Harvard College

Oxford Nanopore Technologies Limited

Oxford Nanopore Inc.

Ping Xie

Charles M Lieber

Justin Millis

Xiaojie Duan

Ken Healy

Bozhi Tian

Ruixuan Gao

Qihua Xiong

Ying Fang

Itzhaq Cohen-Karni

Quan Qing

Thomas J Kempa

Steffen Strehle

Xiaocheng Jiang

A nanopore sensor includes a nanopore disposed in a support structure with a nanopore diameter and having a nanopore fluidic resistance, R. A fluidic passage, is disposed in fluidic connection between a first fluidic reservoir of ionic concentration solution and the nanopore, and includes a passage length having a fluidic passage width, along at least a portion of a fluidic passage length, that is greater than the diameter of the nanopore and less than the fluidic passage length. The fluidic passage has a fluidic passage fluidic resistance, R, of at least about 10% of the nanopore fluidic resistance, R, and no more than about 10 times the nanopore fluidic resistance, R. The nanopore is disposed in fluidic connection between the fluidic passage and a second fluidic reservoir of ionic concentration solution. At least one transistor is operatively connected electrically to sense electrical potential local to the fluidic passage.

Nanopore sensor having a fluidic passage and transistor sensing of local electrical potential at the fluidic passage

Devices for improved nanopore sensing are described. An example device has a structure arranged to separate an analyte reservoir and an outlet chamber. An example device has a structure arranged to separate an analyte reservoir and an outlet chamber. The structure can include an array of nanopore structures, each nanopore structure comprising a passage for fluid connection through the structure between the analyte reservoir and outlet chamber. Control terminals can be arranged for applying a control signal to alter the electrical potential difference across that nanopore structure. Some embodiments include an electronic circuit configured to detect a signal from an electrical transduction element at each nanopore structure. Additional structural features and methods of operating and making the devices are described.

Nanopore sensing device, components and method of operation

A first fluidic solution having a first ionic concentration is provided in a first fluidic reservoir in direct fluidic connection with a nanopore. A second fluidic solution, having a second ionic concentration, is provided in a second fluidic reservoir disposed in fluidic connection with the nanopore through a fluidic passage having at least one fluidic section in which the section length is greater than the section width. The electrical potential local to the fluidic passage is measured, and the resistance of both the fluidic passage the nanopore are determined based on the fluidic passage electrical potential. The fluidic passage resistance is compared with the nanopore resistance and at least one of the first and second ionic concentrations is adjusted based on the comparison. The measuring, determining, comparing, and adjusting steps are conducted until the fluidic passage resistance is between about 0.1 times and about 10 times the nanopore resistance.

Nanopore sensor calibration and operation with a fluidic passage

Methods and apparatus for forming apertures in a solid state membrane using dielectric breakdown are provided. In one disclosed arrangement a plurality of apertures are formed. The membrane comprises a first surface area portion on one side of the membrane and a second surface area portion on the other side of the membrane. Each of a plurality of target regions comprises a recess or a fluidic passage opening out into the first or second surface area portion. The method comprises contacting all of the first surface area portion of the membrane with a first bath comprising ionic solution and all of the second surface area portion with a second bath comprising ionic solution. A voltage is applied across the membrane via first and second electrodes in respective contact with the first and second baths comprising ionic solutions to form an aperture at each of a plurality of the target regions in the membrane.

Methods and apparatus for forming apertures in a solid state membrane using dielectric breakdown

In a method for sensing translocation of a molecule through a nanopore, a molecule in a first fluidic solution in a first fluidic reservoir that is in direct fluidic connection with the nanopore is directed to a nanopore inlet and translocated through the nanopore to a nanopore outlet and through a fluidic passage that is in direct fluidic connection with the nanopore outlet, to a second fluidic solution in a second fluidic reservoir disposed in direct fluidic connection with the fluidic passage. The fluidic passage has at least one fluidic section in which a length of the fluidic section is greater than a width of the fluidic section. Translocation of the molecule through the nanopore is sensed by measuring the electrical potential local to the fluidic passage during the translocation of the molecule.

Nanopore sensing with a fluidic passage

In a nanopore sensor, a nanopore disposed in a support structure has a nanopore diameter and nanopore resistance, R. A fluidic passage, disposed in fluidic connection between a first fluidic reservoir and the nanopore, has a cross-sectional extent, along at least a portion of the fluidic passage length, that is greater than the diameter of the nanopore and that is less than the fluidic passage length. The fluidic passage has a fluidic passage resistance, R, of at least about 10% of the nanopore resistance, R, and no more than about 10 times the nanopore resistance, R. The nanopore is disposed in fluidic connection between the fluidic passage and a second fluidic reservoir. At least one electrical transduction element is disposed at the fluidic passage and electrically connected to produce an indication of electrical potential local to the fluidic passage.

