Systems and methods for manipulating a molecule in a nanopore

• US 20110192723A1
• Filed: 02/08/2010
• Published: 08/11/2011
• Est. Priority Date: 02/08/2010
• Status: Abandoned Application

• Current Assignee: Genia Technologies, Inc. (Roche Holding AG)
• Original Assignee: Genia Technologies, Inc. (Roche Holding AG)
• Inventors: Chen, Roger, Davis, Randy
• Application Number:
  US12/658,601
• Publication Number:
  US 20110192723A1
• Time in Patent Office: Days
• US Class Current: 204/451
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2527/15 Gradients
• CPC Class Codes: C12Q 2563/116 electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: G01N 27/447 using electrophoresis
• 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

Techniques for manipulating a molecule in a nanopore embedded in a lipid bilayer are described. In one example, an acquiring electrical stimulus level is applied across a lipid bilayer wherein a region of the lipid bilayer containing the nanopore is characterized by a resistance and wherein the acquiring electrical stimulus level tends to draw the molecule from a surrounding fluid into the nanopore, a change in the resistance of the lipid bilayer resulting from the acquisition of at least a portion of a molecule into the nanopore is detected, the acquiring electrical stimulus level is changed to a holding electrical stimulus level wherein the portion of the molecule remains in the nanopore upon the changing of the acquiring electrical stimulus level to the holding electrical stimulus level.

Claims

1. A method of manipulating a molecule in a nanopore embedded in a lipid bilayer, including:

applying an acquiring electrical stimulus level across a lipid bilayer wherein a region of the lipid bilayer containing the nanopore is characterized by a resistance and wherein the acquiring electrical stimulus level tends to draw the molecule from a surrounding fluid into the nanopore;

detecting a change in the resistance of the lipid bilayer resulting from the acquisition of at least a portion of a molecule into the nanopore;

changing the acquiring electrical stimulus level to a holding electrical stimulus level wherein the portion of the molecule remains in the nanopore upon the changing of the acquiring electrical stimulus level to the holding electrical stimulus level.

2. The method of claim 1, wherein the nanopore is an alpha-hemolysin nanopore.

3. The method of claim 1, wherein the nanopore is an alpha-hemolysin nanopore embedded in a diphytanoylphosphatidylcholine (DPhPC) lipid bilayer.

4. The method of claim 1, wherein the acquiring electrical stimulus and the holding electrical stimulus each comprises an applied voltage (V) level.

5. The method of claim 1, wherein changing the acquiring electrical stimulus level to a holding electrical stimulus level comprises reducing the acquiring electrical stimulus level to the holding electrical stimulus level.

6. The method of claim 5, wherein reducing the acquiring electrical stimulus level to the holding electrical stimulus level comprises reducing the acquiring electrical stimulus level within 10 ms after detecting the change in resistance of the bilayer resulting from the acquisition of at least a portion of the molecule into the nanopore.

7. The method of claim 1, wherein the molecule comprises a charged or polar polymer.

8. The method of claim 1, wherein the molecule comprises a nucleic acid molecule.

9. The method of claim 1, wherein the molecule comprises a deoxyribonucleic acid (DNA) molecule.

10. The method of claim 1, wherein the molecule comprises a double-stranded deoxyribonucleic acid (dsDNA) molecule.

11. The method of claim 1, wherein the acquiring electrical stimulus level ranges from 100 to 400 mV.

12. The method of claim 1, wherein the holding electrical stimulus level ranges from 50 to 150 mV.

13. The method of claim 1, further including applying a variable progression electrical stimulus to move the molecule through the nanopore.

14. The method of claim 13, wherein the progression voltage level ranges from 100 mV to 200 mV.

15. The method of claim 13, wherein the variable progression electrical stimulus applied to move the molecule through the nanopore discriminates the structural components of the molecule.

16. The method of claim 13, wherein the molecule is a nucleic acid molecule and the progression electrical stimulus is applied to discriminate nucleotide bases of the nucleic acid molecule.

17. The method of claim 13, wherein the variable progression electrical stimulus includes a series of successively more intense electrical pulses.

18. The method of claim 13, wherein the progression electrical stimulus pattern includes an asymmetric reverse “

V”

time profile.

19. The method of claim 13, wherein the molecule is a double stranded DNA, the progression electrical stimulus unzips the double stranded DNA and pulls a single strand of the DNA through the nanopore.

