Non-faradaic, capacitively coupled measurement in a nanopore cell array

• US 9,551,697 B2
• Filed: 10/17/2013
• Issued: 01/24/2017
• Est. Priority Date: 10/17/2013
• Status: Active Grant

• Current Assignee: Genia Technologies, Inc. (Roche Holding AG)
• Original Assignee: Genia Technologies, Inc. (Roche Holding AG)
• Inventors: Chen, Roger J. A.
• Primary Examiner(s): DINH, BACH T
• Application Number:
  US14/056,795
• Publication Number:
  US 20150107996A1
• Time in Patent Office: 1,195 Days
• Field of Search: 435/6.11, 435/6.12
• US Class Current: 1/1
• CPC Class Codes: G01N 27/3278 involving nanosized elements, e.g. nanogaps or nanoparticles nanopores G01N33/48721; magnetic beads G01N27/745
• CPC Class Codes: G01N 27/4473 by electric means
• CPC Class Codes: G01N 27/44743 Introducing samples
• CPC Class Codes: G01N 27/44791 Microapparatus sample containers with integrated microfluidic structures B01L3/5027
• CPC Class Codes: G01N 33/48721 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

Abstract

A method of identifying a molecule is disclosed. A molecule is drawn to a nanopore by applying a first voltage signal to a pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore. The molecule is released from the nanopore by applying a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore. The first period and the second period are determined based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current.

Claims

1. A method of identifying a molecule, comprising:

drawing a molecule to a nanopore by applying a first voltage signal to a pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore, wherein one of the electrodes comprises a property that facilitates non-faradaic conduction, and wherein the one of the electrodes comprises a spongy structure, wherein the spongy structure is formed by electroplating platinum onto a platinum electrode in the presence of a detergent;

releasing the molecule from the nanopore by applying a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determining the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current.

2. The method of claim 1, wherein determining the first period and the second period based at least in part on the net ionic current comprises determining the first period and the second period that reduce the net ionic current.

3. The method of claim 2, wherein determining the first period and the second period that reduce the net ionic current comprises setting the second voltage signal to off.

4. The method of claim 2, wherein determining the first period and the second period that reduce the net ionic current comprises setting the second voltage signal to a signal with a polarity opposite from the first voltage signal.

5. The method of claim 4, wherein the first voltage signal during the first period and the second voltage signal during the second period comprise an AC signal.

6. The method of claim 5, further comprising setting a duty cycle of the AC signal at least in part based on a rectifying characteristic corresponding to the nanopore.

7. The method of claim 5, further comprising setting a duty cycle of the AC signal based at least in part on a sum of charges corresponding to the first ionic current and the charges corresponding to the second ionic current over a combined time period comprising the first period and the second period.

8. The method of claim 5, further comprising setting a duty cycle of the AC signal based at least in part on a magnitude of voltage sufficient to draw the molecule to the nanopore.

9. The method of claim 1, wherein the one of the electrodes comprises a noble metal.

10. The method of claim 1, wherein the one of the electrodes comprises a structure that increases a surface area of the one of the electrodes.

11. The method of claim 1, wherein the one of the electrodes comprises a structure that increases a double layer capacitance.

12. The method of claim 1, wherein the first period and the second period are determined based at least in part on how fast the property of the portion of the molecule changes over time.

13. A system for identifying a molecule, comprising:

a voltage control unit controlling a voltage source;

a pair of electrodes coupled to the voltage source, wherein one of the electrodes comprises a property that facilitates non-faradaic conduction, and wherein the one of the electrodes comprises a spongy structure, wherein the spongy structure is formed by electroplating platinum onto a platinum electrode in the presence of a detergent; and

a measurement circuitry;

wherein the voltage control unit is configured to;

draw a molecule to a nanopore by controlling the voltage source to apply a first voltage signal to the pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

release the molecule from the nanopore by controlling the voltage source to apply a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determine the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current;

and wherein the measurement circuitry is configured to measure the first ionic current.

14. The system of claim 13, wherein determining the first period and the second period based at least in part on the net ionic current comprises determining the first period and the second period that reduce the net ionic current.

15. The system of claim 14, wherein determining the first period and the second period that reduce the net ionic current comprises setting the second voltage signal to off.

16. The system of claim 14, wherein determining the first period and the second period that reduce the net ionic current comprises setting the second voltage signal to a signal with a polarity opposite from the first voltage signal.

17. The system of claim 16, wherein the first voltage signal during the first period and the second voltage signal during the second period comprise an AC signal.

18. The system of claim 17, wherein the voltage control unit is further configured to set a duty cycle of the AC signal at least in part based on a rectifying characteristic corresponding to the nanopore.

