WO2025238377A1

WO2025238377A1 - A flow cell with a light shield and a method

Info

Publication number: WO2025238377A1
Application number: PCT/GB2025/051069
Authority: WO
Inventors: Paul MACKETT; Steven Ireland
Original assignee: Oxford Nanopore Technologies PLC
Current assignee: Oxford Nanopore Technologies PLC
Priority date: 2024-05-17
Filing date: 2025-05-16
Publication date: 2025-11-20
Anticipated expiration: 2026-11-17
Also published as: GB202407100D0

Abstract

A flow cell for use as part of a nanopore array device is described. The flow cell comprises a main body defining a sensing chamber, an array of nanopore sensing elements located within the sensing chamber, and a light shield for inhibiting passage of light. The light shield is moveable relative to the sensing chamber to vary an amount of light that can reach the array of nanopore sensing elements.

Description

A FLOW CELL WITH A LIGHT SHIELD AND A METHOD

FIELD OF THE APPLICATION

The present application relates to a flow cell for use as part of a nanopore array device and a method.

BACKGROUND

The use of nanopores to sense interactions with molecular entities, for example polynucleotides is a powerful technique that has been subject to much recent development. Nanopore array devices have been developed that comprise an array of nanopore sensing elements, thereby increasing data collection by allowing plural nanopore sensing elements to sense interactions in parallel, typically from the same sample.

Nanopore sensing elements may typically employ an electrical signal across a nanopore channel to generate a measurement signal that is interpreted to sense and/or characterise molecular entities as they interact with the nanopore channel. Typically, an electrical signal is applied as a potential difference or current across the nanopore channel that will provide a meaningful measurement signal to be interpreted. The measurement can include, for example, one of ionic current flow, electrical resistance, or voltage. An example of such a device is Oxford Nanopore Technology’s MinlON sequencer, which performs DNA and RNA sequencing.

The flow cell is the part of the nanopore array device which comprises a sensing chamber within which is located the sensor which senses the liquid. An example of a flow cell is Oxford Nanopore Technologies’ MinlON Flow Cell, which comprises a sensor comprising an array of nanopore sensing elements, and electronics for processing a signal produced by the sensor. The MinlON Flow Cell is for use as part of Oxford Nanopore Technology’s MinlON sequencer. The MinlON comprises additional electronics for performing further processing of the signal produced by the sensor. Flow cells are often consumable parts. SUMMARY

A first aspect provides a flow cell for use as part of a nanopore array device, the flow cell comprising: a main body defining a sensing chamber, the main body comprising a surface through which light can pass into the sensing chamber; an array of nanopore sensing elements located within the sensing chamber; and a light shield for inhibiting passage of light through the surface, wherein the light shield is moveable relative to the sensing chamber to vary an amount of light that can reach the array of nanopore sensing elements.

Providing the light shield as part of the flow cell, rather than on a separate part of the nanopore array device may enable existing nanopore array devices which do not have a separate light shield to use the flow cell and thereby benefit from the use of the light shield (discussed further below). In nanopore array devices which have multiple flow cells (and corresponding array of nanopore sensing elements), this may enable the user to block light from reaching some of the array of nanopore sensing elements, whilst allowing light to reach other of the array of nanopore sensing elements. This may be desirable when the multiple flow cells are operating on different schedules to one another.

Providing a light shield may enable a user to vary the amount of light which can reach the nanopore based on the different requirements of the stages of using the flow cell. For example, when loading a liquid into the sensing chamber, it may be desirable to allow light to reach the array of nanopore sensing elements so that the user can check if there are air bubbles present in the array of nanopore sensing elements. The presence of air bubbles may degrade the performance of the array of nanopore sensing elements. When running a test on the flow cell, it may be desirable to reduce the amount of light which can reach the array of nanopore sensing elements because the performance of the array of nanopore sensing elements may be affected by the amount of light to which it is exposed. Without wishing to be bound by theory, this may be due to the presence of light affecting the function of components of the array of nanopore sensing elements. For example, light may reduce the activity of enzymes which move the liquid through the array of nanopore sensing elements.

Optionally, the main body comprises a transparent material.

Optionally, the light shield is formed from an opaque material. Forming the light shield from an opaque material may provide a simple means for the light shield to inhibit the passage of light.

Optionally, the light shield comprises a polariser; and movement of the light shield relative to the sensing chamber causes the polariser to move relative to the sensing chamber to vary the amount of light that can reach the array of nanopore sensing elements.

Optionally, the flow cell comprises a guide configured to guide the movement of the light shield relative to the sensing chamber to vary the amount of light which can reach the array of nanopore sensing elements. As a result, the light shield may be easier to move into a desired position by the user, which may make the flow cell easier to use than if the guide were omitted.

