Systems and methods for characterizing a molecule

• US 8,324,914 B2
• Filed: 02/08/2010
• Issued: 12/04/2012
• Est. Priority Date: 02/08/2010
• Status: Active Grant

• Current Assignee: Roche Sequencing Solutions, Inc. (Roche Holding AG)
• Original Assignee: Genia Technologies, Inc. (Roche Holding AG)
• Inventors: Chen, Roger, Davis, Randy
• Primary Examiner(s): Nguyen, Vincent Q
• Application Number:
  US12/658,604
• Publication Number:
  US 20110193570A1
• Time in Patent Office: 1,030 Days
• Field of Search: 324/693, 324/717, 324/71.1, 324/451, 324/654, 435/616
• US Class Current: 324/717
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• 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 2015/0038 Investigating nanoparticles
• 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 27/447 using electrophoresis
• 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
• CPC Class Codes: Y10T 29/49002 Electrical device making
• CPC Class Codes: Y10T 29/49117 Conductor or circuit manufacturing

Abstract

Techniques for characterizing a molecule are described herein. In one example, a portion of the molecule is trapped in a nanopore, a variable voltage is applied across the nanopore until the trapped portion of molecule is moved within the nanopore, and the molecule is characterized based on the electrical stimulus required to affect movement of at least a portion of the trapped portion of the molecule within the nanopore.

Claims

1. A method of characterizing a molecule including:

trapping a portion of the molecule in a nanopore, wherein the nanopore is one of a plurality of nanopores in a nanopore array, and wherein each of the plurality of nanopores is individually addressable;

applying a variable voltage across the nanopore until the trapped portion of molecule is moved within the nanopore;

characterizing the molecule based on the electrical stimulus required to affect movement of at least a portion of the trapped portion of the molecule within the nanopore.

2. The method of claim 1, wherein the molecule comprises a polymeric molecule.

3. The method of claim 1, wherein the molecule comprises a nucleotide molecule.

4. The method of claim 1, wherein the molecule comprises a DNA molecule.

5. The method of claim 1, wherein the molecule comprises a RNA molecule.

6. The method of claim 1, wherein the molecule comprises a dsDNA molecule and characterizing the molecule includes identifying GC base pairs and/or AT base pairs.

7. The method of claim 1, further including characterizing the molecule based on an electrical signal of the molecule as it moves through the nanopore.

8. The method of claim 7, wherein the electrical signal comprises electrical resistance information of the nanopore as the molecule moves through the nanopore.

9. The method of claim 7, wherein the electrical signal comprises an electrical resistance versus time profile of the nanopore as the molecule moves through the nanopore.

10. The method of claim 7, wherein the electrical signal comprises a current versus time profile of the nanopore as the molecule moves through the nanopore.

11. The method of claim 7, wherein the electrical signal comprises a voltage versus time profile of the nanopore as the molecule moves through the nanopore.

12. The method of claim 7, wherein the electrical signal of the molecule comprises a combined electrical signal combining electrical signal for multiple regions of the molecule.

13. The method of claim 7, wherein characterizing the molecule based on an electrical signal of the molecule as it moves through the nanopore includes characterizing the molecule based on one or more of following:

amplitude, frequency, edge rise time, and edge fall time information of the electrical signal.

14. The method of claim 1, wherein the molecule comprises a nucleotide molecule, and wherein characterizing the molecule includes characterizing a base sequence of at least a portion of the molecule.

15. The method of claim 1, wherein each of the plurality of nanopores is individually controllable.

16. A system for characterizing a molecule including:

a nanopore device configured to;

trap a portion of the molecule in a nanopore, wherein the nanopore is one of a plurality of nanopores in a nanopore array, and wherein each of the plurality of nanopores is individually addressable;

apply a variable voltage across the nanopore until the trapped portion of the molecule is moved within the nanopore;

a processor configured to characterize the molecule based on the electrical stimulus required to affect movement of at least a portion of the trapped portion of the molecule within the nanopore; and

a memory configured to provide the processor with instructions.

