Compositions, systems, and methods for detecting events using tethers anchored to or adjacent to nanopores

• US 9,708,655 B2
• Filed: 06/02/2015
• Issued: 07/18/2017
• Est. Priority Date: 06/03/2014
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Mandell, Jeffrey G., Gunderson, Kevin L., Gundlach, Jens H.
• Primary Examiner(s): Forman, Betty
• Application Number:
  US14/728,721
• Publication Number:
  US 20150344945A1
• Time in Patent Office: 777 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: G01N 27/44743 Introducing samples
• CPC Class Codes: G01N 27/44791 Microapparatus sample containers with integrated microfluidic structures B01L3/5027

Abstract

Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed therebetween. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide. The second event can include adding a second nucleotide to the polynucleotide.

Claims

1. A method including:

providing a nanopore including a first side, a second side, and an aperture extending through the first and second sides;

providing a permanent tether including a head region, a tail region, and an elongated body disposed therebetween,

the head region being anchored to or adjacent to the first or second side of the nanopore,

the elongated body including a reporter region; and

moving the reporter within the aperture toward the first side of the nanopore responsive to a first event occurring adjacent to the first side of the nanopore, wherein the first event comprises addition of a first nucleotide to a polynucleotide;

moving the reporter toward the second side of the nanopore after the first event and before a second event; and

moving the reporter within the aperture responsive to the second event occurring adjacent to the first side of the nanopore, wherein the second event comprises addition of a second nucleotide to the polynucleotide.

2. The method of claim 1, wherein the head region is anchored to the first side of the nanopore.

3. The method of claim 1, wherein the reporter region is translationally moved toward the first side of the nanopore responsive to the first event.

4. The method of claim 3 further including translationally moving the reporter region toward the second side after the first event.

5. The method of claim 1, further including measuring a first current or flux through the aperture or a first optical signal while the reporter region is moved responsive to the first event.

6. The method of claim 1, wherein a protein is disposed adjacent to the first side of the nanopore, and wherein the first event includes a first conformational change of the protein.

7. The method of claim 6, wherein the head region is anchored to the protein.

8. The method of claim 7, wherein the first conformational change moves the head region, and the movement of the head region translationally moves the reporter region.

9. The method of claim 8, wherein the protein includes a polymerase.

10. The method of claim 9, wherein the first conformational change occurs responsive to the polymerase acting upon the first nucleotide.

11. The method of claim 10, wherein the first conformational change moves the head region, and the movement of the head region translationally moves the reporter region.

12. The method of claim 11, further including identifying the first nucleotide based on a measured magnitude or time duration, or both, of a change in a current or flux through the aperture or an optical signal responsive to the translational movement of the reporter region.

13. The method of claim 10, further including translationally moving the reporter region responsive to a second conformational change of the polymerase occurring responsive to the polymerase acting upon the second nucleotide.

14. The method of claim 13, further including identifying the first nucleotide based on a measured magnitude or time duration, or both, of a first change in a current or flux through the aperture or a first optical signal responsive to the translational movement of the reporter region responsive to the first conformational change, and

further including identifying the second nucleotide based on a measured magnitude or time duration, or both, of a second change in the current or flux through the aperture or a second optical signal responsive to the translational movement of the reporter region responsive to the second conformational change.

15. The method of claim 1, wherein a polymerase is disposed adjacent to the first side of the nanopore, wherein the first event includes the polymerase acting upon the first nucleotide.

16. The method of claim 15, wherein the first nucleotide includes an elongated tag including a moiety that interacts with the tether.

17. The method of claim 16, wherein the interaction of the moiety with the tether translationally moves the reporter region.

18. The method of claim 16, wherein the tether includes a first oligonucleotide.

19. The method of claim 18, wherein the moiety includes a second oligonucleotide that hybridizes to the first oligonucleotide.

20. The method of claim 19, wherein the hybridization of the second oligonucleotide to the first oligonucleotide shortens the tether by a first amount.

21. The method of claim 20, further including identifying the first nucleotide based on a measured magnitude or time duration, or both, of a change in a current or flux through the aperture or an optical signal responsive to the shortening of the tether by the first amount.

22. The method of claim 1, wherein polymerase is disposed on the first side, the head region being anchored to the polymerase, the method further including:

further contacting the polymerase with the first nucleotide and with first and second polynucleotides, the polymerase adding the first nucleotide to the first polynucleotide based on a sequence of the second polynucleotide,

the polymerase being modified so as to delay release of pyrophosphate responsive to addition of the first nucleotide to the first polynucleotide.

23. The method of claim 1, wherein a polymerase is disposed on the first side, the head region being anchored to the polymerase, the method further including:

further contacting the polymerase with the first nucleotide and with first and second polynucleotides, the polymerase adding the first nucleotide to the first polynucleotide based on a sequence of the second polynucleotide,

the first nucleotide being coupled to a reversible terminator, and

inhibiting, by the reversible terminator, the polymerase from adding the second nucleotide to the first polynucleotide.

24. The method of claim 23, the method further comprising cleaving the reversible terminator.

25. The method of claim 23, the method further comprising cleaving the reversible terminator by reaction with a chemical agent.

26. The method of claim 25, further comprising flowing fluid past the polymerase to remove the chemical agent.

27. The method of claim 26, further comprising supplying new reagents to the polymerase by fluid flow.

28. The method of claim 27, wherein the reversible terminator is disposed on the first side and wherein a source of the chemical agent is disposed on the second side, the method comprising moving the chemical agent from the second side to the first side through the aperture.