Optionally, the guide comprises a recess configured to receive the light shield; and the light shield is located within the recess. The recess may provide a simple to manufacture and space efficient means for guiding the motion of the light shield.

Optionally, the light shield is moveable relative to the sensing chamber along a first axis to vary the amount of light which can reach the array of nanopore sensing elements; the guide comprises a fin and a groove; the fin is comprised by one of the main body and the light shield; the groove is comprised by the other of the main body and the light shield; and the fin is located within the groove such that movement of the light shield relative to the sensing chamber along a second axis, perpendicular to the first axis, is inhibited. Thereby, the movement of the light shield may be more easily constrained than if the fin and the groove were omitted, which may improve the ease of use of the nanopore array device.

Optionally, the first axis and the second axis extend in the horizontal plane.

Optionally, the light shield is slidable relative to the sensing chamber. Sliding may provide a more compact design for the light shield, and thereby the light shield may be more easily accommodated within the space constraints of the flow cell, than other forms of motion such as if the light shield were pivotable relative to the sensing chamber.

Optionally, the light shield is slidable in the horizontal plane.

Optionally, the flow cell comprises a valve moveable between: an open position in which; and a closed position; and the light shield is coupled to the valve such that movement of the valve causes movement of the light shield relative to the sensing chamber. This may reduce the number of operations the user is required to perform and thereby make the flow cell easier to use, relative to the light shield and valve not being coupled to one another, because the user may only need to move the valve rather than having to move both the valve and the light shield during operation of the flow cell.

Optionally, the flow cell comprises a sensing chamber inlet for allowing a liquid to enter the sensing chamber; a sensing chamber outlet for allowing the liquid to exit the sensing chamber. Optionally, when the valve is in the open position, the valve allows at least one of the liquid to flow through the sensing chamber inlet and the liquid to flow through the sample chamber outlet. Optionally, when the valve is in the closed position, the valve inhibits at least one of the liquid from flowing through the sensing chamber inlet and the liquid from flowing through the sample chamber outlet.

Optionally, the light shield is coupled to the valve such that a movement of the valve from the closed position to the open position causes the light shield to move from the covered position to the uncovered position. Optionally, the light shield is coupled to the valve such that a movement of the valve from the open position to the closed position causes the light shield to move from the uncovered position to the covered position.

Optionally, the light shield and the valve are separate components. Providing the valve and light shield as separate components may enable greater design flexibility when compared to the light shield and valve being a single, integrally formed, component. This greater design flexibility may enable the light shield and the valve to be more easily accommodated within the space constraints on a flow cell, which may typically be tight.

Optionally, one of the light shield and the valve comprises a projection; the other of the light shield and the valve comprises a slot configured to receive the projection and couple the light shield to the valve such that the movement of the valve causes the movement of the light shield relative to the sensing chamber to vary the amount of light which can reach the array of nanopore sensing elements. Using a slot and a projection to couple the valve to the light shield may provide a simple to manufacture and robust mechanism for coupling the valve to the light shield. Optionally, one of the light shield and the valve is configured to move linearly; and the other of the light shield and the valve is configured to rotate. The different rotational and linear motions of the light shield and the valve may be dictated by the space constraints and location of other components of the flow cell. The slot and projection may provide a convenient means for coupling the light shield to the valve whilst accommodating the different rotational and linear motions.

Optionally, the light shield is configured to abut the valve to couple the light shield to the valve such that movement of the valve causes movement of the light shield relative to the sensing chamber to vary the amount of light which can reach the array of nanopore sensing elements. Abutting the valve with the light shield may prove a simple means of coupling the movement of the valve to the movement of the light shield.

Optionally, the light shield is moveable between: an uncovered position in which a first amount of light can reach the array of nanopore sensing elements; and a covered position in which a second amount of light can reach the array of nanopore sensing elements; and the second amount of light is no greater than 50% of the first amount of light. The performance of the array of nanopore sensing elements may improve as the amount of light which can reach the nanopore, when the light shield is in the covered position, decreases. Therefore, by the second amount of light being no greater than 50% of the first amount of light, the performance of the array of nanopore sensing elements may be improved to a greater extent than if the second amount of light were greater than 50% of the first amount of light.

Optionally, the second amount of light is no greater than 40%, 30%. 20%, 10%, 5%, 1%, or 0.1% of the first amount of light. Optionally, in the covered position, no light can reach the array of nanopore sensing elements.

Optionally, when the light shield is in the uncovered position, the light shield overlies no greater than 20% of a total surface area of the array of nanopore sensing elements when viewed in a horizontal plane. This may make air bubbles easier to detect than if the light shield overlies a greater amount of the array of nanopore sensing elements when in the uncovered position, and thereby improve the functionality of the flow cell.