19. The system of claim 17, wherein the voltage control unit is further configured to set a duty cycle of the AC signal based at least in part on a sum of charges corresponding to the first ionic current and the charges corresponding to the second ionic current over a combined time period comprising the first period and the second period.

20. The system of claim 17, wherein the voltage control unit is further configured to set a duty cycle of the AC signal based at least in part on a magnitude of voltage sufficient to draw the molecule to the nanopore.

21. The system of claim 13, wherein the one of the electrodes comprises a noble metal.

22. The system of claim 13, wherein the one of the electrodes comprises a structure that increases a surface area of the one of the electrodes.

23. The system of claim 13, wherein the one of the electrodes comprises a structure that increases a double layer capacitance.

24. The system of claim 13, wherein the first period and the second period are determined based at least in part on how fast the property of the portion of the molecule changes over time.

25. The system of claim 13, wherein the molecule comprises a tagged nucleotide associated with a polymerase, and wherein the first period and the second period are determined based at least in part on a time period during which the tagged nucleotide is associated with a polymerase.

26. A method of identifying a molecule, comprising:

drawing a molecule to a nanopore by applying a first voltage signal to a pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

releasing the molecule from the nanopore by applying a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determining the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, further comprising determining the first period and the second period that reduce the net ionic current, further comprising setting the second voltage signal to a signal with a polarity opposite from the first voltage signal, wherein the first voltage signal and the second voltage signal comprise an AC signal, further comprising setting a duty cycle of the AC signal based at least in part on a sum of charges corresponding to the first ionic current and the charges corresponding to the second ionic current over a combined time period comprising the first period and the second period.

27. The method of claim 26, wherein determining the first period and the second period that reduce the net ionic current comprises setting the second voltage signal to off.

28. The method of claim 26, further comprising setting a duty cycle of the AC signal at least in part based on a rectifying characteristic corresponding to the nanopore.

29. The method of claim 26, further comprising setting a duty cycle of the AC signal based at least in part on a magnitude of voltage sufficient to draw the molecule to the nanopore.

30. The method of claim 26, wherein one of the electrodes comprises a noble metal.

31. The method of claim 26, wherein one of the electrodes comprises a structure that increases a surface area of the one of the electrodes.

32. The method of claim 26, wherein one of the electrodes comprises a structure that increases a double layer capacitance.

33. The method of claim 26, wherein the first period and the second period are determined based at least in part on how fast the property of the portion of the molecule changes over time.

34. The method of claim 26, wherein one of the electrodes comprises a property that facilitates non-faradaic conduction, and wherein the one of the electrodes comprises a spongy structure.

35. A system for identifying a molecule, comprising:

a voltage control unit controlling a voltage source;

a pair of electrodes coupled to the voltage source; and

a measurement circuitry;

wherein the voltage control unit is configured to;

draw a molecule to a nanopore by controlling the voltage source to apply a first voltage signal to the pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

release the molecule from the nanopore by controlling the voltage source to apply a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determine the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, wherein determining the first period and the second period further comprising determining the first period and the second period that reduce the net ionic current, further comprising setting the second voltage signal to a signal with a polarity opposite from the first voltage signal, wherein the first voltage signal and the second voltage signal comprise an AC signal, further comprising setting a duty cycle of the AC signal based at least in part on a sum of charges corresponding to the first ionic current and the charges corresponding to the second ionic current over a combined time period comprising the first period and the second period;

and wherein the measurement circuitry is configured to measure the first ionic current.

36. The system of claim 35, wherein determining the first period and the second period that reduce the net ionic current comprises setting the second voltage signal to off.

37. The system of claim 35, wherein the voltage control unit is configured to set a duty cycle of the AC signal at least in part based on a rectifying characteristic corresponding to the nanopore.

38. The system of claim 35, wherein the voltage control unit is configured to set a duty cycle of the AC signal based at least in part on a magnitude of voltage sufficient to draw the molecule to the nanopore.

39. The system of claim 35, wherein one of the electrodes comprises a noble metal.

40. The system of claim 35, wherein one of the electrodes comprises a structure that increases a surface area of the one of the electrodes.

41. The system of claim 35, wherein one of the electrodes comprises a structure that increases a double layer capacitance.

42. The system of claim 35, wherein the first period and the second period are determined based at least in part on how fast the property of the portion of the molecule changes over time.

43. The system of claim 35, wherein one of the electrodes comprises a property that facilitates non-faradaic conduction, and wherein the one of the electrodes comprises a spongy structure.

