Freestanding Ultrathin Membranes and Transfer-Free Fabrication Thereof

• US 20160282326A1
• Filed: 11/25/2014
• Published: 09/29/2016
• Est. Priority Date: 11/25/2013
• Status: Abandoned Application

• Current Assignee: Northeastern University
• Original Assignee: Northeastern University
• Inventors: Waduge, Pradeep, Larkin, Joseph, Upmanyu, Moneesh, Wanunu, Meni, Kar, Swastik
• Application Number:
  US15/037,863
• Publication Number:
  US 20160282326A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: B82Y 40/00 Manufacture or treatment of nanostructures
• CPC Class Codes: C01B 32/186 by chemical vapour deposition [CVD]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C23C 16/0281 of metallic sub-layers C23C16/029 takes precedence
• CPC Class Codes: C23C 16/26 Deposition of carbon only
• CPC Class Codes: C23C 16/56 After-treatment
• CPC Class Codes: G01N 27/44704 Details; Accessories
• CPC Class Codes: G01N 27/4473 by electric means
• 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

Devices contain freestanding, ultra thin (<10 nm thick) membranes and methods of making such devices. Methods of using devices contain freestanding ultra thin membranes for determining the sequence of a polynucleotide and for desalination of aqueous solutions. A device containing: a substrate having an upper surface, a lower surface, and an aperture, the aperture having one or more walls connecting the upper and lower surfaces and forming a well; and a membrane attached to the lower surface of the substrate and forming a floor of the well, the membrane having a thickness of less than 10 nm. The electrical conductance across the membrane is less than 1 nS/?m2.

Claims

1. A membrane device comprising:

(a) a substrate having an upper surface, a lower surface, and an aperture, the aperture having one or more walls connecting the upper and lower surfaces and forming a well; and

(b) a membrane attached to the lower surface of the substrate and forming a floor of the well, the membrane having a thickness of less than 10 nm and an electrical conductance of less than 1 nS/μ

m².

3. The device of claim any one of claims 1 and 2, wherein the membrane consists essentially of a material selected from the group consisting of Bi₂Se₃, bismuth strontium calcium copper oxide, Bi₄Ti₃O₁₂, boron nitride, boron carbon nitride, (Ca,Sr)₂Nb₃O₁₀, Ca₂Ta₂TiO₁₀, carbon nitride, Cu oxide, Cu₂O, CuO, Cu₂O₃, Eu(OH)₂, fluorographene, GaSe, GaTe, graphene, graphene oxide, InSe, LaNb₂O₇, MnO, MoO₃, MoSe₂, MoS₂, MoTe, Ni(OH)₂, NiSe₂, NbSe₂, NbS₂, RuO₂, TaO₃, TaS₂, TiO, TiS₂, VO, WO₃, WSe₂, W5₂, WTe, ZrSe, and ZrS.

15. The device of any one of claims 1 and 4, wherein the substrate comprises a material selected from the group consisting of silicon nitride, silicon oxide, aluminum oxide, and hafnium oxide.

16. The device of any one of claims 1 and 4, wherein the substrate is about 100 nm thick.

18. The device of claim 44, wherein the passivating layer comprises HfO₂.

20. The device of any one of claims 1 and 4, wherein the well has a diameter of less than 1 μ

m.

38. The device of any one of claims 1, 2, and 4, further comprising a supporting structure attached to the upper surface of the substrate, the supporting structure comprising a window that provides access to the well.

39. The device of any one of claims 1, 2, and 4, further comprising

(a) an insulating layer attached to the upper surface of the substrate;

and

(b) a supporting structure attached to a portion of the insulating layer, the supporting structure and insulating layer comprising a window that provides access to the well.

40. The device of any one of claims 38 and 39, wherein the supporting structure comprises one or more materials selected from the group consisting of silicon, silicon dioxide, glass, quartz, and mica.

41. The device of claim 39, wherein the insulating layer comprises one or more materials selected from the group consisting of silicon, silicon dioxide, glass, quartz, and mica.

42. The device of any one of claims 38 to 41, wherein the supporting structure and insulating layer, if present, comprise a plurality of windows, each window providing access to at least one well.

43. The device of claim 42, wherein the supporting structure comprises one or more scored lines between two or more windows, the scored lines enabling the division of the device into two or more pieces, each piece comprising one or more windows.

44. The device of any one of claims 38 to 43, wherein the device has at least 100 windows.

49. A method of making the membrane device of any one of claims 1 and 2, the method comprising the steps of:

(a) providing a substrate having an upper surface, a lower surface, and an aperture, the aperture having one or more walls connecting the upper and lower surfaces and forming a well;

(b) depositing a passivating layer on the lower surface of the substrate;

(c) forming on the lower surface of the substrate a membrane that extends across the aperture, thereby forming a floor of the well.