Optionally, when the light shield is in the uncovered position, the light shield overlies no greater than 10%, 5%, 1%, or 0.1% of the total surface area of the array of nanopore sensing elements when viewed in the horizontal plane. Optionally, when in the uncovered position, the light shield does not overlie any part of the array of nanopore sensing elements when viewed in the horizontal plane.

The horizontal plane is horizontal when the flow cell is placed on a horizontal surface in an intended use configuration.

Optionally, when the light shield is in the covered position, the light shield overlies no less than 80% of a total surface area of the array of nanopore sensing elements when viewed in a horizontal plane. Thereby, the performance of the array of nanopore sensing elements may be improved to a greater extent than if the light shield overlies a lesser amount of the total surface area of the array of nanopore sensing elements.

Optionally, when the light shield is in the covered position, the light shield overlies no less than 85%, 90%, 95%, 99%, or 99.9% of the total surface area of the array of nanopore sensing elements when viewed in the horizontal plane. Optionally, when the light shield is in the uncovered position, the light shield overlies all of the total surface area of the array of nanopore sensing elements when viewed in the horizontal plane.

Optionally, the array of nanopore sensing elements has a total surface area measured in a horizontal plane; and the light shield has a total surface area measured in the horizontal plane which is no greater than 200% of the total surface area of the array of nanopore sensing elements. A more compact light shield may be more easily integrated onto the flow cell, which are typically subject to tight space constraints, and may be easier for the user to use.

Optionally, the total surface area of the light shield measured in the horizontal plane is no greater than 150%, 125%, 110%, 105%, or 100% of the total surface area of the array of nanopore sensing elements.

Optionally, the total surface area of the light shield measured in the horizontal plane is no less than 100% of the total surface area of the array of nanopore sensing elements. As a result, the light shield may completely cover the array of nanopore sensing elements when in the covered position. Optionally, the nanopore array device comprises a bubble sensor configured to detect a bubble in the sensing chamber. This may improve the likelihood of the bubble being detected when compared with the bubble sensor being omitted.

Optionally, the bubble sensor is configured to detect the bubble in the sensing chamber when the light shield is in the covered position. Thereby, the bubble may still be detectable when the light shield is in the covered position, and thereby when the user may be unable to detect the bubble themselves.

Optionally, the main body has a maximum length of no greater than 120mm. Optionally, the main body has a maximum width of no greater than 40mm. Optionally, the main body has a maximum height of no greater than 30mm.

Optionally, the maximum dimension is a length of the flow cell measured in the horizontal plane.

A second aspect provides a nanopore array device comprising the flow cell according to the first aspect.

Optionally, the light shield comprises a polariser; and a further light shield comprising a further polariser, wherein the light shield and the further light shield are configured such that light which passes through the further polariser is attenuated by the polariser. Thereby, the light shield and further light shield may reduce the amount of light which can reach the nanopore to a greater extent than if the further light shield were omitted.

Optionally, the polariser comprises a first polarisation axis; the further polariser comprises a second polarisation axis; and the first polarisation axis is angularly offset from the second polarisation axis. Optionally, the polarisation axis of the polariser is angularly offset from the polarisation axis of the further polariser when viewed in parallel reference planes. Optionally, the parallel reference planes are parallel to the horizontal plane.

Optionally, the nanopore array device may comprise a plurality of flow cells as claimed in any one of the preceding claims.

Optionally, the nanopore array device comprises a lid; the lid comprises the further light shield; and opening and closing the lid causes the further light shield to move relative to the light shield to vary the amount of light which can reach the array of nanopore sensing elements.

Optionally, the polariser and the further polariser are crossed. As a result, the polarisers may attenuate substantially all external light from reaching the array of nanopore sensing elements.

Optionally, the polarisation axis of the polariser is orthogonal to the polarisation axis of the further polariser.

According to a third aspect of the present invention, there is provided a nanopore array device comprising: a flow cell comprising: a main body defining a sensing chamber; a array of nanopore sensing elements located within the sensing chamber; and a light shield comprising a polariser, a further light shield comprising a further polariser, wherein: the light shield and the further light shield are configured such that light which passes through the further polariser is attenuated by the polariser; and the further light shield is moveable relative to the light shield to vary an amount of light which can reach the array of nanopore sensing elements. Using two polarisers may provide a convenient means for varying the amount of light which can reach the array of nanopore sensing elements. The benefits of varying the amount of light which can reach the array of nanopore sensing elements have been discussed above.

Optionally, the nanopore array device comprises a lid; the lid comprises the further light shield; and opening and closing the lid causes the further light shield to move relative to the light shield to vary the amount of light which can reach the array of nanopore sensing elements. The user may raise the lid when loading the liquid into the sensing chamber. This will move the further light shield (and thereby the further polariser) relative to the light shield (and thereby the polariser) and may allow light to reach the array of nanopore sensing elements so that the user can check if there are air bubbles present in the array of nanopore sensing elements. The user may then shut the lid when running a test on the flow cell, which will move the further light shield relative to the light shield. This may result in the amount of light which can reach the nanopore reducing and thereby may improve the performance of the array of nanopore sensing elements when running the test.

