Method and device for nucleic acid sequencing using a planar waveguide

• US 20090247414A1
• Filed: 04/18/2006
• Published: 10/01/2009
• Est. Priority Date: 04/18/2005
• Status: Abandoned Application

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Obradovic, Bojan, West, John Stephen, Swerdlow, Harold Phillip
• Application Number:
  US11/918,609
• Publication Number:
  US 20090247414A1
• Time in Patent Office: Days
• US Class Current: 506/3
• 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 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

The present invention is concerned with improvements to methods of imaging nucleotides incorporated into polynucleotides and in particular with improved methods of determining the sequence of template nucleic acid molecules using multiple cycle nucleic acid “sequencing-by-synthesis” reactions.

Claims

1. A method of sequencing a template nucleic acid molecule comprising:

immobilizing said template nucleic acid molecule on or proximal to a planar waveguide;

incorporating one or more nucleotides into a strand of nucleic acid complementary to the template nucleic acid and determining the identity of the base present in one or more incorporated nucleotide(s) in order to determine the sequence of the template nucleic acid molecule;

wherein the identity of the base present in said nucleotide(s) is determined by detecting a signal produced by said nucleotide(s) when exposed to an evanescent field generated by coupling of light into said planar waveguide.

2. A method according to claim 1 wherein one or more of the incorporated nucleotides comprise a fluorescent label and the step of determining the identity of the base present in the incorporated nucleotide(s) comprises detecting fluorescence from the fluorescently labelled nucleotide(s) when exposed to evanescent illumination generated by coupling of light into said planar waveguide.

3. The method according to claim 1 wherein the template nucleic acid is present in an array.

4. The method according to claim 3 wherein the array is a clustered array.

5. The method according to claim 3 wherein the array is a single molecule array.

6. The method according to claim 1 wherein at least 2 nucleotides are successively incorporated and the identity of the base present in each of the incorporated nucleotides is determined.

7. The method according claim 6 wherein at least 10 nucleotides are successively incorporated and the identity of the base present in each of the incorporated nucleotides is determined.

8. The method according to claim 7 wherein at least 16 nucleotides are successively incorporated and the identity of the base present in each of the incorporated nucleotides is determined.

9. The method according to claim 8 wherein from 16 to 30 nucleotides are successively incorporated and the identity of the base present in each of the incorporated nucleotides is determined.

10. The method according to claim 1 wherein the identity of the base present in each of the incorporated nucleotide(s) is determined after each nucleotide incorporation.

18. The method according to claim 2 wherein the template nucleic acid is present in an array.

11. A device comprising an array of template nucleic acid molecules immobilised on the surface of a planar wave guide, wherein the array comprises clusters of template nucleic acid strands located at distinct locations on the array, and wherein the device further comprises nucleotides incorporated into strands complementary to the templates, wherein the nucleotides comprise a removable blocking group attached at the 3′

position.

12. A device according to claim 11 which further comprises

a top plate held in liquid seal against at least a portion of the surface of the planar wave guide on which the template nucleic acid molecules are immobilised to form a flow cell enclosing at least one reaction channel,

an inlet port and an outlet port to permit flow of liquid through the flow cell when the device is in use, and

an input coupling grating.

13. A device according to claim 12 which further includes an output coupling grating, wherein the input and output coupling gratings are positioned on either side of a reaction channel.

14. A device according to claim 13 which comprises two or more reaction channels, wherein a coupling grating is positioned between each adjacent pair of reaction channels.

15. A device according to claim 13 wherein the reaction channels are each in fluid communication with a common reagent reservoir.

16. (canceled)

17. A method of determining identity of the base present in a nucleotide incorporated into a polynucleotide molecule immobilised on a planar wave guide comprising:

incorporating a nucleotide into a strand of nucleic acid complementary to the template nucleic acid and determining the identity of the base present in the incorporated nucleotide by detecting a signal produced by said nucleotide when exposed to an evanescent field generated by coupling of light into said planar waveguide.