Methods and systems for monitoring multiple optical signals from a single source

• US 7,805,081 B2
• Filed: 08/11/2005
• Issued: 09/28/2010
• Est. Priority Date: 08/11/2005
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Turner, Stephen, Lundquist, Paul, Zaccarin, Denis
• Primary Examiner(s): Bello; Agustin
• Application Number:
  US11/201,768
• Publication Number:
  US 20070036511A1
• Time in Patent Office: 1,874 Days
• Field of Search: 398202-214, 398118-131
• US Class Current: 398/140
• CPC Class Codes: G01J 3/2803 using photoelectric array detector
• CPC Class Codes: G01J 3/36 Investigating two or more bands of a spectrum by separate detectors
• 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 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates

Abstract

Methods and systems for monitoring a plurality of different optical signals from a single source of such signals, where each such different optical signal is spatially separated from other such signals and directed to different detectors or locations upon a single detector, which direction is generally accomplished through the use of a small number of optical components and/or manipulations.

Claims

1. A method of detecting optical signals, comprising:

simultaneously illuminating over time each of a plurality of fluid confinements on a substrate with an excitation radiation to produce at least first and second optical signals from each fluid confinement;

the at least first and second optical signals produced during the occurrence of different reactions of chemical species, wherein at least one of the chemical species is immobilized on the substrate within each fluid confinement and a chemical species with which it reacts is fluid borne, and the first and second optical signals occurring at different times within each fluid confinement wherein the first optical signal comprises a wavelength different from a wavelength of the at least second optical signal;

passing the at least first and second optical signals through an optical train that transmits the first and second optical signals in divergent paths;

receiving the first and second optical signals at different locations on one optical detector.

2. The method of claim 1, wherein the fluid confinement comprises at least a third optical signal, which comprises a wavelength different from a wavelength of the at least first and second optical signals.

3. The method of claim 2, wherein the third optical signal is spatially separated from the first and second optical signals and directed to a third location on the one optical detector different from the first and second locations.

4. The method of claim 3, wherein the fluid confinement comprises at least a fourth optical signal, which comprises a wavelength different from a wavelength of the at least first, second and third optical signals.

5. The method of claim 4, wherein fourth optical signal is spatially separated from the first, second and third optical signals and directed to a fourth location on the one optical detector different from the first, second and third locations.

6. The method of claim 2, wherein the third optical signal is spatially separated from the first and second optical signals and directed to a first location on a second optical detector.

7. The method of claim 2, wherein the at least first and second optical signals are at least partially concurrent.

8. The method of claim 2, wherein the source comprises at least first and second fluorescent components that emit the first and second optical signals, respectively.

9. The method of claim 8, wherein the first and second fluorescent components comprise first and second fluorescent labels covalently coupled to at least first and second different nucleotide polyphosphates or nucleotide polyphosphate analogs.

10. The method of claim 9, wherein the fluid confinement comprises a zero mode waveguide.

11. The method of claim 10, wherein at least one of the chemical species comprises a complex of polymerase, template nucleic acid and primer sequence complementary to a portion of the template nucleic acid, immobilized within the zero mode waveguide, and wherein first and second optical signals are produced when first and second different nucleotide polyphosphates or nucleotide polyphosphate analogs bearing the first and second fluorescent labels, respectively, are associated with the complex.

12. The method of claim 2, wherein spatially separating the first and second optical signals comprises passing the first and second optical signals through an optical train that directs the first and second optical signals on divergent paths.

13. The method of claim 12, wherein the optical train comprises an optical grating for spatially separating the first and second optical signals.

14. The method of claim 12, wherein the optical train comprises a prism for spatially separating the first and second optical signals.

15. The method of claim 2, further comprising characterizing the first and second optical signals based upon the location on the detector to which they were directed.

16. The method of claim 2, wherein the source comprises an unknown optical signal, the method further comprising characterizing whether the unknown optical signal is the first or second optical signal by a location upon the one detector to which the unknown optical signal is directed.

17. The method of claim 1 wherein the reactions of chemical species comprises DNA sequence identification, DNA hybridization, immunoassays, or enzymatic reactions.

18. An analytical system, comprising:

a plurality of confined reaction regions on a substrate for containing a reaction mixture that each produce at least first and second optical signals by illumination with excitation light of different reactions of chemical species within each confined reaction region, wherein at least one of the chemical species is immobilized on the substrate within the confined reaction region and the a chemical species with which it reacts is fluid borne, such optical signals produced during the reactions, and occurring at different times, wherein the first optical signal comprises a wavelength different from a wavelength of the at least second optical signal;

an excitation light source; and

an optical train in optical communication with the confined reaction regions, for simultaneously directing excitation light from the light source to the plurality of confined reaction regions over time, and receiving the first and second optical signals from the plurality of confined reaction regions and spatially separating the first and second optical signals and directing them to different locations on an optical detector.

19. The analytical system of claim 18, wherein the optical detector comprises a photodiode array.

20. The analytical system of claim 18, wherein the optical detector comprises a charge coupled device (CCD).

21. The analytical system of claim 18, wherein the optical train comprises an optical grating that spatially separates the first and second optical signals directed therethrough.

