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

• US 10,161,001 B2
• Filed: 06/09/2016
• Issued: 12/25/2018
• Est. Priority Date: 07/25/2001
• Status: Expired due to Term

• Current Assignee: The Trustees of Princeton University (Princeton University)
• Original Assignee: The Trustees of Princeton University (Princeton University)
• Inventors: Austin, Robert H., Yu, Zhaoning, Tegenfeldt, Jonas O., Chou, Stephen Y., Cao, Han
• Primary Examiner(s): Bhat, Narayan K
• Application Number:
  US15/178,248
• Publication Number:
  US 20170067102A1
• Time in Patent Office: 929 Days
• 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 nanofluidic chip, comprising:

a) nanochannel array, comprising;

a substrate having a surface;

at least one channel in the surface, wherein the at least one channel has a trench width of less than 100 nanometers and a trench depth of less than 100 nanometers; and

the at least one channel is capable of admitting a fluid;

b) at least one sample reservoir in fluid communication with the at least one channel, said sample reservoir capable of releasing a fluid; and

c) at least one waste reservoir in fluid communication with the at least one channel, said waste reservoir capable of receiving a fluid.

2. The nanofluidic chip of claim 1, wherein the at least one channel is one of a plurality of parallel channels in the surface.

3. The nanofluidic chip of claim 1, wherein the at least one channel is surmounted by sealing material to render the channel at least substantially enclosed.

4. The nanofluidic chip of claim 1 wherein the at least one sample reservoir is formed in the surface of the substrate.

5. The nanofluidic chip of claim 1 further comprising at least one waste reservoir in fluid communication with the at least one channel.

6. The nanofluidic chip of claim 1 capable of transporting a plurality of elongated macromolecules from a sample reservoir and across the at least one channel.

7. The nanofluidic chip of claim 1 further comprising at least one pair of electrodes capable of applying an electric field across the at least one channel in at least one direction.

8. The nanofluidic chip of claim 7 wherein at least two pair of electrodes each provides an electric field in different directions.

9. A system, comprising:

A) a nanofluidic chip, comprising;

a) nanochannel array, comprising;

a substrate having a surface; and

at least one channel in the surface capable of admitting a fluid, wherein the at least one channel has a trench width of less than 100 nanometers and a trench depth of less than 100 nanometers; and

b) at least one sample reservoir in fluid communication with the at least one channel, said sample reservoir capable of releasing a fluid; and

B) an apparatus for detecting at least one signal transmitted from the at least one fluid in the nanochannel array.

10. The nanofluidic chip of claim 9, wherein the at least one channel is one of a plurality of parallel channels in the surface.

11. The nanofluidic chip of claim 9, wherein the at least one channel is surmounted by sealing material to render the channel at least substantially enclosed.

12. The system according to claim 9, further comprising a transporting apparatus to transport a fluid through at the at least one channel.

13. The system according to claim 9, further comprising a sample loading apparatus for loading at least one fluid to the at least one sample reservoir.

14. The system according to claim 9, further comprising a data processor.

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

providing a nanofluidic chip, comprising;

a) nanochannel array, comprising;

a substrate having a surface;

at least one nanochannel in the surface, wherein the at least one channel has a trench width of less than 100 nanometers and a trench depth of less than 100 nanometers; and

the at least one channel is capable of admitting a fluid;

b) at least one sample reservoir in fluid communication with the at least one channel, said sample reservoir capable of releasing a fluid; and

c) at least one waste reservoir in fluid communication with the at least one channel, said waste reservoir capable of receiving a fluid;

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

maintaining the at least one macromolecule in an elongated state within a region of the at least one nanochannel having a substantially constant width;

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

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

16. The method of claim 15, wherein the at least one macromolecule is transported into the nanochannel by applying an electric current.