Nanopore and Carbon Nanotube Based DNA Sequencer

• US 20110168562A1
• Filed: 03/18/2009
• Published: 07/14/2011
• Est. Priority Date: 03/18/2008
• Status: Active Grant

• Current Assignee: Trustees Of Columbia University In The City Of New York (Columbia University), Arizona Board of Regents (University of Arizona)
• Original Assignee: Trustees Of Columbia University In The City Of New York (Columbia University)
• Inventors: Reinhart, Kevin, He, Jin, Lindsay, Stuart, Zhang, Peiming, Nuckolls, Colin, Tang, Jinyao
• Granted Patent: US 8,961,757 B2
• Time in Patent Office: Days
• US Class Current: 204/600
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• 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 a device for analyzing the composition of a heteropolymer comprising a carbon nanotube through which the heteropolymer is driven by electrophoresis. The carbon nanotube also serves as one electrode in a reading circuit. One end of the carbon nanotube is held in close proximity to a second electrode, and each end of the carbon nanotube is functionalized with flexibly-tethered chemical-recognition moieties, such that one will bind one site on the emerging polymer, and the second will bind another site in close proximity, generating an electrical signal between the two electrodes when the circuit is completed by the process of chemical recognition.

Claims

1. A device for measuring a desired characteristics of a biomolecule comprising a carbon nanotube wherein the biomolecule is translocated through the carbon nanotube.

2. The device of claim 1 wherein the biomolecule is a biopolymer selected from the group consisting of DNA, RNA, protein and peptides.

3. The device of claim 1 wherein the biopolymer is DNA and electrophoresis drives the translocation and wherein the interior diameter of the carbon nanotube is about 3 nm or less.

4. The device of claim 1 wherein the carbon nanotube is functionalized with a recognition element that recognizes the polymer and provides a means for measuring the desired characteristic.

5. A device for determining the sequence of a polymer comprising:

a) a carbon nanotube having an interior diameter through which the polymer can travel;

b) a solid surface to support the carbon nanotube;

c) an insulating film layer disposed on top of the carbon nanotube, the insulating film layer comprising at least a first and second well separated by an insulating wall formed by the insulating film layer, and wherein the first and second wells are capable of containing an electrolyte, wherein the first and second well each comprise an electrode or are connected to an electrode;

wherein the carbon nanotube comprises a first portion and a second portion, wherein the first portion contacts the first well and the second portion contacts the second well;

wherein the second portion has a first part and a second part separated by a gap having a first gap end and a second gap end;

wherein the first gap end is functionalized with a first recognition element and the second gap end is functionalized with a second recognition element.

wherein the device further comprises a first electrode that contacts the first part of the second portion of the carbon nanotube and comprises a second electrode that contacts the second part of the second portion of the carbon nanotube;

wherein the first and second electrodes contacting the second portion of the carbon nanotube are independent of the electrodes contacting the wells in the insulating film layer.

6. The device of claim 5 wherein the gap is about 1 nm to about 10 nm wide.

7. The device of claim 5 wherein the carbon nanotube is a single walled carbon nanotube.

8. The device of claim 5 wherein the interior diameter is 3 nm or less and the polymer is DNA or RNA.

9. The device of claim 5 wherein the electrodes comprise palladium.

10. The device of claim 5 wherein the solid support comprises an oxidized silicon wafer and wherein the insulating film layer comprises PMMA.

11. The device of claim 5 further comprising a cover.

12. The device of claim 5 wherein the first and second recognition elements are different.

13. The device of claim 5 wherein the first and second recognition elements are tethered to the carbon nanotube by a flexible linker.

14. The device of claim 13 wherein the flexible linker comprises a hydrocarbon chain.

15. The device of claim 14 wherein the linker is a two methylene chain terminated with an amine.

16. The device of claim 5 wherein the polymer is a nucleic acid and the first recognition element comprises a phosphate grabber and the second recognition element comprises a nucleoside base reader.

17. The device of claim 16 wherein the polymer is DNA and the phosphate grabber comprises guanidinium and the base reader is a reader that can recognize its Watson-Crick base pair complement.

18. The device of claim 16 wherein the polymer is DNA and the phosphate grabber comprises guanidinium and the base reader is either an adenine, guanine, cytosine or thymine reader.

19. The device of claim 16 wherein the polymer is RNA and the phosphate grabber comprises guanidinium and the base reader is either an adenine, guanine, cytosine or uracil reader.

20. A method of fabricating a device suitable for polymer sequencing comprising

a) providing an oxidized silicon wafer support comprising SiO₂ and CoMo-doped mesoporous SiO₂ catalyst particles patterned on one end of the support;

b) growing a carbon nanotube via a chemical vapor deposition process from the CoMo-doped mesoporous SiO₂ catalyst particles using ethanol as a carbon source to produce the carbon nanotube disposed on top of the silicon wafer;

c) cutting a gap in a second portion of the carbon nanotube by oxygen plasma to produce a gap between a first part and a second part of the second portion of the carbon nanotube, wherein the first part has a first gap end and the second part has a second gap end;

wherein the oxygen plasma cutting provides a carboxylated first gap end and a carboxylated second gap end;

d) providing a first electrode to contact a first part of the second portion of the carbon nanotube, and providing an electrode to contact the second part of the second portion of the carbon nanotube;

g) spincasting an insulating layer on the silicon wafer and the carbon nanotube;

h) creating a first and second well in the insulating layer so that the first portion of the carbon nanotube contacts the first well and the second portion of the carbon nanotube contacts the second well; and

i) contacting the first well with a third electrode and contacting the second well with a fourth electrode, wherein the third and fourth electrodes do not physically contact the carbon nanotube.

21. The method of claim 20 wherein the insulating layer comprises PMMA.

22. The method of claim 20 wherein the carbon nanotube is a single walled carbon nanotube.

23. The method of claim 20 wherein the carbon nanotube has an interior diameter of about 3 nm or less.

24. The method of claim 20 wherein the gap is about 1-10 nm wide.

25. The method of claim 20 comprising further functionalizing the first gap end with a guanidinium and the second gap end with a base reader.

26. The method of claim 25 wherein the guanidinium and the base reader are connected to the carbon nanotube with a flexible linker.

27. The method of claim 26 wherein the flexible linker comprise a two methylene chain linked via an amide bond to the carboxyl residue at the first and second gap ends of the carbon nanotube.

28. A method of fabricating a device suitable for polymer sequencing comprising

a) providing a oxidized silicon wafer support comprising SiO₂ and CoMo-doped mesoporous SiO₂ catalyst particles patterned on one end of the support;

b) growing a carbon nanotube via a chemical vapor deposition process from the CoMo-doped mesoporous SiO₂ catalyst particles using ethanol as a carbon source to produce the carbon nanotube disposed on top of the silicon wafer;

c) providing an aluminum mask over the carbon nanotube wherein the aluminum mask is patterned to expose a section of the carbon nanotube;

d) removing the exposed section of the carbon nanotube with an oxygen plasma to expose a bare silicon wafer support, wherein the amount removed is between 1-10 nm, and wherein the non-exposed section of the carbon nanotube is protected from the oxygen plasma etch by the aluminum mask;

e) depositing a metal layer over both the aluminum mask and the bare silicon wafer support;

f) removing the aluminum mask with tetramethylammonium hydroxide to create a gap between the end of the nanotube and the metal layer.

29. The device manufactured by the method of claim 28.