22. The analytical system of claim 21, wherein the optical train comprises an optical grating that spatially separates the first, second and third optical signals directed therethrough.

23. The analytical system of claim 22, wherein the optical train comprises an optical grating that spatially separates the first, second, third and fourth optical signals directed therethrough.

24. The analytical system of claim 18, wherein the optical train comprises a first prism that spatially separates the at least first and second optical signals.

25. The analytical system of claim 24, wherein the optical train further comprises at least a second prism in series with the first prism.

26. The analytical system of claim 25, wherein at least one of the first and second prisms is rotatable around an optical axis of the optical train to adjust a dispersion profile of the optical signals passing therethrough.

27. The analytical system of claim 18, wherein the confined reaction region comprise wells in a multiwell plate.

28. The analytical system of claim 18, wherein confined reaction region comprises a feature on a molecular array.

29. The analytical system of claim 18, wherein the confined reaction regions comprise zero mode waveguides.

30. The analytical system of claim 18, further comprising a processor operably coupled to the detector for individually or collectively recording the first and second optical signals incident upon the different locations on the detector and characterizing the first and second optical signals based upon the different location on the detector upon which said optical signals were incident.

31. An analytical system, comprising:

a plurality of confined reaction regions on a substrate for containing a reaction mixture that produces in each confined region at least first and second optical signals resulting from the illumination of different reactions of chemical species occurring in each confined region, wherein at least one of the chemical species is immobilized on the substrate within the confined reaction region and a chemical species with which it reacts is fluid borne, such optical signals produced during the reactions, and occurring at different times, wherein the first optical signal comprises a wavelength different from a wavelength of the at least second optical signal;

an optical train in optical communication with the confined reaction region, for simultaneously illuminating over time each of the plurality of confined reaction regions, and for receiving the first and second optical signals from the plurality of confined reaction regions and spatially separating the first and second optical signals and directing them to different locations on an optical detector, wherein said optical train comprises a replaceable modular optical component that spatially separates the first and second optical signals passing therethrough.

32. The analytical system of claim 31, wherein the replaceable modular component comprises at least a first prism.

33. The analytical system of claim 32, wherein at least one of the first and second prisms are rotatable around an optical axis of the optical train.

34. The analytical system of claim 31, wherein the modular component comprises at least the first prism and a second prism.

35. The analytical system of claim 31, wherein the replaceable modular component comprises an optical grating.

36. The analytical system of claim 31, further comprising a library of a plurality of replaceable modular components, wherein each of the plurality of modular components has a different dispersion profile for different optical signals.

37. A method of detecting optical signals, comprising:

simultaneously illuminating a plurality of fluid confinements on a substrate over time to produce first and second optical signals from each fluid confinement;

the first and second optical signals produced during different reactions of chemical species in each fluid confinement, and occurring at different times within each fluid confinement, wherein at least one of the chemical species is immobilized on the substrate within the fluid confinement and a chemical species with which it reacts is fluid borne, and wherein the first optical signal comprises an optical characteristic different from an optical characteristic of the at least second optical signal;

passing optical signals through an optical train that transmits the first and second optical signals in divergent paths; and

receiving the first and second optical signals from each of the plurality of fluid confinement at different locations on one optical detector.

38. A method of detecting optical signals, comprising:

simultaneously illuminating a plurality of fluid confinements on a substrate over time to produce first and second optical signals from each fluid confinement;

the at least first and second optical signals produced during different reactions of chemical species in each fluid confinement, wherein at least one of the chemical species is immobilized to the substrate within the fluid confinement and a chemical species with which it reacts is fluid borne, and the at least first and second optical signals occurring at different times within the fluid confinements, wherein the first optical signal comprises a wavelength different from a wavelength of the at least second optical signal; and

directing the first and second optical signals from each of the plurality of fluid confinements to different locations on one optical detector.

39. A method of detecting optical signals, comprising:

simultaneously illuminating a plurality of fluid confinements on a substrate over time to produce first and second optical signals from each fluid confinements;

wherein each different optical signal is produced from the illumination of a different reaction of chemical species in each fluid confinements, wherein at least one of the chemical species is immobilized on the substrate within each fluid confinement and a chemical species with which it reacts is fluid borne, such optical signals produced during the reactions, and occurring at a different time and comprises a wavelength different from each other optical signal; and

spatially separating the plurality of different optical signals from each of the plurality of fluid confinements and directing them to discrete locations on one optical detector.

40. A method of detecting optical signals, comprising:

illuminating a fluid confinements on a substrate continuously over time to produce at least first and second optical signals;

the at least first and second optical signals produced from the illumination of different reactions of chemical species, wherein at least one of the chemical species is immobilized on the substrate within each fluid confinement and a chemical species with which it reacts is fluid borne, such optical signals produced during the reactions, and occurring at different times, and wherein the first optical signal comprises a wavelength different from a wavelength of the at least second optical signal; and

spatially separating the first and second optical signals and directing the first and second optical signals to first and second different locations on a first optical detector.