Biomolecule sequencing devices, systems and methods

• US 10,557,167 B2
• Filed: 03/02/2017
• Issued: 02/11/2020
• Est. Priority Date: 09/18/2013
• Status: Active Grant

• Current Assignee: Osaka University
• Original Assignee: Quantum Biosystems Inc.
• Inventors: Kawai, Tomoji, Taniguchi, Masateru, Ohshiro, Takahito, Oldham, Mark, Nordman, Eric
• Primary Examiner(s): Hollington, Jermele M
• Application Number:
  US15/448,317
• Publication Number:
  US 20180023132A1
• Time in Patent Office: 1,076 Days
• Field of Search: None
• 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 27/04 by investigating resistance
• 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: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

Devices, systems and methods for sequencing protein samples are provided. In some examples, currents generated when a monomer passes through between electrodes of a nanogap electrode pair are measured for each of several different distances, so that monomers are identified when compared to a reference physical quantity of a known monomer, which may be obtained from a current measured with a similar inter-electrode distance(s) at which each of plural kinds of monomers are identifiable and ordered with predetermined accuracy and based on a detected physical quantity obtained from a tunneling current, which may be further normalized by the use of one or more reference substances.

Claims

1. A system for detecting a biomolecule using at least one pair of nanogap electrodes, comprising:

a fluid flow unit comprising at least one pump for directing a plurality of monomers with reference substances bound thereto to the at least one pair of nanogap electrodes, wherein the reference substances comprise a first reference substance bound to a first monomer and a second reference substance bound to a second monomer, wherein the first reference substance is different than the second reference substance; and

a computer processor coupled to the at least one pair of nanogap electrodes and programmed to;

(a) measure tunneling nanocurrent signals resulting from the plurality of monomers with reference substances bound thereto using the at least one pair of nanogap electrodes, wherein the tunneling nanocurrent signals correspond to the reference substances, wherein the first reference substance and the second reference substance correspond to different tunneling nanocurrent signals; and

(b) identify a monomer of the plurality of monomers with reference substances bound thereto based on the tunneling nanocurrent signals measured in (a).

2. The system of claim 1, wherein the monomer of the plurality of monomers with reference substances bound thereto is identified based upon a reference physical quantity of the monomer.

3. The system of claim 1, wherein the reference substances are electrically conductive.

4. The system of claim 1, wherein the tunneling nanocurrent signals of the reference substances are measured for at least about one second.

5. The system of claim 1, wherein the at least one pair of nanogap electrodes is normalized using the reference substances.

6. The system of claim 1, wherein the biomolecule is between electrodes of the at least one pair of nanogap electrodes.

7. The system of claim 1, wherein the monomer of the plurality of monomers with reference substances bound thereto is bound to the biomolecule, and wherein the computer processor is further programmed to detect the reference substances using the tunneling nanocurrent signals measured in (a).

8. The system of claim 1, wherein the reference substances comprise subunits.

9. The system of claim 1, wherein the plurality of monomers with reference substances bound thereto comprises native nucleotide bases and/or modified nucleotide bases.

10. The system of claim 1, wherein the plurality of monomers with reference substances bound thereto is incorporatable.

11. The system of claim 10, wherein the monomer of the plurality of monomers with reference substances bound thereto comprises a portion of a double stranded nucleic acid.

12. The system of claim 11, wherein the portion of the double stranded nucleic acid is sequenced.

13. A method of detecting a biomolecule, comprising:

(a) providing a plurality of monomers with reference substances bound thereto, wherein the reference substances comprise a first reference substance bound to a first monomer and a second reference substance bound to a second monomer, wherein the first reference substance is different than the second reference substance;

(b) using at least one pair of nanogap electrodes to measure tunneling nanocurrent signals resulting from the plurality of monomers with reference substances bound thereto, the tunneling nanocurrent signals corresponding to the reference substances, wherein the the first reference substance and the second reference substance correspond with different tunneling nanocurrent signals; and

(c) identifying a monomer of the plurality of monomers with reference substances bound thereto based on the tunneling nanocurrent signals measured in (b).

14. The method of claim 13, wherein the identifying of the monomer of the plurality of monomers with reference substances bound thereto is based upon a reference physical quantity of the monomer.

15. The method of claim 13, wherein the reference substances are electrically conductive.

16. The method of claim 13, wherein the tunneling nanocurrent signals of the reference substances are measured for at least about one second.

17. The method of claim 13, further comprising normalizing the at least one pair of nanogap electrodes using the reference substances.

18. The method of claim 13, wherein the biomolecule is between electrodes of the at least one pair of nanogap electrodes.

19. The method of claim 13, wherein the monomer of the plurality of monomers with reference substances bound thereto is bound to the biomolecule, and wherein the method further comprises detecting the reference substances using the tunneling nanocurrent signals measured in (b).

20. The method of claim 13, wherein the reference substances comprise subunits.

21. The method of claim 13, wherein the plurality of monomers with reference substances bound thereto comprises native nucleotide bases and/or modified nucleotide bases.

22. The method of claim 13, wherein the plurality of monomers with reference substances bound thereto is incorporatable.

23. The method of claim 22, wherein the monomer of the plurality of monomers with reference substances bound thereto comprises a portion of a double stranded nucleic acid.

24. The method of claim 23, wherein the portion of the double stranded nucleic acid is sequenced.