Apparatus and method for biopolymer identification during translocation through a nanopore

• US 7,410,564 B2
• Filed: 01/27/2003
• Issued: 08/12/2008
• Est. Priority Date: 01/27/2003
• Status: Expired due to Term

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Flory, Curt A.
• Primary Examiner(s): NOGUEROLA, ALEXANDER STEPHAN
• Application Number:
  US10/352,675
• Publication Number:
  US 20040144658A1
• Time in Patent Office: 2,024 Days
• Field of Search: 204601-605, 204451-455, 204/409, 204/403.01, 205/775, 205/777.5
• US Class Current: 205/777.5
• CPC Class Codes: B82Y 10/00 Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• 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: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: G01N 15/134 Devices using two or more apertures
• 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

The present invention provides an apparatus and method for identifying and sequencing a biopolymer translocating a nanopore. The apparatus of the present invention provides a first electrode, a second electrode and a potential means for applying a bias ramping potential across the electrodes to produce resonant tunneling of current carriers between the two electrodes. As the bias potential is ramped across the electrodes the increase in tunneling current occurs as the carrier energy sequentially matches the conduction band energies of the translocating biopolymer. This technique allows for real-time identification and sequencing of a biopolymer as the band energy spectra of the individual portions of the bipolymer are recorded, differentiated and identified. A method for identifying the biopolymer is also disclosed.

Claims

1. An apparatus for detecting a biopolymer in a nanopore, comprising:

(a) a first electrode;

(b) a second electrode adjacent to said first electrode;

(c) a nanopore adjacent to said first electrode and said second electrode and positioned to allow said biopolymer to be positioned between said first electrode and said second electrode; and

(d) potential means for electrically connecting said first electrode and said second electrode for applying a ramping voltage over an energy spectrum of the biopolymer from said first electrode, through a portion of said biopolymer in said nanopore, to said second electrode to produce a signal indicative of said portion of said biopolymer;

wherein ramp-time of the applied voltage is short compared to a nucleotide translocation time through the nanopore.

2. The apparatus of claim 1, wherein the first and second electrodes are ring electrodes, the apparatus further comprising a substrate for positioning said first electrode and said second electrode.

3. The apparatus of claim 1, further comprising at least a first substrate for positioning said first electrode.

4. The apparatus of claim 1, further comprising at least a second substrate for positioning said second electrode.

5. The apparatus of claim 1, further comprising at least a first substrate for positioning a nanopore.

6. The apparatus of claim 1, further comprising a means for signal detection for detecting said signal produced from said portion of said biopolymer.

7. The apparatus of claim 1, wherein said biopolymer is a charged polymer.

8. The apparatus of claim 6, wherein said biopolymer is selected from the group consisting of carbohydrates, proteins, nucleic acids, lipids, glycans, polynucleotides, proteoglycans and polypeptides.

9. A method for identifying a biopolymer translocating through a nanopore, comprising:

(a) applying a ramping voltage over an energy spectrum of the biopolymer from a first electrode through a portion of said biopolymer to a second electrode to identify said portion of said biopolymer positioned in said nanopore;

wherein ramp-time of the applied voltage is short compared to a nucleotide translocation time through the nanopore.

10. The method of claim 9, wherein said ramping voltage produces an electrical current, and wherein said electrical current is a tunneling current with an energy level that matches at least one conduction band energy of a portion of said biopolymer.

11. The method of claim 10, wherein said tunneling current is in resonance with said conduction band energies of a portion of said biopolymer.

12. The method of claim 9, further comprising translocating said biopolymer through said nanopore to identify each of said translocating portions of said biopolymer.

13. An apparatus for detecting a biopolymer translocating a nanopore, comprising:

(a) a first electrode having a first nanopore;

(b) a second electrode adjacent to said first electrode having a second nanopore wherein said first nanopore of said first electrode is positioned with said second nanopore of said second electrode so that said biopolymer may translocate through said first nanopore and said second nanopore; and

(c) potential means for electrically connecting said first electrode and said second electrode for applying a ramping voltage over an energy spectrum of the biopolymer from said first electrode through a portion of said biopolymer to said second electrode to produce a detectable signal indicative of a portion of said biopolymer translocating said first nanopore and said second nanopore;

wherein ramp-time of the applied voltage is short compared to a nucleotide translocation time through the nanopore.

14. The apparatus of claim 13, wherein the center point of said nanopore of said first electrode is positioned coaxially with the center point of said nanopore of said second electrode.

15. The apparatus of claim 14, wherein said first electrode is positioned above said second electrode.

16. The apparatus of claim 13, further comprising a substrate for positioning said first electrode and said second electrode.

17. The apparatus of claim 13, further comprising at least a first substrate for positioning said first electrode.

18. The apparatus of claim 13, further comprising at least a second substrate for positioning said second electrode.

19. An apparatus for detecting a portion of a biopolymer translocating a nanopore, comprising:

(a) a first electrode;

(b) a second electrode spaced from said first electrode to define a nanopore between said first electrode and said second electrode, said nanopore designed for receiving a translocating biopolymer, said first electrode being in electrical connection with said second electrode; and

(c) potential means for electrically connecting said first electrode and said second electrode for applying a ramping voltage over an energy spectrum of the biopolymer from said first electrode, across said biopolymer to said second electrode to produce a signal indicative of a portion of said biopolymer translocating said nanopore;

wherein ramp-time of the applied voltage is short compared to a nucleotide translocation time through the nanopore.

20. The apparatus of claim 19, wherein said biopolymer is translocated in a stepwise fashion through said nanopore defined between said first electrode and said second electrode.

21. A method for identifying a biopolymer in a nanopore defined between a first and second electrode, comprising:

applying a ramping voltage over an energy spectrum of the biopolymer from a first electrode through a portion of a biopolymer to a second electrode to scan energy levels until the energy levels of said first electrode, said biopolymer and said second electrode are in resonance, said ramping potential to produce a detectable signal to identify said portion of said biopolymer positioned in said nanopore;

wherein ramp-time of the applied voltage is short compared to a nucleotide translocation time through the nanopore.

22. The method of claim 21, wherein monomers of the biopolymer comprise a quantum well comprising an identifiable energy level spectrum that is separated by energy barriers from the electrodes.

23. An apparatus for detecting a biopolymer in a nanopore, comprising:

(a) a first electrode;

(b) a second electrode adjacent to said first electrode;

(c) a nanopore adjacent to said first electrode and said second electrode and positioned to allow said biopolymer to be positioned between said first electrode and said second electrode; and

(d) potential means for electrically connecting said first electrode and said second electrode for applying a ramping voltage over an energy spectrum of the biopolymer from said first electrode, through a portion of said biopolymer in said nanopore, to said second electrode to produce a signal indicative of said portion of said biopolymer,

wherein ramp-time of the applied voltage is short compared to a nucleotide translocation time through the nanopore; and

wherein said ramping voltage induces resonant tunneling.

24. The apparatus of claim 23, further comprising at least a first substrate for positioning a nanopore.

25. The apparatus of claim 23, further comprising a means for signal detection for detecting said signal produced from said portion of said biopolymer.

26. A method for identifying a biopolymer translocating through a nanopore, comprising:

(a) applying a ramping voltage over an energy spectrum of the biopolymer from a first electrode through a portion of said biopolymer to a second electrode to identify said portion of said biopolymer positioned in said nanopore;

wherein ramp-time of the applied voltage is short compared to a nucleotide translocation time through the nanopore; and

wherein said ramping voltage induces resonant tunneling.