Methods for measuring analytes using nanofabricated device

• US 11,391,719 B2
• Filed: 12/21/2017
• Issued: 07/19/2022
• Est. Priority Date: 06/30/2015
• Status: Active Grant

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: Roche Sequencing Solutions, Inc. (Roche Holding AG)
• Inventors: Henck, Steven
• Primary Examiner(s): Kessel, Maris R
• Assistant Examiner(s): Tran, Vivian A
• Application Number:
  US15/851,608
• Publication Number:
  US 20180120287A1
• Time in Patent Office: 1,671 Days
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• 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

Abstract

Devices for sequencing linear biomolecules (e.g., DNA, RNA, polypeptides, proteins, and the like) using quantum tunneling effects, and methods of making and using such devices, are provided. A nanofabricated device can include a small gap formed by depositing a thin film between two electrodes, and subsequently removing the film using an etching process. The width of the resulting gap can correspond with the size of a linear biomolecule such that when a part of the biomolecule (e.g., a nucleobase or amino acid) is present in the gap, a change in tunneling current, voltage, or impedance can be measured and the part of the biomolecule identified. The gap dimensions can be precisely controlled at the atomic-scale by, for example, atomic layer deposition (ALD) of the sacrificial film. The device can be made using existing integrated circuit fabrication equipment and facilities, and multiple devices can be formed on a single chip.

Claims

1. A device for sequencing a linear biomolecule using quantum tunneling, the device comprising:

a substrate having a top surface;

a first electrode disposed on and in contact with a first portion of the top surface of the substrate;

a first dielectric layer disposed on and in contact with a second portion of the top surface of the substrate, wherein a top surface of the first dielectric layer and a top surface of the first electrode are substantially coplanar;

a second electrode, wherein;

a first portion of the second electrode is disposed on and in contact with the top surface of the first dielectric layer, and

a second portion of the second electrode is suspended over the first electrode, wherein the second portion suspended over the first electrode spans from a first end of the first electrode to an opposite end of the first electrode and is continuous; and

a gap defined by the top surface of the first electrode, a bottom surface of the second electrode, the top surface of the first dielectric layer, a first side surface of the second electrode, and a second side surface of the second electrode, wherein a width of the gap corresponds to a size of the linear biomolecule such that a quantum tunneling current is transmitted between the first electrode and the second electrode when;

a voltage is applied across the first electrode and the second electrode; and

a part of the linear biomolecule is present in the gap;

wherein;

the substrate comprises a second dielectric layer in contact with a bottom surface of the first electrode;

a bottom surface of the first dielectric layer and the bottom surface of the first electrode are substantially coplanar; and

the second dielectric layer is in contact with the bottom surface of the first dielectric layer.

2. The device of claim 1, wherein the substrate comprises a semiconductor substrate on which the second dielectric layer is disposed.

3. The device of claim 1, wherein the width of the gap is 0.8 to 5.0 nm.

4. The device of claim 1, wherein the first electrode and the second electrode are oriented orthogonally to one another.

5. The device of claim 1, further comprising circuitry electrically coupled to the first electrode and the second electrode, wherein the circuitry is configured to:

apply the voltage across the first electrode and the second electrode; and

measure;

the quantum tunneling current transmitted between the first electrode and the second electrode;

the voltage across the first electrode and the second electrode;

or

an impedance between the first electrode and the second electrode.

6. The device of claim 1, wherein the first electrode and the second electrode each individually comprises a material selected from a group consisting of metals, semiconductors, carbon, conductive ceramics, and conductive polymers.

7. The device of claim 1, wherein the first dielectric layer comprises a material selected from the group consisting of oxides, dielectric ceramics, polymers, carbonates, glasses, and minerals.

8. The device of claim 1, wherein:

the bottom surface of the second electrode is between the first side surface of the second electrode and the second side surface of the second electrode,

a first edge of the bottom surface of the second electrode is a first edge of the first side surface of the second electrode, and

a second edge of the bottom surface of the second electrode is a first edge of the second side surface of the second electrode.

9. The device of claim 8, wherein the first electrode is disposed within a cavity of the first dielectric layer such that two side surfaces of the first electrode contact the first dielectric layer.

10. The device of claim 9, wherein an edge of the top surface of the first electrode contacts an edge of the top surface of the first dielectric layer.

11. The device of claim 10, wherein a second edge of the first side surface of the second electrode contacts the top surface of the first dielectric layer.

12. The device of claim 11, wherein a second edge of the second side surface of the second electrode contacts the top surface of the first dielectric layer.

13. The device of claim 1, wherein the gap is formed by:

depositing a sacrificial layer on the top surface of the first electrode,

depositing the second electrode onto the sacrificial layer and onto the top surface of the first dielectric layer, and

removing the sacrificial layer.

14. The device of claim 1, wherein the first dielectric layer comprises a piezoelectric element comprising a material that expands in volume in response to an applied electromagnetic field.

15. The device of claim 1, wherein the first dielectric layer and the second dielectric layer comprise different materials.

16. The device of claim 1, wherein the first electrode consists of gold.

17. The device of claim 1, further comprising a via, wherein the via is disposed through the second dielectric layer and is electrically coupled to the first electrode.

18. A sequencing method comprising:

a) providing the device according to claim 1;

b) applying the voltage across the first electrode and the second electrode;

c) introducing the part of the linear biomolecule into the gap;

d) measuring;

the quantum tunneling current transmitted between the first electrode and the second electrode; and

/or

the voltage across the first electrode and the second electrode; and

/or

an impedance between the first electrode and the second electrode; and

e) identifying, based on the measured quantum tunneling current, the measured voltage, or the measured impedance, the part of the linear biomolecule introduced into the gap.