Systems, methods and apparatus for single molecule sequencing

• US 7,709,808 B2
• Filed: 05/16/2007
• Issued: 05/04/2010
• Est. Priority Date: 05/16/2006
• Status: Expired due to Fees

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Oldham, Mark F., Menchen, Steven M., Nordman, Eric S., Reel, Richard T., Boege, Steven J.
• Primary Examiner(s): Porta; David P
• Assistant Examiner(s): BOOSALIS, FANI POLYZOS
• Application Number:
  US11/749,411
• Publication Number:
  US 20080105831A1
• Time in Patent Office: 1,084 Days
• Field of Search: 250/458.1, 250/483.1, 250/368, 250/487.1, 250/459.1, 359/569, 422/82.08, 422/82.11
• US Class Current: 250/458.1
• CPC Class Codes: G01N 2021/6432 Quenching
• 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
• CPC Class Codes: G01N 21/648 using evanescent coupling or surface plasmon coupling for the excitation of fluorescence

Abstract

An embodiment generally relates to a system for analysis of an analyte. The system can include a transparent substrate. The system also includes an excitation light source configured to induce an evanescent wave excitation of a fluorescently labeled molecule near the access to the transparent substrate and a detector for detecting the fluorescently labeled molecule.

Claims

1. A system for analysis of an analyte, the system comprising:

a substrate;

an exclusion layer deposited on the substrate, the exclusion layer having a hole reaching a portion of the substrate;

a fluid sample contacting the substrate through the hole;

an excitation light source configured to induce an evanescent wave field with a penetration depth that is below a top surface of the exclusion layer, wherein the evanescent wave field energizes a first inorganic absorber bound to the substrate; and

a detector configured to detect light emissions.

2. The system of claim 1, wherein the inorganic absorber is a quantum dot.

3. The system of claim 1, wherein the inorganic absorber is an upconverting phosphor.

4. The system of claim 1, wherein the evanescent wave is induced by internal reflection.

5. The system of claim 1, wherein the substrate and the fluid sample each have different index of refraction from the other.

6. The system of claim 1, wherein the inorganic absorber creates an energy transfer zone at a first wavelength.

7. The system of claim 6, further comprising:

an enzyme, wherein a first portion of the enzyme is bound to a fluorescently labeled moiety and a second portion of the enzyme is attached to the first inorganic absorber, wherein the first inorganic absorber transfers excitation energy to the fluorescently labeled moiety at a first wavelength.

8. The system of claim 7, further comprising a second inorganic absorber that is attached to a third portion of the enzyme, wherein the second inorganic absorber is configured to be energized by the evanescent wave field and transfer excitation energy to the fluorescently labeled moiety at a second wavelength.

9. The system of claim 7, wherein the fluorescently labeled moiety includes a fluorescent dye component, a quencher component and a nucleotide component.

10. The system of claim 9, wherein the fluorescent dye component is configured to fluoresce upon cleavage from the quencher component and the nucleotide component.

11. A system for analysis of analyte, the system comprising:

a transparent substrate coated with a metal layer;

an exclusion coating deposited on the metal layer;

a fluorescently labeled molecule configured to diffuse into a hole in the exclusion coating; and

an excitation light source configured to produce plasmon-coupled emission with a penetration depth that is below a top surface of the exclusion coating.

12. The system of claim 11, wherein the exclusion coating is implemented with an index of refraction material higher than a material of the substrate.

13. The system of claim 11, wherein the plasmon coupled emission form an energy transfer zone in the hole in the exclusion coating.

14. The system of claim 13, wherein a cone of emission light is formed in response the fluorescently labeled molecule entering the energy transfer zone.

15. A luminescence detection system, the system comprising a resonant optical cavity, wherein luminophore emission is elicited by evanescent excitation established within the boundary of the resonant optical cavity.

16. The system of claim 15, wherein the resonant optical cavity further comprises:

an excitation light source configured to produce light at a selected wavelength;

a substrate; and

a plurality of mirrors, wherein one mirror is position to reflect and deflect light from the excitation light source to the substrate which reflects the light to the second mirror, which reflects the light and redirects the light substantially the reverse direction as the incoming light.

17. The system of claim 15, further comprising:

an excitation light source configured to produce light at a selected wavelength;

a total internal reflection interface; and

a plurality of mirrors, wherein the resonant optical cavity is bounded by the plurality of mirrors and the total internal reflection interface.

18. The system of claim 17, wherein the light from the excitation light source enters the resonant optical cavity at the Brewster'"'"'s angle to induce total internal reflection.

19. The system of claim 17, wherein the light from the excitation light source enters the resonant optical cavity at normal incidence.

20. The system of claim 15, further comprising:

a plurality of light source, each source configured to produce associated light at a selected wavelength;

a plurality of total internal reflection interface;

a plurality of mirrors further comprising of a plurality of subsets of mirrors, each subset of mirrors associated with a light source, wherein a plurality of resonant cavities are formed, each resonant cavity bounded by an associated subset of mirrors and associated total internal reflection interface and supplied with light from an associated light source.