Use of longitudinally displaced nanoscale electrodes for voltage sensing of biomolecules and other analytes in fluidic channels

• US 8,882,980 B2
• Filed: 09/03/2009
• Issued: 11/11/2014
• Est. Priority Date: 09/03/2008
• Status: Active Grant

• Current Assignee: NABsys, Inc.
• Original Assignee: NABsys, Inc.
• Inventors: Ling, Xinsheng, Bready, Barrett, Oliver, John S., Jouzi, Maryam, Petrossian, Leo
• Primary Examiner(s): Van, Luan
• Assistant Examiner(s): ROSENWALD, STEVEN ERIC
• Application Number:
  US12/553,667
• Publication Number:
  US 20100096268A1
• Time in Patent Office: 1,895 Days
• Field of Search: 204/192.22, 204/433, 204/450, 205/549, 205/645, 422500-570
• US Class Current: 204/452
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• 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 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
• CPC Class Codes: Y10S 977/957 Of chemical property or presence

Abstract

Devices and methods for detecting an analyte are provided. Devices for voltage sensing of analytes may comprise a fluidic channel defined in a substrate, a pair of sensing electrodes disposed in a fluidic channel for sensing voltage therein, and a pair of electromotive electrodes for applying potential along the fluidic channel. The pair of sensing electrodes may include a first and second sensing electrode disposed at two discrete locations along the length of the fluidic channel and the pair of electromotive electrodes may be disposed at a first end and a second end of the fluidic channel. The fluidic channel may include a nanochannel or a microchannel. Methods for detecting an analyte may include the steps of disposing the analyte in a fluidic channel; applying a potential along the fluidic channel to generate an electrophoretic force therein such that the analyte is translocated from a first end of the fluidic channel to a second end of the fluidic channel; and measuring a voltage signal between a pair of sensing electrodes disposed in the fluidic channel as the analyte moves past the sensing electrodes.

Claims

1. A device for voltage sensing of analytes, the device comprising:

a fluidic channel defined by a trench in a substrate;

a pair of sensing electrodes disposed in the channel for sensing voltage therein, the pair of sensing electrodes comprising a first and a second sensing electrode disposed at two discrete laterally offset locations along a length of the fluidic channel, the pair of sensing electrodes being connected to a voltmeter for measuring a voltage sensed by the pair of sensing electrodes, and the pair of sensing electrodes not being connected to a voltage source; and

a pair of electromotive electrodes disposed at a first end and a second end of the fluidic channel for applying a potential along the fluidic channel,

wherein the fluidic channel comprises a nanochannel or a microchannel.

2. The device of claim 1, wherein the substrate comprises a material selected from the group consisting of silicon, silicon dioxide, fused silica, and gallium arsenide.

3. The device of claim 1, wherein each of the sensing and electromotive pairs of electrodes comprises a material selected from the group consisting of platinum, gold, chrome, titanium, silver chloride, silver, and graphene.

4. The device of claim 1, wherein the first sensing electrode is disposed on a first side of the fluidic channel and the second sensing electrode is disposed on an opposing side of the fluidic channel.

5. The device of claim 1, wherein each of the first and second sensing electrodes is disposed on a first side of the fluidic channel.

6. The device of claim 1, wherein each of the first and second sensing electrodes transverses the fluidic channel.

7. The device of claim 1, wherein the first sensing electrode transverses the fluidic channel and the second sensing electrode is disposed on a side of the fluidic channel.

8. The device of claim 1, wherein the electromotive pair of electrodes comprises macroscopic electrodes for generating a constant, changing, or oscillating electrophoretic force in the fluidic channel for translocation of an analyte disposed therein.

9. The device of claim 1, further comprising a plurality of fluidic channels.

10. The device of claim 1, further comprising a voltage amplifier disposed on the substrate.

11. The device of claim 1, wherein the fluidic channel has a width selected from a range of 1 nm to 5 μ

m.

