Nanopore arrays

• US 9,759,711 B2
• Filed: 02/05/2013
• Issued: 09/12/2017
• 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:
  US13/759,701
• Publication Number:
  US 20140221249A1
• Time in Patent Office: 1,680 Days
• Field of Search: 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 method of analyzing molecules using a nanopore array including a plurality of cells included on a semiconductor chip, comprising:

causing one nanopore to be formed in a lipid bilayer formed in each of at least a portion of the plurality of the cells, comprising delivering a nanopore forming reagent by a fluidic system to the plurality of cells such that one nanopore may be formed in each of the at least a portion of the plurality of the cells, wherein the plurality of the cells comprises a thousand or more cells;

in each of the plurality of the cells;

applying by a pair of electrodes and an electrical circuit a first electrical stimulus, wherein the first electrical stimulus is applied across a lipid bilayer if it has been formed in the particular cell, and sensing by the electrical circuit a first electrical measurement in response to the first electrical stimulus; and

determining by a processor 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 not determined within a fixed period, terminating the method, and in the event that formation of one nanopore in each of at least the threshold number of cells is determined within the fixed period, begin causing 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 and disabling any subsequent electrical stimulus from being applied to the particular disabled cell;

causing the molecules to interact with the formed nanopores in the cells that are not disabled, comprising delivering by the fluidic system a solution containing the molecules to the plurality of cells such that the molecules may interact with the formed nanopores;

in each of the cells that have been determined as having one formed nanopore;

applying, by the pair of electrodes and the electrical circuit a second electrical stimulus, sensing by the electrical circuit a second electrical measurement in response to the second electrical stimulus, and determining a property of the molecules based at least in part on the second electrical measurement; and

determining 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.

2. The method of claim 1, wherein causing the molecules to interact with the formed nanopores in the cells that are not disabled comprises sending signals from a master controller to the chip.

3. The method 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;

in each of the plurality of the cells, sensing by the electrical circuit a third electrical measurement; and

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 method 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 method of claim 3, wherein determining whether to begin to cause the nanopores to be formed comprises determining by the processor 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 method of claim 1, further comprising determining a state for each cell.

7. The method of claim 6, wherein the 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 method 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 method of claim 1, further comprising:

determining that a particular cell is mal-functioning; and

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

10. The method of claim 1, further comprising causing a first stimulus to be applied to a first group of cells and causing a second stimulus to be applied to a second group of cells.

11. The method of claim 1, wherein causing the nanopores to be reformed so that the cells with the reformed nanopores may be reused to interact with additional molecules comprises:

causing a detection of any contents of interest in the cells; and

in response to the detection of any contents of interest in the cells, causing the contents of interest to be flushed out of the cells by the fluidic system into a storage device prior to causing the nanopores to be reformed.

12. The method of claim 1, wherein causing the nanopores to be reformed comprises causing one or more cells to be rinsed.

13. The method of claim 1, further comprising causing a detection of any contents of interest in the cells.

14. The method of claim 13, further comprising causing the detected contents of interest to be extracted from the cells.