposed to said channel; and

a molecular beacon coupled to said mobile or said immobilized chemical species.

36. The device of claim 35, wherein said molecular beacon is coupled to said immobilized chemical species and comprises a single-stranded bi-labeled florescent probe held in a hairpin-loop conformation by complementary stem sequences near both ends of said probe.

37. The device of claim 35, wherein said molecular beacon is coupled to said mobile chemical species and comprises a single-stranded bi-labeled florescent probe held in a hairpin-loop conformation by complementary stem sequences near both ends of said probe.

38. The device of claim 35, wherein said molecular beacon comprises a florescence reporter.

39. The device of claim 35, wherein said molecular beacon comprises a moiety at one end of said immobilized chemical species and a non-florescent quenching moiety at another end of said immobilized chemical species.