Compositions, systems, and methods for detecting the presence of polymer subunits using chemiluminescence

• US 10,633,694 B2
• Filed: 09/10/2015
• Issued: 04/28/2020
• Est. Priority Date: 09/12/2014
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Boyanov, Boyan, Qiang, Liangliang, Gunderson, Kevin L., Klausing, Kay, Pickering, Lea, Delattre, Cyril, Khurana, Tarun
• Primary Examiner(s): Martinell, James
• Application Number:
  US15/507,465
• Publication Number:
  US 20170356030A1
• Time in Patent Office: 1,692 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2563/103 luminescence
• CPC Class Codes: C12Q 2563/125 the label being enzymatic, i.e. proteins, and non proteins, such as nucleic acid with enzymatic activity

Abstract

Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.

Claims

1. A composition including:

a substrate;

a first polynucleotide coupled to the substrate;

a second polynucleotide hybridized to the first polynucleotide;

a catalyst coupled to a first nucleotide at the 3′

end of the second polynucleotide, wherein the catalyst is operable to cause a chemiluminogenic molecule to emit a photon, wherein the first nucleotide is coupled to a first moiety, and the catalyst is coupled to a second moiety, wherein the first nucleotide and the catalyst are coupled via the first and second moieties; and

a polymerase capable of extending the second polynucleotide hybridized to the first polynucleotide.

2. The composition of claim 1, wherein the catalyst is selectively cleavable from the first nucleotide.

3. The composition of claim 1, wherein the catalyst includes a luciferase.

4. The composition of claim 3, wherein the chemiluminogenic molecule comprises luciferin or coelenterazine.

5. The composition of claim 1, wherein the catalyst includes a peroxide generator.

6. The composition of claim 5, wherein the peroxide generator comprises a peroxide catalyst selected from the group consisting of an enzyme, a metallic catalyst, an organic catalyst, and a metalorganic catalyst;

and wherein the chemiluminogenic molecule comprises a substituent selected from the group consisting of luminol, a luminol derivative, and acridinium.

7. A system comprising:

the composition of claim 1, wherein the catalyst coupled to a first nucleotide is a first catalyst;

a plurality of nucleotides comprising;

a first subset of nucleotides comprising the first moiety,

a second subset of nucleotides comprising a third moiety,

a third subset of nucleotide comprising a fourth moiety, and

a fourth subset of nucleotides comprising a fifth moiety;

wherein the second moiety of the first catalyst is capable of selectively coupling to one, two or three moieties selected from the first, third, fourth, or fifth moieties;

a second catalyst coupled to a sixth moiety, wherein the sixth moiety is capable of selectively coupling to one, two or three moieties selected from the first, third, fourth, or fifth moieties;

a cleaving agent capable of selectively cleaving one or more linkages between the second moiety and any one of the first, third, fourth or fifth moieties, or between the sixth moiety and any one of the first, third, fourth, or fifth moieties; and

circuitry configured to detect the photon emitted by the chemiluminogenic molecule.

8. A method for sequencing a nucleic acid, comprising:

providing the composition of claim 1, wherein the catalyst coupled to a first nucleotide is a first catalyst; and

contacting the first catalyst with a first chemiluminogenic molecule, such that the first chemiluminogenic molecule emits a photon.

9. The method of claim 8 further comprising extending the second polynucleotide by adding a second nucleotide to the first nucleotide in the presence of the polymerase.

10. The method of claim 9, further comprising selectively cleaving the first catalyst from the first nucleotide before the contacting the polymerase with the first and second polynucleotides.

11. The method of claim 10, further comprising extending the second polynucleotide by adding the second nucleotide to the first nucleotide after the contacting the polymerase with the first and second polynucleotides.

12. The method of claim 11, further including coupling a second catalyst to the second nucleotide.

13. The method of claim 8, wherein the catalyst includes a luciferase.

14. The method of claim 13, wherein the chemiluminogenic molecule comprises luciferin or coelenterazine.

15. The method of claim 8, wherein the catalyst includes a peroxide generator.

16. The method of claim 15, wherein the peroxide generator comprises a peroxide catalyst selected from the group consisting of an enzyme, a metallic catalyst, an organic catalyst, and a metalorganic catalyst;

and wherein the chemiluminogenic molecule comprises a substituent selected from the group consisting of luminol, a luminol derivative, and acridinium.

17. The method of claim 8, further including detecting the photon emitted by the first chemiluminogenic molecule, thereby detecting the presence of the first nucleotide.

18. The method of claim 8, wherein the providing comprises:

incorporating the first nucleotide into the polynucleotide by contacting the polynucleotide with a plurality of nucleotides in the presence of the polymerase, wherein the plurality of nucleotides comprises;

a first subset of nucleotides comprising the first moiety,

a second subset of nucleotides comprising a third moiety,

a third subset of nucleotide comprising a fourth moiety, and

a fourth subset of nucleotides comprising a fifth moiety; and

contacting the first nucleotide with the catalyst coupled to the second moiety, wherein the second moiety is capable of selectively coupling to at least the first moiety, and optionally to one or two moieties selected from the third, fourth, or fifth moieties; and

determining the identity of the first nucleotide by;

(i) the contacting the catalyst with a first chemiluminogenic molecule, such that the first chemiluminogenic molecule emits a photon;

(ii) detecting the presence of the catalyst coupled to the incorporated nucleotide,

(iii) contacting the first nucleotide with a second catalyst coupled to a sixth moiety, wherein the sixth moiety is capable of selectively coupling to one, two or three moieties selected from the first, third, fourth, or fifth moieties,

(v) detecting the presence or absence of the second catalyst coupled to the first nucleotide,

(vi) contacting the first nucleotide with a cleaving agent, wherein the cleaving agent is capable of selectively cleaving one or more linkages between the second moiety and any one of the first, third, fourth or fifth moieties, or between the sixth moiety and any one of the first, third, fourth, or fifth moieties,

(vii) detecting the presence or absence of the first or second catalyst coupled to the incorporated nucleotide, thereby determining the identity of the incorporated nucleotide.