System and method for nucleic acids sequencing by phased synthesis

• US 8,747,751 B2
• Filed: 06/10/2009
• Issued: 06/10/2014
• Est. Priority Date: 06/16/2008
• Status: Expired due to Fees

• Current Assignee: LDIP, LLC
• Original Assignee: PLC Diagnostics, Inc.
• Inventors: Duer, Reuven, Herron, James
• Primary Examiner(s): Babic, Christopher M
• Assistant Examiner(s): Flinders, Jeremy C
• Application Number:
  US12/481,799
• Publication Number:
  US 20090312188A1
• Time in Patent Office: 1,826 Days
• Field of Search: 385/12, 385/14, 385/15, 385/30, 385/40, 435/6.1, 435/288.7, 422/82.08, 422/82.11
• US Class Current: 422/82.11
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00704 integrated with the reactor apparatus
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2523/319 Photocleavage, photolysis, photoactivation
• CPC Class Codes: C12Q 2535/107 Maxam and Gilbert method, i.e. sequential release and detection of nucleotides
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 2021/6441 with two or more labels
• 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
• CPC Class Codes: G02B 27/56 : Optics using evanescent waves, i.e. inhomogeneous waves
• CPC Class Codes: G02B 6/24 : Coupling light guides

Abstract

A system and methods of sequencing a nucleic acid by detecting the identity of a fluorescent nucleotide analogue incorporated at the 3′ end of a growing nucleic acid strand are provided. The system may include a substrate comprising a plurality of substantially parallel excitation waveguides, and a plurality of substantially parallel collection waveguides, the excitation waveguides and collection waveguides crossing to form a two-dimensional array of intersection regions, a plurality of optical sensing sites in optical communication with the intersection regions, one or more switchable light sources and a detector coupled to the light dispersive module. Methods of using these systems are also described.

Claims

1. A scanning sensor system for sequencing a nucleic acid comprising:

a substrate comprising a plurality of substantially parallel excitation waveguides, and a plurality of substantially parallel collection waveguides, the excitation waveguides and collection waveguides crossing to form a two-dimensional array of intersection regions where an excitation waveguide and a collection waveguide cross and provide evanescent optical communication with an optical sensing site adjacent each crossing;

wherein each optical sensing site is adjacent to and in optical communication with one of the excitation waveguides and one of the collection waveguides at the intersection regions, so that the excitation waveguides couple into the optical sensing site through an evanescent electromagnetic field and the collection waveguides couple into the optical sensing sites through an evanescent electromagnetic field;

one or more switchable light sources, comprising a scanning light source input and a photo-cleaving light source input, coupled to and in optical communication with the excitation waveguides of the substrate;

a light dispersive module coupled to and in optical communication with the collection waveguides of the substrate, and comprising an array of elements; and

a detector coupled to and in optical communication with the light dispersive module.

2. The system of claim 1, wherein a scanning light source is coupled to a first switchable light source coupled to and in optical communication with the excitation waveguides at a first side of the substrate and a photo-cleaving light source is coupled to a second switchable light source coupled to and in optical communication with the excitation waveguides at a second side of the substrate.

3. The system of claim 1 or claim 2, wherein the dispersive module is configured to disperse light from one or more of the collection waveguides to a plurality of elements in the detector.

4. The system of claim 3, wherein the dispersive module is configured to disperse light from a given collection waveguide to four or more elements in the detector.

5. The system of claim 4, wherein the light dispersed from the dispersive module comprises a plurality of light wavelengths.

6. The system of claim 5, wherein the plurality of wavelengths comprises four or more light wavelengths.

7. The system of claim 1 or claim 2, wherein the photo-cleaving light source emits light having a wavelength ranging between 400 nm and 2000 nm.

8. The system of claim 7, wherein the photo-cleaving light source input is coupled to an ultra-violet light source.

9. The system of claim 8, wherein the ultra-violet light source emits light having a wavelength ranging between 100 nm and 400 nm.

12. The system of claim 1, wherein the optical sensing site is a well.

13. The system of claim 1, wherein the optical sensing site is above the collection waveguide and the excitation waveguide.

14. The system of claim 1, wherein the optical sensing site is in a different layer than the collection waveguide and the excitation waveguide.

10. A scanning sensor system for sequencing a nucleic acid comprising:

a substrate comprising a plurality of excitation waveguides and a plurality of collection waveguides, the excitation waveguides and collection waveguides arranged in a lateral plane so that the excitation waveguides and collection waveguides cross to form a two-dimensional array of intersection regions where the crossing of each excitation waveguide and collection waveguide provides evanescent optical communication with an optical sensing site adjacent to one of the excitation waveguides and one of the collection waveguides at each crossing, further wherein the excitation waveguides are single-mode in a vertical dimension and multimode in a lateral dimension;

wherein the plurality of optical sensing sites are each in optical communication with the excitation waveguide and collection waveguide so that the excitation waveguides couple into the optical sensing sites through an evanescent electromagnetic field and the collection wave guides couple into the optical sensing sites through an evanescent electromagnetic field;

one or more switchable light sources, comprising a scanning light source input and a photo-cleaving light source input, coupled to and in optical communication with the excitation waveguides of the substrate;

a light dispersive module coupled to and in optical communication with the collection waveguides of the substrate, and comprising an array of elements; and

a detector coupled to and in optical communication with the light dispersive module.

11. A scanning sensor system for sequencing a nucleic acid comprising:

a substrate comprising a plurality of excitation waveguides, and a plurality of collection waveguides, the excitation waveguides and collection waveguides crossing to form a two-dimensional array of intersection regions where an excitation waveguide and a collection waveguide cross and provide evanescent optical communication with an optical sensing site;

a plurality of optical sensing sites wherein each optical sensing site is adjacent to and in optical communication with one of the excitation waveguides and one of the collection waveguides, so that the excitation waveguides couple into the optical sensing sites through an evanescent electromagnetic field and the collection waveguides couple into the optical sensing sites through an evanescent electromagnetic field;

one or more switchable light sources, comprising a scanning light source input and a photo-cleaving light source input, coupled to and in optical communication with the excitation waveguides of the substrate;

a light dispersive module coupled to and in optical communication with the collection waveguides of the substrate, and comprising an array of elements; and

a detector coupled to and in optical communication with the light dispersive module.