Nanopore sensor having a fluidic passage for local electrical potential measurement

To sense the translocation of a molecule through a nanopore, there is directed to an inlet of the nanopore, having a nanopore fluidic resistance, R, a molecule disposed in a cis fluidic ionic solution having a cis fluidic access resistance, R. The molecule is caused to translocate through the nanopore from the inlet of the nanopore to an outlet of the nanopore and to a trans fluidic ionic solution having a trans fluidic access resistance, R. The trans fluidic access resistance, R, is of the same order of magnitude as the nanopore fluidic resistance, R, and both Rand Rare at least an order of magnitude greater than the cis fluidic access resistance, R. An indication of local electrical potential is produced at a site within the nanopore sensor that is on the trans fluidic ionic solution-side of the nanopore, to sense translocation of the molecule through the nanopore.

Method for nanopore sensing with local electrical potential measurement

There is provided a nanopore sensor including cis and trans fluidic reservoirs. A nanopore is provided in a support structure separating the cis and trans reservoirs. The nanopore has an inlet in fluidic connection with the cis fluidic reservoir and an outlet in fluidic connection with the trans fluidic reservoir. The cis fluidic reservoir has a fluidic access resistance, R, the trans fluidic reservoir has a fluidic access resistance, R, and the nanopore has a fluidic resistance, R. Ris of the same order of magnitude as Rand both Rand Rare at least an order of magnitude greater than R. An electrical transduction element is disposed at a nanopore sensor site that exposes the transduction element to the trans reservoir. An electrical circuit is connected to the electrical transduction element for producing an electrical signal indicative of changes in electrical potential local to the trans reservoir.

Nanopore sensing by local electrical potential measurement

There is provided a multi-channel nanopore sensor having a plurality of independent nanopore sensors. Each independent nanopore sensor includes a nanopore disposed in a support structure. A fluidic connection is between a first fluidic reservoir, common to all of the independent nanopore sensors, and an inlet to the nanopore, with a first ionic solution of a first ionic concentration disposed in the first fluidic reservoir. A fluidic connection is between a second fluidic reservoir, common to all of the independent nanopore sensors, and an outlet from the nanopore, with a second ionic solution of a second ionic concentration, different than the first ionic concentration, disposed in the second fluidic reservoir. An electrical transduction element, disposed in contact with that ionic solution having a lower ionic concentration, is arranged at a site that produces an electrical signal indicative of electrical potential local to that ionic solution having a lower ionic concentration.

Multi-channel nanopore sensing by local electrical potential measurement

A nanopore sensor is provided, including a nanopore disposed in a support structure. A fluidic passage is disposed between a first fluidic reservoir and the nanopore to fluidically connect the first fluidic reservoir to the nanopore through the fluidic passage. The fluidic passage has a passage length that is greater than the passage width. A second fluidic reservoir is fluidically connected to the nanopore, with the nanopore providing fluidic communication between the fluidic passage the second reservoir. Electrodes are connected to impose an electrical potential difference across the nanopore. At least one electrical transduction element is disposed in the nanopore sensor with a connection to measure the electrical potential that is local to the fluidic passage.

Nanopore sensor including fluidic passage

There is provided a method for sensing the translocation of a molecule through a nanopore. In the method, there is directed to an inlet of a nanopore a molecule that is disposed in a first ionic solution of a first ionic concentration. The molecule is caused to translocate through the nanopore from the inlet of the nanopore to an outlet of the nanopore and into a second ionic solution of a second ionic concentration that is different than the first ionic concentration. An electrical potential, local to that ionic solution, of the first and second ionic solutions, which has a lower ionic concentration, is measured while the molecule is caused to translocate through the nanopore.

A solid state molecular sensor having an aperture extending through a thickness of a sensing material is configured with a continuous electrically-conducting path extending in the sensing material around the aperture. A supply reservoir is connected to provide a molecular species, having a molecular length, from the supply reservoir to an input port of the aperture. A collection reservoir is connected to collect the molecular species from an output port of the aperture after translocation of the molecular species from the supply reservoir through the sensing aperture. The sensing aperture has a length between the input and output ports, in the sensing material, that is substantially no greater than the molecular length of the molecular species from the supply reservoir. An electrical connection to the sensing material measures a change in an electrical characteristic of the sensing material during the molecular species translocation through the aperture.

High-resolution molecular sensor

There is provided a nanopore disposed in a support structure, with a fluidic connection between a first fluidic reservoir and an inlet to the nanopore and a second fluidic connection between a second fluidic reservoir and an outlet from the nanopore. A first ionic solution of a first buffer concentration is disposed in the first reservoir and a second ionic solution of a second buffer concentration, different than the first concentration, is disposed in the second reservoir, with the nanopore providing the sole path of fluidic communication between the first and second reservoirs. An electrical connection is disposed at a location in the nanopore sensor that develops an electrical signal indicative of electrical potential local to at least one site in the nanopore sensor as an object translocates through the nanopore between the two reservoirs.

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Needham, MA, United States of America

Ping Xie