20. The method of claim 13, further including applying a reverse progression electrical stimulus to the region of lipid bilayer containing nanopore to allow the molecule to reverse progress through the nanopore.

21. The method of claim 20, wherein the reverse progression electrical stimulus has the same polarity as the acquiring electrical stimulus, and wherein the magnitude of the reverse progression electrical stimulus is smaller than the magnitude of the acquiring electrical stimulus but larger than the magnitude of the holding electrical stimulus.

22. The method of claim 20, where the reverse progression electrical stimulus has the opposite polarity as the acquiring electrical stimulus.

23. The method of claim 20, wherein the molecule is a double stranded DNA molecule, the progression electrical stimulus unzips the double stranded DNA and pulls a single strand of the DNA through the nanopore, and the single strand DNA re-anneals to a double strand as the DNA reverse progresses through the nanopore.

24. The method of claim 20, wherein an electrical signature of the molecule is recorded during the reverse progression of the molecule.

25. A system for manipulating a molecule in a nanopore embedded in a lipid bilayer, including:

a variable voltage source configured to apply an acquiring electrical stimulus level across a lipid bilayer wherein a region of the lipid bilayer containing the nanopore is characterized by a resistance and wherein the acquiring electrical stimulus level tends to draw the molecule from a surrounding fluid into the nanopore;

a sensing circuit configured to detect a change in the resistance of the lipid bilayer resulting from the acquisition of at least a portion of a molecule into the nanopore;

wherein the variable voltage source is further configured to change the acquiring electrical stimulus level to a holding electrical stimulus level upon the changing of the acquiring electrical stimulus level to the holding electrical stimulus level wherein the portion of the molecule remains in the nanopore.

26. The system of claim 25, wherein the nanopore is an alpha-hemolysin nanopore.

27. The system of claim 25, wherein the nanopore is an alpha-hemolysin nanopore embedded in a diphytanoylphosphatidylcholine (DPhPC) lipid bilayer.

28. The system of claim 25, wherein the acquiring electrical stimulus and the holding electrical stimulus each comprises an applied voltage (V) level.

29. The system of claim 25, wherein changing the acquiring electrical stimulus level to a holding electrical stimulus level comprises reducing the acquiring electrical stimulus level to the holding electrical stimulus level.

30. The system of claim 29, wherein reducing the acquiring electrical stimulus level to the holding electrical stimulus level comprises reducing the acquiring electrical stimulus level within 10 ms after detecting the change in resistance of the bilayer resulting from the acquisition of at least a portion of the molecule into the nanopore.

31. The system of claim 25, wherein the molecule comprises a charged or polar polymer.

32. The system of claim 25, wherein the molecule comprises a nucleic acid molecule.

33. The system of claim 25, wherein the molecule comprises a deoxyribonucleic acid (DNA) molecule.

34. The system of claim 25, wherein the molecule comprises a double-stranded deoxyribonucleic acid (dsDNA) molecule.

35. The system of claim 25, wherein the acquiring electrical stimulus level ranges from 100 to 400 mV.

36. The system of claim 25, wherein the holding electrical stimulus level ranges from 50 to 150 mV.

37. The system of claim 25, further including applying a variable progression electrical stimulus to move the molecule through the nanopore.

38. The system of claim 37, wherein the progression voltage level ranges from 100 to 200 mV.

39. The system of claim 37, wherein the variable progression electrical stimulus applied to move the molecule through the nanopore discriminates the structural components of the molecule.

40. The system of claim 37, wherein the molecule is a nucleic acid molecule and the progression electrical stimulus is applied to discriminate nucleotide bases of the nucleic acid molecule.

41. The system of claim 37, wherein the variable progression electrical stimulus includes a series of successively more intense electrical pulses.

42. The system of claim 37, wherein the progression electrical stimulus pattern includes an asymmetric reverse “

V”

time profile.

43. The system of claim 37, wherein the molecule is a double stranded DNA, the progression electrical stimulus unzips the double stranded DNA and pulls a single strand of the DNA through the nanopore.

44. The system of claim 37, further including applying a reverse progression electrical stimulus to the region of lipid bilayer containing nanopore to allow the molecule to reverse progress through the nanopore.

45. The system of claim 44, wherein the reverse progression electrical stimulus has the same polarity as the acquiring electrical stimulus, and wherein the magnitude of the reverse progression electrical stimulus is smaller than the magnitude of the acquiring electrical stimulus but larger than the magnitude of the holding electrical stimulus.

