Scanning optical detection system

• US 6,309,601 B1
• Filed: 05/01/1997
• Issued: 10/30/2001
• Est. Priority Date: 11/01/1993
• Status: Expired due to Fees

• Current Assignee: Nanogen, Inc.
• Original Assignee: Nanogen, Inc.
• Inventors: Juncosa, Robert D., Wu, Lei, Cormack, Robert H., Butler, William F.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/846,876
• Time in Patent Office: 1,643 Days
• Field of Search: 422/50, 422/68.1, 422/69, 422/82.05, 422/82.08, 422/82.09, 435/6, 435/7.1, 436/501, 935/77, 935/78, 935/88
• US Class Current: 422/68.1
• 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 19/0093 Microreactors, e.g. miniaturised or microfabricated reactors laboratory containers with capillary fluid transport in microfabricated channels or chambers B01L3/5027
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00527 Sheets
• 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 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00614 Delimitation of the attachment areas
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00686 Automatic
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00713 Electrochemical synthesis
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B01L 2200/025 : Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/143 : Quality control, feedback systems
• CPC Class Codes: B01L 2300/0636 : Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0645 : Electrodes
• CPC Class Codes: B01L 2300/0816 : Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0838 : Capillaries
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2400/0421 : electrophoretic flow
• CPC Class Codes: B01L 3/5027 : by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502761 : specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 10/00 : Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 5/00 : Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07K 1/04 : on carriers C07K1/003, C07K1/006 take precedence
• CPC Class Codes: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C12Q 1/6813 : Hybridisation assays
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6825 : Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2565/515 : characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C12Q 2565/607 : being a sensor, e.g. electrode
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6458 : Fluorescence microscopy fluorescence microscopes per se G02B21/0076 and G02B21/16
• CPC Class Codes: G01N 21/76 : Chemiluminescence; Bioluminescence
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules
• CPC Class Codes: G11C 13/04 : using optical elements ; using other beam accessed elements, e.g. electron or ion beam
• CPC Class Codes: G11C 19/00 : Digital stores in which the information is moved stepwise, e.g. shift registers
• CPC Class Codes: H01L 25/50 : Multistep manufacturing processes of assemblies consisting of devices, each device being of a type provided for in group H01L27/00 or H01L29/00 H01L21/50 takes precedence
• CPC Class Codes: H01L 2924/00 : Indexing scheme for arrangements or methods for connecting or disconnecting semiconductor or solid-state bodies as covered by H01L24/00
• CPC Class Codes: H01L 2924/0002 : Not covered by any one of groups H01L24/00, H01L24/00 and H01L2224/00

Abstract

An optical detection system is adapted for detection of biological reactions. An excitation source illuminates a portion of an object to be examined, the portion preferably comprising one microlocation out of an array of microlocations. An intervening optical detection platform serves to direct the excitation radiation to the portion of the object to be illuminated. A detector receives the emitted radiation from the object to be examined, the detector being characterized in that the diameter of the region examined by the detector is the same as or smaller than the diameter of the illuminated region, and comprises less than the entire surface of the object to be examined, and most preferably images a whole or a part of a single microlocation. In operation, a microscopy system is formed in which the excitation radiation is substantially in focus at the surface of the object to be examined. In one aspect of this invention, the optical detection platform includes an excitation detector that measures reflected excitation radiation from the object to be examined. This information is compared to prestored information regarding the location of the microlocations and interstitial regions on the object to be examined, whereby alignment information is obtained. The excitation radiation may then be precisely directed to a given microlocation or portion thereof to perform the examining through the system.

Claims

1. A system for optical detection of emitted radiation from one or more microlocations separated by interstitial regions on an object to be examined, comprising:

a light source providing excitation radiation characterized in that the diameter of the excitation radiation when illuminating the object is of the same diameter or less than the diameter of the microlocation to be examined,

a confocal scanning system adapted to receive the excitation radiation and direct it to the object and to provide reflected radiation and emitted radiation from the microlocation,

a first detector adapted to receive the reflected radiation and generate an output,

a position detection system configured to receive the output of the first detector and based on the output determine position information regarding one or more microlocations,

a control system coupled to the position detection system which utilizes the position information to cause the confocal scanning system to direct excitation radiation to substantially only one microlocation at a time and substantially not to the interstitial regions on the object, wherein the location of the microlocation is predetermined based on position information, and

a second detector operatively positioned to receive the emitted radiation from the microlocation.