17. The system of claim 16, wherein the molecule comprises a polymeric molecule.

18. The system of claim 16, wherein the molecule comprises a nucleotide molecule.

19. The system of claim 16, wherein the molecule comprises a DNA molecule.

20. The system of claim 16, wherein the molecule comprises a RNA molecule.

21. The system of claim 16, wherein the molecule comprises a dsDNA molecule and characterizing the molecule includes identifying GC base pairs and/or AT base pairs.

22. The system of claim 16,

wherein the nanopore device is further configured to detect an electrical signal of the molecule as it moves through the nanopore;

and

wherein the processor is further configured to characterize the molecule based on the electrical signal of the molecule as it moves through the nanopore.

23. The system of claim 22, wherein the electrical signal comprises electrical resistance information of the nanopore as the molecule moves through the nanopore.

24. The system of claim 22, wherein the electrical signal comprises an electrical resistance versus time profile of the nanopore as the molecule moves through the nanopore.

25. The system of claim 22, wherein the electrical signal comprises a current versus time profile of the nanopore as the molecule moves through the nanopore.

26. The system of claim 22, wherein the electrical signal comprises a voltage versus time profile of the nanopore as the molecule moves through the nanopore.

27. The system of claim 22, wherein the electrical signal of the molecule comprises a combined electrical signal combining electrical signal for multiple regions of the molecule.

28. The system of claim 22, wherein characterizing the molecule based on an electrical signal of the molecule as it moves through the nanopore includes characterizing the molecule based on one or more of following:

amplitude, frequency, edge rise time, and edge fall time information of the electrical signal.

29. The system of claim 16, wherein the molecule comprises a nucleotide molecule, and wherein characterizing the molecule includes characterizing a base sequence of at least a portion of the molecule.

30. The system of claim 16, wherein each of the plurality of nanopores is individually controllable.

31. A system for characterizing a molecule including:

means for trapping a portion of the molecule in a nanopore, wherein the nanopore is one of a plurality of nanopores in a nanopore array, and wherein each of the plurality of nanopores is individually addressable;

means for applying a variable voltage across the nanopore until the trapped portion of molecule is moved within the nanopore;

means for characterizing the molecule based on the electrical stimulus required to affect movement of at least a portion of the trapped portion of the molecule within the nanopore.

32. The system of claim 31, wherein the molecule comprises a polymeric molecule.

33. The system of claim 31, wherein the molecule comprises a nucleotide molecule.

34. The system of claim 31, wherein the molecule comprises a DNA molecule.

35. The system of claim 31, wherein the molecule comprises a RNA molecule.

36. The system of claim 31, wherein the molecule comprises a dsDNA molecule and characterizing the molecule includes identifying GC base pairs and/or AT base pairs.

37. The system of claim 31, further including means for characterizing the molecule based on an electrical signal of the molecule as it moves through the nanopore.

38. The system of claim 37, wherein the electrical signal comprises electrical resistance information of the nanopore as the molecule moves through the nanopore.

39. The system of claim 37, wherein the electrical signal comprises an electrical resistance versus time profile of the nanopore as the molecule moves through the nanopore.

40. The system of claim 37, wherein the electrical signal comprises a current versus time profile of the nanopore as the molecule moves through the nanopore.

41. The system of claim 37, wherein the electrical signal comprises a voltage versus time profile of the nanopore as the molecule moves through the nanopore.

42. The system of claim 37, wherein the electrical signal of the molecule comprises a combined electrical signal combining electrical signal for multiple regions of the molecule.

43. The system of claim 37, wherein characterizing the molecule based on an electrical signal of the molecule as it moves through the nanopore includes characterizing the molecule based on one or more of following:

amplitude, frequency, edge rise time, and edge fall time information of the electrical signal.

44. The system of claim 31, wherein the molecule comprises a nucleotide molecule, and wherein characterizing the molecule includes characterizing a base sequence of at least a portion of the molecule.

45. The system of claim 31, wherein each of the plurality of nanopores is individually controllable.