Compositions, systems, and methods for sequencing polynucleotides using tethers anchored to polymerases adjacent to nanopores

Patent metadata

Field	Value
Publication number	US-2024376535-A1
Application number	US-202418620915-A
Country	US
Kind code	A1
Filing date	Mar 28, 2024
Priority date	Jun 3, 2015
Publication date	Nov 14, 2024
Grant date	—

Abstract

A composition includes a nanopore including first and second sides and an aperture, nucleotides each including an elongated tag, and a first polynucleotide that is complementary to a second polynucleotide. A polymerase can be disposed adjacent to the first side of the nanopore and configured to add nucleotides to the first polynucleotide based on a sequence of the second polynucleotide. A permanent tether can include a head region anchored to the polymerase, a tail region, and an elongated body disposed therebetween that occurs in the aperture of the nanopore. A first moiety can be disposed on the elongated body that binds to the elongated tag of a first nucleotide upon which the polymerase is acting. A reporter region can be disposed on the elongated body that indicates when the first nucleotide is complementary or is not complementary to a next nucleotide in the sequence of the second polynucleotide.

First claim

What is claimed:

1 . A system including a composition and a measurement circuit, the composition including:
a nanopore including a first side, a second side, and an aperture extending through the first and second sides; a plurality of nucleotides, wherein each of the nucleotides comprises an elongated tag that corresponds to the type of nucleotide, the elongated tag being sufficiently long and narrow to be disposed within at least a portion of the aperture of the nanopore; first and second polynucleotides, the first polynucleotide being complementary to the second polynucleotide; a polymerase disposed adjacent to the first side of the nanopore, the polymerase configured to add nucleotides of the plurality of nucleotides to the first polynucleotide based on a sequence of the second polynucleotide; a permanent tether including a head region, a tail region, and an elongated body disposed therebetween, the head region being anchored to the polymerase, wherein the elongated body occurs in the aperture of the nanopore; a first moiety disposed on the elongated body, wherein the first moiety is configured to bind to the elongated tag of a first nucleotide upon which the polymerase is acting; and a reporter region disposed on the elongated body; wherein the reporter region is configured to indicate whether the first nucleotide is complementary or is not complementary to a next nucleotide in the sequence of the second polynucleotide; the measurement circuit being configured to measure a first signal state through the aperture generated responsive to the polymerase acting upon the first nucleotide and based upon the binding of the first moiety of the permanent tether with the elongated tag of the first nucleotide, the first nucleotide being identifiable based on the measured first signal state; and to measure a second signal state through the aperture it being determinable, based upon the second signal state, that the first nucleotide is complementary or is not complementary to the next nucleotide of the second polynucleotide.

2 . The system of claim 1 , wherein the polymerase acting upon the first nucleotide comprises the polymerase binding the first nucleotide.

3 . The system of claim 1 , wherein the first signal state comprises an electrical signal or an optical signal.

4 . The system of claim 2 , the reporter region being configured to generate the second signal state, the second signal state responsive to the polymerase successfully incorporating the first nucleotide into the first polynucleotide in response to the polymerase.

5 . The system of claim 4 , said reporter region being configured to generate the second signal state responsive to release of pyrophosphate responsive to the polymerase successfully incorporating the first nucleotide into the first polynucleotide.

6 . The system of claim 5 , the polymerase being modified so as to delay release of the pyrophosphate responsive to incorporation of the first nucleotide into the first polynucleotide.

7 . The system of claim 6 , wherein the polymerase comprises modified recombinant Phi29, B103,Ga-1, Pza, Phi15, BS32, M2y, Nf, G1, Cp-1, Prd 1, Pze, Sf5, Cp-5, Cp-7, Pr4, Pr5, Pr722, or L17polymerase.

8 . The system of claim 6 , wherein the polymerase comprises a modified recombinant Phi 29DNA polymerase having at least one amino acid substitution or substitution combination selected from the group consisting of an amino acid substitution at position 484, an amino acid substitution at position 198, and an amino acid substitution at position 381.

9 . The system of claim 6 , wherein the polymerase comprises a modified recombinant Phi 29DNA polymerase having at least one amino acid substitution or substitution combination selected from the group consisting of E375Y, K512Y, T368F, A484E, A484Y, N387L, T372Q, T372L, K478Y, 1370W, F198W, and L381A.

10 . The system of claim 2 , said reporter region being configured to produce said second signal state, said second signal state being responsive to a conformation change of said polymerase.

11 . The system of claim 10 , the amplitude and duration of the polymerase conformation change in response to the first nucleotide being complementary or not complementary to the next nucleotide of the second polynucleotide, the amplitude or duration of the second signal state or both being varied based on the conformation of the polymerase.

12 . The system of claim 1 , wherein the second signal state comprises an electrical signal.

13 . The system of claim 1 , wherein the second signal state comprises an optical signal.

14 . The system of claim 1 , wherein the elongated label comprises a first nucleotide sequence and the first portion comprises a second nucleotide sequence complementary to a first nucleotide sequence of the elongated label.

15 . The system of claim 1 , wherein the first signal state is based on the elongate label, the first nucleotide being identified based on the first signal state.

16 . The system of claim 1 , wherein the second signal state is based on a location of the reporter region within the aperture.

17 . The system of claim 13 , wherein the permanent tether further comprises a second portion, the first portion and the second portion of the tether being configured to hybridize to one another to form a hairpin structure.

18 . The system of claim 17 , further comprising a voltage source configured to apply a voltage between said first and second sides.

Assignees

• Illumina Inc

Inventors

• Gunderson Kevin L
• Mandell Jeffrey G

Classifications

• G01N33/48721

  Investigating individual macromolecules, e.g. by translocation through nanopores (Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68) · CPC title

• C12Q1/6839

  Triple helix formation or other higher order conformations in hybridisation assays · CPC title

• G01N33/49

  Blood {(chemical methods for determining blood cell populations G01N33/5094; chemical analysis of blood groups or blood types G01N33/80)} · CPC title

• C12Q2565/631

  being a biochannel or pore · CPC title

• C12Q2565/607

  being a sensor, e.g. electrode · CPC title