50. A method of making the membrane device of any one of claims 1 and 2, the method comprising the steps of:

(a) providing a substrate having an upper surface, a lower surface, and an aperture, the aperture having one or more walls connecting the upper and lower surfaces and forming a well;

(b) depositing a passivating layer on the lower surface of the substrate;

(c) depositing a sacrificial layer having an upper surface and a lower surface on the passivating layer and across the aperture, thereby forming a floor of the well;

(d) forming on the upper surface of the sacrificial layer and/or the passivating layer a membrane that extends across the aperture; and

(e) removing the sacrificial layer, leaving the membrane as the floor of the well.

51. The method of any one of claims 49 and 50, wherein the substrate comprises a material selected from the group consisting of silicon nitride, silicon oxide, aluminum oxide, and hafnium oxide.

52. The method of any one of claims 49 and 50, wherein the passivating layer comprises a material selected from the group consisting of HfO₂, TiO₂, and Al₂O₃.

53. The method of claim 52, wherein the passivating layer comprises HfO₂.

54. The method of any one of claims 49 and 50, wherein the passivating layer is from about 5 nm to about 15 nm thick.

55. The method of claim 50, wherein the step (c) is performed by thermal evaporation.

56. The method of claim 50, wherein the sacrificial layer comprises a material selected from the group consisting of Cu, Fe, Ni, Pd, and Pt.

57. The method of claim 56, wherein the sacrificial layer comprises Cu.

58. The method of claim 50, wherein the sacrificial layer is less than 0.5 μ

m thick.

59. The method of claim 58, wherein the sacrificial layer is about 200 nm thick.

60. The method of any one of claims 49 and 50, wherein each membrane consists essentially of a material selected from the group consisting of Bi₂Se₃, bismuth strontium calcium copper oxide, Bi₄Ti₃O₁₂, boron nitride, boron carbon nitride, (Ca,Sr)₂Nb₃O₁₀, Ca₂Ta₂TiO₁₀, carbon nitride, Cu oxide, Cu₂O, CuO, Cu₂O₃, Eu(OH)₂, fluorographene, GaSe, GaTe, graphene, graphene oxide, InSe, LaNb₂O₇, MnO, MoO₃, MoSe₂, MoS₂, MoTe, Ni(OH)₂, NiSe₂, NbSe₂, NbS₂, RuO₂, TaO₃, TaS₂, TiO, TiS₂, VO, WO₃, WSe₂, WS₂, WTe, ZrSe, and ZrS.

61. The method of claim 60, wherein the membrane consists of graphene.

62. The method of claim 61, wherein the graphene membrane is formed by carbon vapor deposition using methane and hydrogen gases.

63. The method of claim 57, wherein the sacrificial layer is removed by dissolving the Cu in ammonium persulfate.

64. The method of any one of claims 49 and 50, wherein the method comprises making a plurality of membrane devices.

65. The method of claim 64, wherein at least 80% of the graphene membranes produced by the method are intact.

66. The method of claim 64, wherein at least 80% of the graphene membranes produced by the method have a conductance of less than 1 nS/μ

m²

67. The method of any one of claims 49 and 50, further comprising the step of creating one or more nanopores in the membrane.

68. The method of claim 67, wherein the nanopores are created using an electron beam.

2. A membrane device comprising:

(a) a substrate having an upper surface, a lower surface, and an aperture, the aperture having one or more walls connecting the upper and lower surfaces and forming a well;

(b) a passivating layer coating the lower surface of the substrate; and

(c) a membrane attached to the passivating layer and forming a floor of the well, the membrane having a thickness of less than 10 nm and an electrical conductance of less than 1 nS/μ

m².

17. The device of any one of claims 2 and 4, wherein the passivating layer comprises material selected from the group consisting of HfO₂ and TiO₂.

19. The device of any one of claims 2 and 4, wherein the layer of passivating layer is about 10 nm thick.

4. A nanopore membrane device comprising:

(a) a substrate having an upper surface, a lower surface coated with a passivating layer, and an aperture, the aperture having one or more walls connecting the upper and lower surfaces and forming a well; and

(b) a membrane attached to the passivating layer and forming a floor of the well, the membrane having a thickness of less than 10 nm and comprising a nanopore, wherein the background conductance of the membrane is less than less than 1 nS/μ

m².