2. The system of claim 1 wherein the excitation source is a laser.

3. The system of claim 2 wherein the laser is a single laser source.

4. The system of claim 1 wherein the scanning system is an x-y scanning system.

5. The system of claim 4 wherein the x-y scanning system includes a mirror adapted to reflect the excitation radiation, the reflected radiation and the emitted radiation.

6. The system of claim 1 wherein the second detector further includes an aperture.

7. The system of claim 6 wherein the aperture comprises a pinhole aperture.

8. The system of claim 7 wherein the pinhole aperture corresponds to a microlocation with a diameter in the range from substantially 20 microns to 80 microns.

9. The system of claim 8 wherein the pinhole aperture corresponds to a microlocation with a diameter of substantially 50 microns.

10. The system of claim 1 further including a focusing motor which is capable of moving the position detection system and the aperture.

11. The system of claim 1 further including a rejection filter disposed between the confocal scanning system and the second detector.

12. The system of claim 11 wherein the rejection filter rejects excitation radiation to a factor of 10⁷.

13. The system of claim 11 wherein the rejection filter rejects excitation radiation to a factor of 10¹⁰.

14. The system of claim 1 further including a data acquisition system.

15. The system of claim 1 further including a display.

16. The system of claim 1 further including a laser power monitor positioned to receive excitation radiation and output an indication of laser power.

17. The system of claim 16 wherein the output of the laser power monitor is connected to the control system.

18. The system of claim 1, wherein the position information is x-y position information.

19. A system for optical detection of emitted radiation from at least one microlocation on an object including one or more microlocations to be examined, comprising:

at least one light source providing excitation radiation characterized in that the diameter of the excitation radiation when illuminating the object is of the same diameter or less than the diameter of the microlocation to be examined,

a confocal scanning system adapted to receive excitation energy and selectively direct the excitation energy to at least one microlocation thereon and to provide reflected radiation from the microlocation and emitted radiation from the microlocation,

a first detector adapted to receive the reflected radiation and generate an output,

a position detection system configured to receive the output of the first detector and based on the output determine position information regarding at least one microlocation,

a control system coupled to the position detection system which causes, for each microlocation to be examined, the confocal scanning system to generally align with the microlocation, direct excitation radiation to the microlocation only when the confocal scanning system is aligned with the microlocation, and collect emitted radiation from the microlocation before moving to a next microlocation to be examined, and

a second detector operatively positioned to receive the emitted radiation from the microlocation.

20. The system of claim 19 wherein the excitation source is a laser.

21. The system of claim 19 wherein the scanning system is an x-y scanning system.

22. The system of claim 19 wherein the second detector includes an aperture through which the emitted radiation travels.

23. The system of claim 22 wherein the aperture comprises a pinhole aperture.

24. The system of claim 23 wherein the pinhole aperture corresponds to a microlocation with a diameter in the range from substantially 20 microns to 80 microns.

25. The system of claim 19 further including a laser power monitor positioned to receive excitation radiation and output an indication of laser power.

26. The system of claim 19, wherein the control system uses the position information to selectively control the order in which microlocations are examined.

27. A system for optical detection of emitted radiation from microlocations on an object to be examined, comprising:

a light source configured to generate light,

a confocal scanning system adapted to receive the light and direct it to the object and to receive excitation radiation and direct it to one or more microlocations and to provide reflected radiation and emitted radiation from the microlocation,

an excitation radiation source configured to generally only direct excitation radiation to the confocal scanning system when the confocal scanning system is aligned with a microlocation, the excitation radiation characterized in that the diameter of the excitation radiation when illuminating the microlocation is of the same diameter or less than the diameter of the microlocation to be examined,

a first detector adapted to receive the reflected radiation and generate an output,

a position detection system configured to receive the output of the first detector and based on the output determine position information regarding one or more microlocations,

a control system coupled to the position detection system which causes the confocal scanning system to selectively align with the one or more microlocations based on the position information, wherein the one or more microlocations in sum are a subset of all the microlocations available for scanning on the object, and

a second detector operatively positioned to receive the emitted radiation from the one or more microlocations, the second detector characterized in that the diameter of a microlocation examined by the detector is less than or equal to the diameter of the excitation radiation.