44. A method of identifying a molecule, comprising:

drawing a molecule to a nanopore by applying a first voltage signal to a pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

releasing the molecule from the nanopore by applying a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determining the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, further comprising determining the first period and the second period that reduce the net ionic current, further comprising setting the second voltage signal to a signal with a polarity opposite from the first voltage signal, wherein the first voltage signal and the second voltage signal comprise an AC signal, further comprising setting a duty cycle of the AC signal at least in part based on a rectifying characteristic corresponding to the nanopore.

45. A system for identifying a molecule, comprising:

a voltage control unit controlling a voltage source;

a pair of electrodes coupled to the voltage source; and

a measurement circuitry;

wherein the voltage control unit is configured to;

draw a molecule to a nanopore by controlling the voltage source to apply a first voltage signal to the pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

release the molecule from the nanopore by controlling the voltage source to apply a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determine the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, wherein determining the first period and the second period further comprising determining the first period and the second period that reduce the net ionic current, further comprising setting the second voltage signal to a signal with a polarity opposite from the first voltage signal, wherein the first voltage signal and the second voltage signal comprise an AC signal, further comprising setting a duty cycle of the AC signal at least in part based on a rectifying characteristic corresponding to the nanopore;

and wherein the measurement circuitry is configured to measure the first ionic current.

46. A method of identifying a molecule, comprising:

drawing a molecule to a nanopore by applying a first voltage signal to a pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

releasing the molecule from the nanopore by applying a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determining the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, further comprising determining the first period and the second period that reduce the net ionic current, further comprising setting the second voltage signal to a signal with a polarity opposite from the first voltage signal, wherein the first voltage signal and the second voltage signal comprise an AC signal, further comprising setting a duty cycle of the AC signal based at least in part on a magnitude of voltage sufficient to draw the molecule to the nanopore.

47. A system for identifying a molecule, comprising:

a voltage control unit controlling a voltage source;

a pair of electrodes coupled to the voltage source; and

a measurement circuitry;

wherein the voltage control unit is configured to;

draw a molecule to a nanopore by controlling the voltage source to apply a first voltage signal to the pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

release the molecule from the nanopore by controlling the voltage source to apply a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determine the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, wherein determining the first period and the second period further comprising determining the first period and the second period that reduce the net ionic current, further comprising setting the second voltage signal to a signal with a polarity opposite from the first voltage signal, wherein the first voltage signal and the second voltage signal comprise an AC signal, further comprising setting a duty cycle of the AC signal based at least in part on a magnitude of voltage sufficient to draw the molecule to the nanopore;

and wherein the measurement circuitry is configured to measure the first ionic current.

48. A method of identifying a molecule, comprising:

drawing a molecule to a nanopore by applying a first voltage signal to a pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

releasing the molecule from the nanopore by applying a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determining the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, wherein the first period and the second period are determined based at least in part on how fast the property of the portion of the molecule changes over time.

49. A system for identifying a molecule, comprising:

a voltage control unit controlling a voltage source;

a pair of electrodes coupled to the voltage source; and

a measurement circuitry;

wherein the voltage control unit is configured to;

draw a molecule to a nanopore by controlling the voltage source to apply a first voltage signal to the pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

release the molecule from the nanopore by controlling the voltage source to apply a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determine the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, wherein the first period and the second period are determined based at least in part on how fast the property of the portion of the molecule changes over time;

and wherein the measurement circuitry is configured to measure the first ionic current.

50. A method of identifying a molecule, comprising:

drawing a molecule to a nanopore by applying a first voltage signal to a pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

releasing the molecule from the nanopore by applying a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determining the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, wherein the molecule comprises a tagged nucleotide associated with a polymerase, and wherein the first period and the second period are determined based at least in part on a time period during which the tagged nucleotide is associated with a polymerase.

51. A system for identifying a molecule, comprising:

a voltage control unit controlling a voltage source;

a pair of electrodes coupled to the voltage source; and

a measurement circuitry;

wherein the voltage control unit is configured to;

draw a molecule to a nanopore by controlling the voltage source to apply a first voltage signal to the pair of electrodes during a first period, wherein the first voltage signal causes a first ionic current through the nanopore that is indicative of a property of a portion of the molecule proximate to the nanopore;

release the molecule from the nanopore by controlling the voltage source to apply a second voltage signal to the pair of electrodes during a second period, wherein the second voltage signal causes a second ionic current through the nanopore; and

determine the first period and the second period based at least in part on a net ionic current through the nanopore comprising the first ionic current and the second ionic current, wherein the molecule comprises a tagged nucleotide associated with a polymerase, and wherein the first period and the second period are determined based at least in part on a time period during which the tagged nucleotide is associated with a polymerase;

and wherein the measurement circuitry is configured to measure the first ionic current.