Nanochannel arrays and their preparation and use for high throughput macromolecular analysis

• US 9,678,038 B2
• Filed: 11/15/2013
• Issued: 06/13/2017
• Est. Priority Date: 07/25/2001
• Status: Active Grant

• Current Assignee: The Trustees of Princeton University (Princeton University)
• Original Assignee: The Trustees of Princeton University (Princeton University)
• Inventors: Austin, Robert H., Tegenfeldt, Jonas O., Chou, Stephen Y., Yu, Zhaoning, Cao, Han
• Primary Examiner(s): Ball, J. Christopher
• Application Number:
  US14/081,322
• Publication Number:
  US 20150136601A1
• Time in Patent Office: 1,306 Days
• Field of Search: None
• CPC Class Codes: B01J 2219/00274 Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
• CPC Class Codes: B01L 2200/0663 Stretching or orienting elongated molecules or particles
• CPC Class Codes: B01L 2200/12 Specific details about manufacturing devices
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 2300/0861 Configuration of multiple channels and/or chambers in a single devices
• CPC Class Codes: B01L 2300/0896 Nanoscaled
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0418 electro-osmotic flow [EOF]
• CPC Class Codes: B01L 2400/086 using baffles or other fixed flow obstructions
• CPC Class Codes: B01L 3/502707 characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B81B 1/002 Holes characterised by their shape, in either longitudinal or sectional plane
• CPC Class Codes: B81B 2201/058 Microfluidics not provided for in B81B2201/051 - B81B2201/054
• CPC Class Codes: B81B 2203/0338 Channels
• CPC Class Codes: B81C 1/00071 Channels
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/648 using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
• 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: Y10S 977/704 : Nucleic acids, e.g. DNA or RNA
• CPC Class Codes: Y10S 977/88 : with arrangement, process, or apparatus for testing
• CPC Class Codes: Y10S 977/883 : Fluidic self-assembly, FSA

Abstract

Nanochannel arrays that enable high-throughput macromolecular analysis are disclosed. Also disclosed are methods of preparing nanochannel arrays and nanofluidic chips. Methods of analyzing macromolecules, such as entire strands of genomic DNA, are also disclosed, as well as systems for carrying out these methods.

Claims

1. A method of analyzing at least one macromolecule, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel;

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

detecting at least one signal transmitted from the at least one elongated macromolecule within the nanochannel; and

correlating the detected signal to at least one property of the at least one macromolecule;

wherein the macromolecule is DNA and the detected signals are correlated to the base pair sequence of said DNA; and

wherein the nanochannel is surmounted by sealing material to render the nanochannel at least substantially enclosed.

2. The method of claim 1, wherein the sealing material is optically transparent.

3. The method of claim 2, wherein at least one signal is transmitted through the optically transparent sealing material.

4. A method of analyzing at least one macromolecule, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel;

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

detecting at least one signal transmitted from the at least one elongated macromolecule within the nanochannel; and

correlating the detected signal to at least one property of the at least one macromolecule;

wherein the macromolecule is DNA and the detected signals are correlated to the base pair sequence of said DNA; and

wherein the at least one macromolecule has an elongated length in nanochannel of greater than 150 nanometers.

5. A method of analyzing at least one macromolecule, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel;

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

detecting at least one signal transmitted from the at least one elongated macromolecule within the nanochannel; and

correlating the detected signal to at least one property of the at least one macromolecule;

wherein the macromolecule is DNA and the detected signals are correlated to the base pair sequence of said DNA; and

wherein the at least one macromolecule is a DNA fragment from a restriction fragment length polymorphism analysis.

6. A method of analyzing at least one macromolecule, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel;

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

detecting at least one signal transmitted from the at least one elongated macromolecule within the nanochannel; and

correlating the detected signal to at least one property of the at least one macromolecule;

wherein the macromolecule is DNA and the detected signals are correlated to the base pair sequence of said DNA; and

wherein the at least one macromolecule is at least one chromosome.

7. The method of claim 6, wherein the at least one chromosome is analyzed to determine the presence of at least one single nucleotide polymorphism.

8. A method of analyzing at least one macromolecule, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel;

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

detecting at least one signal transmitted from the at least one elongated macromolecule within the nanochannel; and

correlating the detected signal to at least one property of the at least one macromolecule; and

illuminating the at least one macromolecule within the nanochannel;

wherein the macromolecule is DNA and the detected signals are correlated to the base pair sequence of said DNA.

9. A method of maintaining at least one macromolecule in an elongated state, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel; and

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

wherein the at least one macromolecule is a DNA fragment from a restriction fragment length polymorphism analysis.

10. The method of claim 9, wherein the at least one macromolecule is transported into the nanochannel by applying an electric current.

11. The method of claim 9, wherein the trench width of the nanochannel is less than about 150 nanometers.

12. The method of claim 9, wherein the trench depth of the nanochannel is less than about 200 nanometers.

13. The method of claim 9, wherein the width of the nanochannel is substantially constant along the length of the nanochannel.

14. The method of claim 9, wherein the nanochannel is in the material of a surface.

15. The method of claim 9, wherein the nanochannel is surmounted by sealing material to render the nanochannel at least substantially enclosed.

16. The method of claim 9, wherein the at least one macromolecule has an elongated length in the nanochannel of greater than 150 nanometers.

17. The method of claim 9, wherein the at least one macromolecule is DNA having greater than 10 base pairs.

18. A method of analyzing at least one macromolecule, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel;

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

detecting at least one signal transmitted from the at least one elongated macromolecule within the nanochannel; and

correlating the detected signal to at least one property of the at least one macromolecule;

wherein the at least one macromolecule is a DNA fragment from a restriction fragment length polymorphism analysis.

19. A method of analyzing at least one macromolecule, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel;

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

detecting at least one signal transmitted from the at least one elongated macromolecule within the nanochannel; and

correlating the detected signal to at least one property of the at least one macromolecule;

wherein the at least one macromolecule is at least one chromosome.

20. The method of claim 19, wherein the at least one chromosome is analyzed to determine the presence of at least one single nucleotide polymorphism.

21. A method of maintaining at least one macromolecule in an elongated state, comprising the steps of:

transporting at least one macromolecule in a fluid sample into a nanochannel, such that the at least one macromolecule is in an elongated state within the nanochannel; and

maintaining the at least one macromolecule in an elongated state within the nanochannel without application of a shear force;

wherein the at least one macromolecule is at least one chromosome.

22. The method of claim 21, wherein the at least one macromolecule is transported into the nanochannel by applying an electric current.

23. The method of claim 21, wherein the trench width of the nanochannel is less than about 150 nanometers.

24. The method of claim 21, wherein the trench depth of the nanochannel is less than about 200 nanometers.

25. The method of claim 21, wherein the width of the nanochannel is substantially constant along the length of the nanochannel.

26. The method of claim 21, wherein the nanochannel is in the material of a surface.

27. The method of claim 21, wherein the nanochannel is surmounted by sealing material to render the nanochannel at least substantially enclosed.

28. The method of claim 21, wherein the at least one macromolecule is DNA having greater than 10 base pairs.