28. The system of claim 27 wherein the scanning system is an x-y scanning system.

29. The system of claim 27 further including a focusing motor.

30. The system of claim 27 further including a laser power monitor positioned to receive excitation radiation and output an indication of laser power.

31. A system for optical detection of emitted radiation from microlocations on an object to be examined, comprising:

a light source providing excitation radiation characterized in that the diameter of the excitation radiation when illuminating the microlocation is of the same diameter or less than the diameter of the microlocation to be examined,

a confocal scanning system adapted to receive the excitation radiation and direct it to the microlocation and to provide reflected radiation and emitted radiation from the microlocation,

a first detector adapted to receive the reflected radiation and a position detection system, the first detector having an output connected to a position detection system,

a second detector operatively positioned to receive the emitted radiation from the microlocation, the detector characterized in that the diameter examined by the detector is less than or equal to the diameter of the excitation radiation,

a control system coupled to the position detection system which causes the confocal scanning system to direct excitation radiation to a specific microlocation, and

a rejection filter disposed between the confocal scanning system and the second detector, wherein the rejection filter rejections excitation radiation to a factor of 10⁷.

32. A system for optical detection of emitted radiation from microlocations on an object to be examined, comprising:

a light source providing excitation radiation characterized in that the diameter of the excitation radiation when illuminating the microlocation is of the same diameter or less than the diameter of the microlocation to be examined,

a confocal scanning system adapted to receive the excitation radiation and direct it to the microlocation and to provide reflected radiation and emitted radiation from the microlocation,

a first detector adapted to receive the reflected radiation and a position detection system, the first detector having an output connected to a position detection system,

a second detector operatively positioned to receive the emitted radiation from the microlocation, the detector characterized in that the diameter examined by the detector is less than or equal to the diameter of the excitation radiation,

a control system coupled to the position detection system which causes the confocal scanning system to direct excitation radiation to a specific microlocation, and

a rejection filter disposed between the confocal scanning system and the second detector, wherein the rejection filter rejections excitation radiation to a factor of 10¹⁰.

33. A system for optical detection of emitted radiation from microlocations on an object to be examined, comprising:

a light source providing excitation radiation characterized in that the diameter of the excitation radiation when illuminating the microlocation is of the same diameter or less than the diameter of the microlocation to be examined,

a confocal scanning system adapted to receive the excitation radiation and direct it to the microlocation and to provide reflected radiation and emitted radiation from the microlocation,

a first detector adapted to receive the reflected radiation and a position detection system, the first detector having an output connected to a position detection system,

a second detector operatively positioned to receive the emitted radiation from the microlocation, the detector characterized in that the diameter examined by the detector is less than or equal to the diameter of the excitation radiation,

a control system coupled to the position detection system which causes the confocal scanning system to direct excitation radiation to a specific microlocation, and

a laser power monitor positioned to receive excitation radiation and output an indication of laser power.

34. A system for optical detection of emitted radiation from microlocations on an object to be examined, comprising:

a light source providing excitation radiation characterized in that the diameter of the excitation radiation when illuminating the microlocation is of the same diameter or less than the diameter of the microlocation to be examined,

a confocal scanning system adapted to receive the excitation radiation and direct it to the microlocation and to provide reflected radiation and emitted radiation from the microlocation,

a first detector adapted to receive the reflected radiation and a position detection system, the first detector having an output connected to a position detection system,

a second detector operatively positioned to receive the emitted radiation from the microlocation, the detector characterized in that the diameter examined by the detector is less than or equal to the diameter of the excitation radiation,

a control system coupled to the position detection system which causes the confocal scanning system to direct excitation radiation to a specific microlocation, and

a laser power monitor connected to the control system and positioned to receive excitation radiation and output an indication of laser power.