46. The system of claim 44, where the reverse progression electrical stimulus has the opposite polarity as the acquiring electrical stimulus.

47. The system of claim 44, wherein the molecule is a double stranded DNA molecule, the progression electrical stimulus unzips the double stranded DNA and pulls a single strand of the DNA through the nanopore, the single strand DNA re-anneal to a double strand as the DNA reverse progresses through the nanopore.

48. The system of claim 44, wherein an electrical signature of the molecule is recorded during the reverse progression of the molecule.

49. A system for manipulating a molecule in a nanopore embedded in a lipid bilayer, to including:

means for applying an acquiring electrical stimulus level across a lipid bilayer wherein a region of the lipid bilayer containing the nanopore is characterized by a resistance and wherein the acquiring electrical stimulus level tends to draw molecule from a surrounding fluid into the nanopore;

means for detecting a change in the resistance of the lipid bilayer resulting from the acquisition of at least a portion of a molecule into the nanopore;

means for changing the acquiring electrical stimulus level to a holding electrical stimulus level wherein the portion of the molecule remains in the nanopore upon the changing of the acquiring electrical stimulus level to the holding electrical stimulus level.

50. The system of claim 49, wherein the nanopore is an alpha-hemolysin nanopore.

51. The system of claim 49, wherein the nanopore is an alpha-hemolysin nanopore embedded in a diphytanoylphosphatidylcholine (DPhPC) lipid bilayer.

52. The system of claim 49, wherein the acquiring electrical stimulus and the holding electrical stimulus each comprises an applied voltage (V) level.

53. The system of claim 49, wherein changing the acquiring electrical stimulus level to a holding electrical stimulus level comprises reducing the acquiring electrical stimulus level to the holding electrical stimulus level.

54. The system of claim 53, wherein reducing the acquiring electrical stimulus level to the holding electrical stimulus level comprises reducing the acquiring electrical stimulus level within 10 ms after detecting the change in resistance of the bilayer resulting from the acquisition of at least a portion of the molecule into the nanopore.

55. The system of claim 49, wherein the molecule is a charged or polar polymer.

56. The system of claim 49, wherein the molecule is a nucleic acid molecule.

57. The system of claim 49, wherein the molecule is a deoxyribonucleic acid (DNA) molecule.

58. The system of claim 49, wherein the molecule is a double-stranded deoxyribonucleic acid (dsDNA) molecule.

59. The system of claim 49, wherein the acquiring electrical stimulus level ranges from 100 to 400 mV.

60. The system of claim 49, wherein the holding electrical stimulus level ranges from 50 to 150 mV.

61. The system of claim 49, further including means for applying a variable progression electrical stimulus to move the molecule through the nanopore.

62. The system of claim 61, wherein the progression voltage level ranges from 100 mV to 200 mV.

63. The system of claim 61, wherein the variable progression electrical stimulus applied to move the molecule through the nanopore discriminates the structural components of the molecule.

64. The system of claim 61, wherein the molecule is a nucleic acid molecule and the progression electrical stimulus is applied to discriminate nucleotide bases of the nucleic acid molecule.

65. The system of claim 61, wherein the variable progression electrical stimulus includes a series of successively more intense electrical pulses.

66. The system of claim 61, wherein the progression electrical stimulus pattern includes an asymmetric reverse “

V”

time profile.

67. The system of claim 61, wherein the molecule is a double stranded DNA, the progression electrical stimulus unzips the double stranded DNA and pulls a single strand of the DNA through the nanopore.

68. The system of claim 61, further including means for applying a reverse progression electrical stimulus to the region of lipid bilayer containing nanopore to allow the molecule to reverse progress through the nanopore.

69. The system of claim 68, wherein the reverse progression electrical stimulus has the same polarity as the acquiring electrical stimulus, and wherein the magnitude of the reverse progression electrical stimulus is smaller than the magnitude of the acquiring electrical stimulus but larger than the magnitude of the holding electrical stimulus.

70. The system of claim 68, wherein the reverse progression electrical stimulus has the opposite polarity as the acquiring electrical stimulus.

71. The system of claim 68, wherein the molecule is a double stranded DNA molecule, the progression electrical stimulus unzips the double stranded DNA and pulls a single strand of the DNA through the nanopore, the single strand DNA re-anneal to a double strand as the DNA reverse progresses through the nanopore.

72. The system of claim 68, wherein an electrical signature of the molecule is recorded during the reverse progression of the molecule.