12. The device of claim 1, wherein the fluidic channel has a depth selected from a range of 1 nm to 5 μ

m.

13. The device of claim 1, wherein the fluidic channel has a length selected from a range of 1 μ

m to 10 cm.

14. A method for detecting an analyte, the method comprising the steps of:

disposing the analyte in a fluidic channel defined by a trench in a substrate;

applying a potential along the fluidic channel;

translocating the analyte from a first end of the fluidic channel to a second end of the fluidic channel; and

measuring a voltage signal between a pair of sensing electrodes disposed in the fluidic channel for sensing voltage therein as the analyte moves past the pair of sensing electrodes, the pair of sensing electrodes comprising a first and a second electrode disposed at two discrete laterally offset locations along a length of the fluidic channel, the pair of sensing electrodes being connected to a voltmeter for measuring a voltage sensed by the pair of sensing electrodes and the pair of sensing electrodes not being connected to a voltage source,

wherein the fluidic channel comprises a nanochannel or a microchannel.

15. The method of claim 14, wherein applying a potential along the fluidic channel comprises generating an electrophoretic force therein.

16. The method of claim 14, wherein translocating the analyte comprises using a pressure differential.

17. The method of claim 14, wherein translocating the analyte comprises using a chemical gradient.

18. The method of claim 14, wherein the analyte comprises a biopolymer selected from the group consisting of deoxyribonucleic acids, ribonucleic acids, and polypeptides.

19. The method of claim 18, wherein the biopolymer comprises a single-stranded molecule.

20. The method of claim 14, wherein the analyte comprises a biopolymer having at least one probe attached thereto.

21. The method of claim 20, wherein the voltage signal changes when the biopolymer moves through a volume between the sensing electrodes and further changes when the portion of the biopolymer containing the probe moves through the volume between the sensing electrodes.

22. The method of claim 21, further comprising recording a time between voltage signal changes.

23. The method of claim 22, wherein a duration of a change in the voltage signal indicates a presence of a probe, further comprising using the voltage signal to determine a distance between two probes on the biopolymer.

24. The method of claim 14, further comprising using a duration of a change in the voltage signal to determine a length of the analyte.

25. A method for determining a sequence of a biopolymer, the method comprising:

disposing an analyte in a fluidic channel defined by a trench in a substrate;

applying a potential along the fluidic channel;

translocating the analyte from a first end of the fluidic channel to a second end of the fluidic channel; and

measuring an electrical signal between a pair of sensing electrodes disposed in the fluidic channel for sensing an electrical property therein as the analyte moves past the pair of sensing electrodes, the electrical property corresponding to locations along the biopolymer, the pair of sensing electrodes comprising a first and a second electrode disposed at two discrete laterally offset locations along a length of the fluidic channel, the pair of sensing electrodes being connected to voltmeter for measuring the electrical property sensed by the pair of sensing electrodes, and the pair of sensing electrodes not being connected to a voltage source,

wherein the fluidic channel comprises a nanochannel or a microchannel.

26. The method of claim 25, wherein applying a potential along the fluidic channel comprises generating an electrophoretic force therein.

27. The method of claim 25, wherein translocating the analyte comprises using a pressure differential.

28. The method of claim 25, wherein translocating the analyte comprises using a chemical gradient.

29. The method of claim 25, wherein preparing the analyte comprises hybridizing the biopolymer with a probe.

30. The method of claim 29, wherein a change in the electrical property corresponds to a location along the hybridized biopolymer containing the probe.

31. The method of claim 25, wherein the biopolymer comprises a double-stranded biopolymer target molecule.

32. The method of claim 31, further comprising preparing the analyte by contacting the target molecule with a first probe having a first probe specificity for recognition sites of the target molecule to form a first plurality of local ternary complexes, the first probe having a first predicted recognition site sequence.

33. The method of claim 32, further comprising using the electrical property to determine positional information of the first plurality of local ternary complexes.

34. The method of claim 33, wherein the positional information includes a parameter corresponding to a spatial distance between two local ternary complexes.

