Nucleotide analogs for sequencing

• US 10,428,379 B2
• Filed: 03/12/2014
• Issued: 10/01/2019
• Est. Priority Date: 03/15/2013
• Status: Active Grant

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Hayden, Mark A., Huff, Jeffrey, Eshoo, Mark W., Picuri, John
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US14/775,067
• Publication Number:
  US 20160032376A1
• Time in Patent Office: Days
• Field of Search: 536 41, 536 231, 536 266, 435 61
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2523/319 Photocleavage, photolysis, photoactivation
• CPC Class Codes: C12Q 2525/117 incorporating modified base
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2563/113 the label being electroactive, e.g. redox labels
• CPC Class Codes: C12Q 2563/116 electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
• CPC Class Codes: C12Q 2563/137 Metal/ion, e.g. metal label

Abstract

Provided herein is technology relating to sequencing nucleic acids, but not exclusively, to compositions, methods, systems, and kits related to nucleotides comprising an electrochemically detectable moiety and one or more photolabile synthesis-inhibiting moieties.

Claims

1. A nucleotide analog comprising:

a) a nucleotide comprising a phosphate moiety, a base, and a sugar;

b) a photocleavable terminating moiety attached to the nucleotide by a first photocleavable linker, wherein said photocleavable terminating moiety is electrochemically detectable by accepting or donating at least one electron during an electrochemical reaction; and

c) a second photocleavable terminating moiety attached to the nucleotide by a second photocleavable linker.

2. The nucleotide analog of claim 1 wherein the electrochemically detectable, photocleavable terminating moiety is attached to the phosphate moiety, base, or sugar of the nucleotide.

3. The nucleotide analog of claim 1 wherein the nucleotide is adenine, cytosine, guanine, thymine, or uracil;

and/or the phosphate moiety is a triphosphate, a diphosphate, or a monophosphate.

4. The nucleotide analog of claim 1 wherein said electrochemically detectable, photocleavable terminating moiety is a group imparting polymerase termination properties to the nucleotide analog.

10. A kit for sequencing a nucleic acid, the kit comprising four nucleotide analogs according to claim 1, wherein a first nucleotide analog comprises an adenine nucleotide, a second nucleotide analog comprises a cytosine nucleotide, a third nucleotide analog comprises a guanine nucleotide, and a fourth nucleotide analog comprises a thymine or a uracil nucleotide.

11. The kit according to claim 10, wherein the first nucleotide analog comprises a first electrochemically detectable moiety or a first fluorescently detectable moiety, the second nucleotide analog comprises a second electrochemically detectable moiety or a second fluorescently detectable moiety, the third nucleotide analog comprises a third electrochemically detectable moiety or a third fluorescently detectable moiety, and the fourth nucleotide analog comprises a fourth electrochemically detectable moiety or a fourth fluorescently detectable moiety.

12. The kit according to claim 10 further comprising a polymerase.

5. A method for sequencing a nucleic acid, the method comprising:

1) hybridizing a primer to a nucleic acid to form a hybridized primer/nucleic acid complex;

2) providing a plurality of nucleotide analogs, each nucleotide analog comprising a nucleotide and a photocleavable terminating moiety attached to the nucleotide, wherein said photocleavable terminating moiety is electrochemically detectable by accepting or donating at least one electron during an electrochemical reaction;

3) reacting the hybridized primer/nucleic acid complex and the nucleotide analog with a polymerase to add the nucleotide analog to the primer by a polymerase reaction to form an extended product comprising an incorporated nucleotide analog;

4) querying the extended product to identify the incorporated nucleotide analog;

5) exposing the extended product to a light source providing a first wavelength of light to remove an electrochemically detectable, photocleavable terminating moiety from the incorporated nucleotide analog; and

wherein each nucleotide analog further comprises a second photocleavable terminating moiety attached to the nucleotide and the method further comprises exposing the extended product to a light source providing a second wavelength of light to remove a second photocleavable terminating moiety from the incorporated nucleotide analog.

6. The method of claim 5 further comprising repeating the reacting, querying, and exposing steps one or more additional cycles to identify a plurality of bases in the nucleic acid, wherein the reacting step of cycle n+1 comprises reacting the extended product of cycle n and a nucleotide analog with the polymerase to add the nucleotide analog to the extended product of cycle n by a polymerase reaction to form an extended product of cycle n+1 comprising an incorporated nucleotide analog.

7. The method of claim 5 further providing a substrate comprising a zero mode waveguide and locating the polymerase within an observation volume of the zero mode waveguide.

8. The method of claim 5 wherein the querying is performed with an electrical detection element or a fluorescence detection element.

9. The method of claim 5 wherein the electrochemically detectable, photocleavable terminating moiety is a group imparting polymerase termination properties to the nucleotide analog and the method further comprises inhibiting a reacting step when an incorporated nucleotide comprises a photocleavable terminating moiety.