Biomolecule sequencing devices, systems and methods

• US 9,644,236 B2
• Filed: 03/04/2016
• Issued: 05/09/2017
• 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): Valone, Thomas
• Application Number:
  US15/061,871
• Publication Number:
  US 20160319342A1
• Time in Patent Office: 431 Days
• Field of Search: 324693
• 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 sequencing a biomolecule having a plurality of monomers, comprising:

a channel including a plurality of sets of nanogap electrodes, wherein each set of said plurality of sets of nanogap electrodes includes two nanogap electrodes, and wherein at least a subset of said plurality of sets of nanogap electrodes has different inter-electrode distances;

a fluid flow unit for directing said biomolecule through said channel; and

a computer processor coupled to said nanogap electrodes and programmed to;

(a) measure signals with said plurality of sets of nanogap electrodes that correspond to nanocurrents as said biomolecule is directed through said channel, which signals correspond to said plurality of monomers of said biomolecule; and

(b) identify said plurality of monomers by comparing said signals measured in (a) to one or more references.

2. The system of claim 1, wherein said computer processor is programmed to identify said plurality of monomers using a predetermined relationship between a relative value of said signals and said one or more references.

3. The system of claim 1, wherein said plurality of sets of nanogap electrodes comprises a first set of nanogap electrodes and a second set of nanogap electrodes having different inter-electrode distances.

4. The system of claim 1, wherein said computer processor is programmed to use an inter-electrode distance of a given set of nanogap electrodes to interpolate a nanocurrent for another inter-electrode distance.

5. The system of claim 1, wherein said computer processor is programmed to generate a consensus sequence of said biomolecule using data from multiple measurements with said plurality of sets of nanogap electrodes using individual monomer quality calls.

6. The system of claim 1, wherein each of said plurality of sets of nanogap electrodes has an inter-electrode distance that is suitable to detect at most a subset of said plurality of monomers of said biomolecule.

7. The system of claim 1, wherein said computer processor is programmed to measure signals corresponding to nanocurrents for said plurality of sets of nanogap electrodes at different inter-electrode distances.

8. The system of claim 1, wherein said computer processor is programmed to measure signals from at most a subset of said plurality of sets of nanogap electrodes, and identify a given monomer of said plurality of monomers with said signals measured with at most said subset of said plurality of sets of nanogap electrodes.

9. The system of claim 1, wherein said inter-electrode distances are from about 0.5 times to five times a molecular diameter of a given subunit of said biomolecule.

10. The system of claim 1, wherein said biomolecule is a peptide molecule.

11. The system of claim 1, wherein said biomolecule is a nucleic acid molecule.

12. The system of claim 1, wherein said nanocurrents comprise tunneling currents.

13. The system of claim 1, wherein said fluid flow unit is configured to direct at least one reference sample through said channel.

14. The system of claim 13, wherein said fluid flow unit comprises one or more pumps for directing said biomolecule and/or said reference sample through said channel.

15. The system of claim 14, wherein said one or more pumps are micropumps.

16. The system of claim 13, wherein said computer processor is programmed to measure said one or more references when said at least one reference sample is directed through said channel.

17. The system of claim 13, wherein said fluid flow unit is configured to alternately and sequentially direct said biomolecule and said at least one reference sample through said channel.

18. The system of claim 13, wherein said reference sample is a reference peptide sample with a predetermined sequence of one or more monomers.

19. The system of claim 13, wherein said reference sample comprises subunits that have the same orientation with respect to a space between two nanogap electrodes of at least one of said plurality of sets of nanogap electrodes when said reference sample is directed through said channel.

20. The system of claim 13, wherein said reference sample has a substantially spherical shape.

21. The system of claim 20, wherein said reference sample comprises metal nanoparticles or fullerenes.