35. The method of claim 33, wherein preparing the analyte further comprises contacting the target molecule with a second probe having a second probe specificity for recognition sites of the target molecule to form a second plurality of local ternary complexes, the second probe having a second predicted recognition site sequence.

36. The method of claim 35, further comprising using the electrical property to determine positional information of the second plurality of local ternary complexes.

37. The method of claim 36, further comprising aligning positional information of at least the first and second plurality of local ternary complexes to determine a DNA sequence of the target.

38. The method of claim 25, wherein the biopolymer comprises a double-stranded nucleic acid target molecule having a plurality of binding sites disposed along the sequence thereof

39. The method of claim 38, wherein preparing the analyte comprises adding a plurality of probe molecules having a first sequence specificity to the double-stranded nucleic acid target molecule.

40. The method of claim 39, further comprising incubating the probe molecules having the first sequence specificity and the target molecule so as to effectuate preferential binding of the first probe molecules to both a first binding site and a second binding site of the target molecule.

41. The method of claim 40, further comprising using the voltage signal to measure a parameter related to a distance between the first binding site and the second binding site.

42. The method of claim 25, further comprising preparing the analyte by contacting the biopolymer with a first probe to create at least one probe-target complex at a recognition site of the biopolymer for which the first probe has a known specificity, while leaving uncomplexed, regions of the biopolymer for which the first probe is not specific.

43. The method of claim 42, wherein preparing the analyte further comprises contacting the biopolymer with a second probe to create at least one probe-target complex at a recognition site of the biopolymer for which the second probe has a known specificity, while leaving uncomplexed, regions of the target for which the second probe is not specific.

44. The method of claim 43, further comprising using the electrical property to detect and record complexed and uncomplexed regions of the biopolymer to create a first probe map of the first probe and a second probe map of the second probe, the first probe map and the second probe map incorporating information on the relative position of the hybridization of the probes.

45. The method of claim 44, further comprising determining a candidate sequence by ordering at least two probe sequences using positional information or a combination of overlapping sequences of the probe molecules and positional information.

46. The method of claim 44, wherein the first and second probe maps further incorporate information on an error of the positional information for each probe.

47. The method of claim 46, further comprising determining a candidate sequence by ordering at least two probe sequences using positional information and parameters relating to the error in positional information or a combination of overlapping sequences of the probe molecules and positional information and error in positional information.

48. A device for sensing electrical properties of analytes, the device comprising:

a fluidic channel defined by a trench in a substrate;

a pair of sensing electrodes disposed in the channel for sensing an electrical property therein, the pair of sensing electrodes comprising a first and a second sensing electrode disposed at two discrete laterally offset locations along a length of the fluidic channel, the pair of sensing electrodes being connected to a voltmeter for measuring the electrical property sensed by the pair of sensing electrodes and the pair of sensing electrodes not being connected to a voltage source; and

a pair of electromotive electrodes disposed at a first end and a second end of the fluidic channel for applying a potential along the fluidic channel,

wherein the fluidic channel comprises a nanochannel or a microchannel.

49. The device of claim 48, wherein the first sensing electrode is disposed on a first side of the fluidic channel and the second sensing electrode is disposed on an opposing side of the fluidic channel.

50. The device of claim 48, wherein each of the first and second sensing electrodes is disposed on a first side of the fluidic channel.

51. The device of claim 48, wherein each of the first and second sensing electrodes transverses the fluidic channel.

52. The device of claim 48, further comprising a plurality of fluidic channels.

53. The device of claim 48, further comprising a voltage amplifier disposed on the substrate.

54. The device of claim 48, wherein the fluidic channel has a width selected from a range of 1 nm to 5 μ

m.

55. The device of claim 48, wherein the fluidic channel has a depth selected from a range of 1 nm to 5 μ

m.

56. The device of claim 48, wherein the fluidic channel has a length selected from a range of 1 μ

m to 10 cm.