Nanopore arrays

• US 10,012,637 B2
• Filed: 03/17/2017
• Issued: 07/03/2018
• Est. Priority Date: 02/05/2013
• Status: Active Grant

• Current Assignee: Roche Sequencing Solutions, Inc. (Roche Holding AG)
• Original Assignee: Genia Technologies, Inc. (Roche Holding AG)
• Inventors: Chen, Roger J. A., Fullagar, David J.
• Primary Examiner(s): Dines, Karla A
• Application Number:
  US15/462,483
• Publication Number:
  US 20170254797A1
• Time in Patent Office: 473 Days
• Field of Search: 435 611, 204450, 506 12
• 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: G11C 16/34 Determination of programming status, e.g. threshold voltage, overprogramming or underprogramming, retention
• CPC Class Codes: G11C 7/00 Arrangements for writing information into, or reading information out from, a digital store G11C5/00 takes precedence; auxiliary circuits for stores using semiconductor devices G11C11/4063, G11C11/413

Abstract

A method of analyzing molecules using a nanopore array including a plurality of cells included on a chip is disclosed. Nanopores are caused to be formed in at least a portion of the plurality of the cells. A first physical measurement of the nanopores is evaluated. It is determined whether to cause the molecules to interact with the nanopores. At least a portion of the nanopores is caused to interact with the molecules. A second physical measurement of the nanopores that indicates a property of the molecules is evaluated. It is determined whether to cause the nanopores to be reformed so that the cells may be reused to interact with additional molecules.

Claims

1. A system for analyzing molecules using a chip comprising a nanopore array comprising a plurality of cells, comprising:

a processor configured to;

cause one nanopore to be formed in each of at least a portion of the plurality of the cells;

receive a first electrical measurement from each of the plurality of the cells, wherein the first electrical measurement is sensed by an electrical circuit in the particular cell; and

determine formation of one nanopore in each of at least a threshold number of cells based at least in part on the sensed first electrical measurements, wherein the threshold number of cells comprise a portion of the plurality of the cells, and in the event that formation of one nanopore in each of at least the threshold number of cells is determined within a fixed period, begin to cause the molecules to interact with the formed nanopores, comprising;

disabling the cells that have been determined as not having one formed nanopore, comprising disabling each of the disabled cells from drawing a current to the particular disabled cell;

causing the molecules to interact with the formed nanopores in the cells that are not disabled; and

receiving from each of the cells that have been determined as having one formed nanopore a second electrical measurement, wherein the second electrical measurement is sensed by the electrical circuit in the particular cell, and determining a property of the molecules based at least in part on the second electrical measurement; and

a memory coupled to the processor and configured to provide the processor with instructions.

2. The system of claim 1, wherein causing the molecules to interact with the formed nanopores in the cells that are not disabled comprises sending signals by the processor to the chip.

3. The system of claim 1, wherein causing one nanopore to be formed in each of at least a portion of the plurality of the cells comprises:

causing lipid bilayers to be formed;

receiving a third electrical measurement from each of the plurality of the cells, wherein the third electrical measurement is sensed by the electrical circuit in the particular cell;

determining whether to begin to cause the nanopores to be formed, wherein the nanopores are formed in at least a portion of the lipid bilayers.

4. The system of claim 3, wherein causing lipid bilayers to be formed comprises causing a lipid bilayer forming reagent to be deposited within the plurality of cells.

5. The system of claim 3, wherein determining whether to begin to cause the nanopores to be formed comprises determining formation of one lipid bilayer in each of at least a second threshold number of cells based at least in part on the sensed third electrical measurements.

6. The system of claim 1, wherein the processor is further configured to determine a state for each cell.

7. The system of claim 6, wherein a state for each cell includes one of the following:

a lipid bilayer is not formed, a lipid bilayer is formed, and a nanopore is formed.

8. The system of claim 6, wherein the determining of the state for each cell is based at least in part on a measurement received from the nanopore array.

9. The system of claim 1, wherein the processor is further configured to:

determine that a particular cell is mal-functioning; and

cause the cell to be disabled and at least some other cells to remain enabled.

10. The system of claim 1, wherein the processor is further configured to cause a first stimulus to be applied to a first group of cells and cause a second stimulus to be applied to a second group of cells.

11. The system of claim 1, wherein causing one nanopore to be formed in each of at least a portion of the plurality of the cells comprises causing a nanopore forming reagent to be deposited within the plurality of cells.

12. The system of claim 1, wherein causing the molecules to interact with the formed nanopores comprises causing the molecules to be deposited within the plurality of cells.

13. The system of claim 1, wherein the processor is further configured to determine whether to begin to cause the nanopores to be reformed so that the cells with the reformed nanopores may be reused to interact with additional molecules.

14. The system of claim 13, wherein causing the nanopores to be reformed comprises causing contents in one or more cells to be flushed out of the cells.

15. The system of claim 13, wherein causing the nanopores to be reformed comprises causing one or more cells to be rinsed.

16. The system of claim 13, wherein the processor is further configured to cause a detection of any contents of interest in the cells.

17. The system of claim 16, wherein the processor is further configured to cause the detected contents of interest to be extracted from the cells.