5. The device of claim 4, wherein the membrane is less than about 5 nm thick.

6. The device of claim 4, wherein the membrane is less than about 1 nm thick.

7. The device of claim 4, wherein the membrane comprises a plurality of nanopores.

8. The device of claim 7, wherein each nanopore has a diameter of about equal length.

9. The device of any one of claims 4 and 8, wherein each nanopore has diameter of about 0.6 nm.

10. The device of any one of claims 4 and 8, wherein each nanopore has diameter of about 0.9 nm.

11. The device of any one of claims 4 and 8, wherein each nanopore has diameter of about 1.5 nm.

12. The device of any one of claims 4 and 8, wherein each nanopore has diameter of about 2.5 nm.

13. The device of any one of claims 4 and 8, wherein each nanopore has diameter of about 7.5 nm.

14. The device of any one of claims 4 and 8, wherein each nanopore has diameter of about 20 nm.

21. The device of claim any one of claims 4 and 7, wherein the membrane consists essentially of a material selected from the group consisting of Bi₂Se₃, bismuth strontium calcium copper oxide, Bi₄Ti₃O₁₂, boron nitride, boron carbon nitride, (Ca,Sr)₂Nb₃O₁₀, Ca₂Ta₂TiO₁₀, carbon nitride, Cu oxide, Cu₂O, CuO, Cu₂O₃, Eu(OH)₂, fluorographene, GaSe, GaTe, graphene, graphene oxide, InSe, LaNb₂O₇, MnO, MoO₃, MoSe₂, MoS₂, MoTe, Ni(OH)₂, NiSe₂, NbSe₂, NbS₂, RuO₂, TaO₃, TaS₂, TiO, TiS₂, VO, W0₃, WSe₂, WS₂, WTe, ZrSe, and ZrS.

22. The device of claim 21, wherein the membrane consists essentially of graphene.

23. The device of claim 22, wherein the graphene membrane is less than five atomic layers thick.

24. The device of claim 22, wherein the graphene at each nanopore has been chemically stabilized to minimize reactivity of the graphene with molecules, ions, and solutes that pass through the nanopore.

25. The device of claim 24, wherein the graphene has been stabilized by hydrogenation, hydroxylation, or treatment with a functionalized peptide or surfactant.

26. The device of claim 22, further comprising a plurality of amphiphilic molecules non-covalently bound to a surface of the graphene membrane internal to the well and a surface of each membrane external to the well.

27. The device of claim 26, wherein the amphiphilic molecules comprise a hydrophobic portion comprising pyrene.

28. The device of claim 26, wherein the amphiphilic molecule comprises a hydrophilic portion comprising ethylene glycol.

29. The device of claim 22, further comprising a hydrophilic layer attached to the surface of the graphene membrane external to the well and to the lower surface of the substrate.

30. The device of claim 29, wherein the hydrophilic layer comprises a material selected from the group consisting of Al₂O₃, TiO₂, SiO₂, HfO₂.

31. The device of claim 29, wherein the hydrophilic layer is less than about 10 nm thick.

32. The device of claim 29, further comprising a nanopore in the hydrophilic layer which is aligned with the nanopore in the graphene membrane.

33. The device of claim 32, further comprising a lipid bilayer non-covalently bound to the hydrophilic layer, the lipid bilayer covering the nanopore.

34. The device of claim 33, further comprising a biological nanopore situated in a region of the lipid bilayer covering the nanopore.

35. The device of claim 22, further comprising a first lipid monolayer non-covalently bound to a surface of the graphene membrane internal to the well and a second lipid monolayer non-covalently bound to a surface of the graphene membrane external to the well, the first and second lipid monolayers covering each nanopore, thereby forming a lipid bilayer spanning each nanopore.

36. The device of claim 35, further comprising a biological nanopore disposed in said lipid bilayer.

37. The device of any of claims 34 and 36, wherein the biological nanopore is selected from the group consisting of alpha-hemolysin, MspA porin, and ClyA porin.

45. An apparatus for sequencing of a polynucleotide, the apparatus comprising:

(a) the device of claim 4, wherein the membrane is disposed between a first fluid reservoir and a second fluid reservoir;

(b) an electrode pair comprising a first electrode disposed in the first fluid reservoir and a second electrode disposed in the second fluid reservoir; and

(c) a circuit capable of detecting an electrical signal that correlates with the sequence of the polynucleotide.

