BIOMOLECULE SEQUENCING DEVICES, SYSTEMS AND METHODS

• US 20160319342A1
• Filed: 03/04/2016
• Published: 11/03/2016
• Est. Priority Date: 09/18/2013
• Status: Active Grant

• Current Assignee: Osaka University
• Original Assignee: Osaka University, Quantum Biosystems Inc.
• Inventors: Taniguchi, Masateru, Ohshiro, Takahito, Kawai, Tomoji, Oldham, Mark, Nordman, Eric
• Granted Patent: US 9,644,236 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• 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 method for sequencing a biomolecule having a plurality of monomers, comprising:

(a) directing said biomolecule through 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;

(b) measuring 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

(c) identifying with a computer processor said plurality of monomers by comparing said signals measured in (b) to one or more references.

2. The method of claim 1, wherein said identifying comprises using a predetermined relationship between a relative value of said signals and said one or more references.

3. The method 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 gap distances.

4. The method of claim 1, further comprising using an inter-electrode distance of a given set of nanogap electrodes to interpolate a nanocurrent for another inter-electrode distance.

5. The method of claim 1, further comprising generating a consensus sequence of said biomolecule using data from multiple measurements with said plurality of sets of nanogap electrodes using individual monomer quality calls.

8. The method of claim 1, wherein each set of said 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.

10. The method of claim 1, further comprising measuring signals corresponding to nanocurrents for said plurality of sets of nanogap electrodes at different inter-electrode distances.

11. The method of claim 1, further comprising measuring signals from at most a subset of said plurality of sets of nanogap electrodes, and identifying 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.

12. The method of claim 1, wherein said nanocurrents include tunneling currents.

6. (canceled)

7. (canceled)

9. (canceled)

13. 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.

14-20. -20. (canceled)

21. A method for sequencing a peptide sample having one or more monomers, comprising:

(a) directing said peptide sample and at least one reference sample through a channel including at least one set of nanogap electrodes having an inter-electrode distance that is variable, wherein said reference sample has a predetermined signal profile corresponding to a nanocurrent measured by said nanogap electrodes;

(b) measuring signals with said nanogap electrodes at different inter-electrode distances that correspond to nanocurrents as said protein sample and reference sample are directed through said channel, which signals include reference signals associated with said reference sample; and

(c) identifying with a computer processor said one or more monomers by comparing said signals measured in (b) to said reference signals.

22. The method of claim 21, wherein said reference sample is separate from said peptide sample.

24. The method of claim 21, wherein said reference sample comprises subunits that have the same orientation with respect to a space between the nanogap electrodes when the reference sample is passed through between the nanogap electrodes.

25. The method of claim 21, wherein said reference sample has a substantially spherical shape.

26. The method of claim 25, wherein said reference sample comprises metal nanoparticles or fullerenes.

33. The method of claim 21, wherein said reference sample is associated with a first pulse duration and said peptide sample is associated with a second pulse duration which is different from said first pulse duration.

34. The method of claim 21, wherein said signal profile comprises a magnitude of a signal.

35. The method of claim 34, wherein said magnitude of said signal is a predetermined magnitude.

37. The method of claim 21, wherein (b) further comprises (i) changing said inter-electrode distance of said nanogap electrodes and (ii) making separate measurements of said signals at said different inter-electrode distances.

23. (canceled)

27-32. -32. (canceled)

36. (canceled)

38. (canceled)

39. A system for sequencing a peptide sample having one or more monomers, comprising:

a channel including at least one set of nanogap electrodes having an inter-electrode distance that is variable;

a fluid flow unit for directing said peptide sample and at least one reference sample through said channel, wherein said reference sample has a predetermined signal profile corresponding to a nanocurrent measured by said nanogap electrodes; and

a computer processor coupled to said nanogap electrodes and programmed to (i) measure signals with said nanogap electrodes at variable inter-electrode distances that correspond to nanocurrents as said peptide sample and reference sample are directed through said channel, and (ii) identify said one or more monomers by comparing said signals measured in (i) to said reference signals.

40-48. -48. (canceled)