46. An apparatus for sequencing of a polynucleotide, the apparatus comprising:

(a) the device of any one of claims 22 and 24, wherein the graphene membrane is disposed between a first fluid reservoir and a second fluid reservoir;

(b) a first electrode pair comprising a first electrode disposed in the first fluid reservoir and a second electrode disposed in the second fluid reservoir, wherein the first electrode pair is capable of applying an electrical field between the fluid reservoirs and across the graphene membrane;

(c) a second electrode pair comprising first and second electrodes in contact with the graphene membrane on opposite sides of the nanopore, wherein the second electrode pair is capable of applying an electrical field laterally through the graphene membrane and across the nanopore of said device; and

(d) a circuit capable of detecting an electrical signal from the second electrode pair that correlates with the sequence of the polynucleotide.

47. The apparatus of any one of claims 45 and 46, further comprising a processor for processing signals from the electrodes.

48. The apparatus of claim 47, wherein the processor is capable of identifying a polynucleotide, a component of a polynucleotide, or a precursor of a polynucleotide from a signal provided by the electrical sensor.

69. A method of determining a sequence of bases of a polynucleotide, the method comprising the steps of:

(a) providing the apparatus of claim 45;

(b) adding an aqueous solution comprising the polynucleotide to the first reservoir and adding an aqueous solution to the second reservoir;

(c) applying an electrical field between the first and second electrodes, wherein the electrical field causes one or more charged molecules to transit through the nanopore;

(d) measuring a signal due to the transit of the one or more charged molecules through the nanopore; and

(e) determining the sequence of bases of the polynucleotide from a previously determined correlation between identities of the bases and the signal.

70. The method of claim 69, wherein the signal is a change in current through the nanopore.

71. The method of claim 69, wherein the signal is optical.

72. The method of claim 69, wherein the one or more charged molecules that transit through the nanopore are one or more copies of the polynucleotide.

73. The method of claim 72, wherein the polynucleotide is single-stranded.

74. The method of claim 72, wherein the polynucleotide is double-stranded.

75. The method of claim 72, wherein the polynucleotide comprises both single-stranded portions and double-stranded portions.

76. The method of claim 69, wherein at least four charged molecules transit through the nanopore, wherein the at least four charged molecules comprise four unique synthetic molecules corresponding to each of four naturally-occurring bases in a polynucleotide, wherein each synthetic molecule confers a change in current as it passes through the nanopore, the change in current due to each synthetic molecule being distinct from the change in current due to each of the other three synthetic molecules.

77. The method of claim 69, wherein the first electrode is an anode and the second electrode is a cathode.

78. The method of claim 69, wherein the first electrode acts is a cathode and the second electrode is an anode.

79. The method of claim 69, wherein the first electrode alternates between being an anode and a cathode and the second electrode alternates between being a cathode and an anode.

80. The method of claim 72, wherein the one or more copies of the polynucleotide transit through the nanopore in a direction determined by an electromotive force provided by the electrical field.

81. The method of claim 72, wherein the one or more copies of the polynucleotide transit through the nanopore against an electromotive force provided by the electrical field.

82. The method of claim 72, wherein the one or more copies of the polynucleotide transit through the nanopore alternately with and against an electromotive force provided by the electrical field.

83. The method of any one of claims 81 and 82, wherein a force driving transit of the one or more copies of the polynucleotide against the electromotive force is provided by a magnetic field.

84. The method of claim 83, wherein the polynucleotide is bound to a magnetic bead.

85. The method of any one of claims 81 and 82, wherein a physical force driving transit of the one or more copies of the polynucleotide against the electromotive force is provided by a polynucleotide polymerase.

86. The method of claim 69, wherein the apparatus comprises an enzyme in the first reservoir.

87. The method of claim 86, wherein the enzyme is selected from the group consisting of a DNA polymerase, RNA polymerase, DNA exonuclease, RNA exonuclease, DNA helicase, and RNA helicase.

88. The method of claim 87, wherein the enzyme is a DNA polymerase or RNA polymerase.

89. The method of any one claims 86 to 88, wherein the enzyme is bound to the membrane adjacent to the nanopore.

92. A method of determining a sequence of bases of a polynucleotide, the method comprising the steps of:

(a) providing the apparatus of claim 46;

(b) adding an aqueous solution comprising the polynucleotide to the first fluid reservoir and adding an aqueous solution to the second fluid reservoir;

(c) applying an electrical field between the first pair of electrodes, wherein the electrical field causes one or more charged molecules to transit through the nanopore;

(d) applying an electrical field between the second pair of electrodes;

(e) measuring a signal between the second pair of electrodes due to the transit of the one or more charged molecules through the nanopore; and

(f) determining the sequence of bases of the polynucleotide from a previously determined correlation between identities of the bases and the signal.

90. The method of 88, wherein the apparatus comprises a primer capable of hybridizing with the polynucleotide.

91. The method of claim 90, wherein the primer is bound to the membrane adjacent to the nanopore.