Optionally, the polariser and the further polariser are crossed. Optionally, the polarisation axis of the polariser is orthogonal to the polarisation axis of the further polariser.

Optionally, the further light shield is moveable relative to the light shield to vary an amount of light which can reach the array of nanopore sensing elements by varying the angular offset between the polarisation axis and the further polarisation axis.

According to a fourth aspect of the present invention, there is provided a method comprising: providing a flow cell for use as part of a nanopore array device according to the first aspect of the present invention; and moving the light shield relative to the sensing chamber to vary an amount of light that can reach the array of nanopore sensing elements.

The array of nanopore sensing elements comprises an array of nanopores provided in a corresponding array of membranes. Each membrane may have a single nanopore inserted into it. The nanopore may typically be a protein nanopore provided in an amphipathic membrane wherein the nanopore provides a channel through the membrane extending from one side to the other. The membrane is typically supported on a support structure separating a cis chamber from a trans chamber. An array of support structures for supporting the array of membranes may have a common cis chamber and an array of trans chambers. The flow cell may be provided with an ionic liquid in the cis chamber covering the nanopores and ionic liquids in the trans chambers. During use, the ionic liquid in the cis chamber may be removed or displaced by a liquid containing the analyte to be sensed by the nanopore array. The cis and trans chambers may contain respective electrodes and ionic flow through the membrane may be measured over time during translocation of the analyte through a nanopore under an applied potential difference across the nanopore. The ionic liquid may comprise an alkali metal halide such as potassium or rubidium chloride. The ionic liquid may further comprise a buffer such as HEPES or Tris-HCl buffer. The pH may vary from 4.0 to 12.0 and is preferably about 7.5. The analyte may for example comprise a polynucleotide, a polypeptide, a protein or a polysaccharide. The polynucleotide may be chosen for example from DNA or RNA. The polynucleotide may be made up of deoxyribonucleotide bases or ribonucleotide bases. Nucleic acids may also include synthetic nucleic acids (XNA), such as hexitol nucleic acid (HNA), cyclohexene nucleic acid (CeNA), threose nucleic acid (TNA), glycerol nucleic acid (GNA), locked nucleic acid (LNA) and peptide nucleic acid (PNA). The translocation of the analyte through the nanopore may be controlled, for example by a binding protein. Suitable polynucleotide binding proteins for controlling translocation of polynucleotides for use in the flow cell are known in the art and include polymerases, exonucleases, helicases and topoisomerases. A preferred enzyme is a helicase which may be or be derived from a Hel308 helicase, a RecD helicase, such as Tral helicase or a TrwC helicase, a XPD helicase or a Dda helicase. The helicase may be any of the helicases, modified helicases or helicase constructs disclosed in WO2013/057495, WO 2013/098562, WO2013098561, WO 2014/013259; WO 2014/013262 and WO 2014013260. Binding proteins such as unfoldases are also known in the art and may be used for controlling the translocation of polypeptides through a nanopore.

The flow-cell may comprise, during use, the binding protein and/or the analyte.

The protein nanopore may be selected for example from a number of known pores such as those derived from P-barrel pores or a-helix bundle pores, such as a-hemolysin, anthrax toxin and leukocidins, and outer membrane proteins/porins of bacteria, such as Mycobacterium smegmatis porin (Msp). The transmembrane protein pore may be derived from derived from Spl or haemolytic protein fragaceatoxin C (FraC). The pore may be derived from CsgG, examples of which are disclosed in WO 2016/034591.

The amphipathic membrane may be chosen for example from a lipid bilayer or polymer. The polymer may be a di or triblock copolymer such as disclosed in WO2014064444 and US6723814.

Optional features of aspects may be equally applied to other aspects, where appropriate. BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 is a perspective view of an example sequencing instrument;

Figure 2 is a perspective view of a flow cell of the example sequencing instrument;

Figure 3 is a perspective view of a bottom surface of the flow cell;

Figure 4 is a perspective view of a main body of the flow cell;

Figure 5 is a top down view of a sensing chamber, a connection channel, a waste collection channel, a waste channel, and a sensor of the flow cell;

Figure 6 is a magnified view of part of the top surface of the flow cell;

Figure 7 is enlarged top down view of a contact surface of the top surface of the main body of the flow cell;

Figure 8 is a sectioned view of the main body of the flow cell along a plane which is parallel to a vertical plane;

Figure 9 is an enlarged perspective view of a guide recess of the top surface of the main body of the flow cell;

Figure 10 is a schematic diagram of the sensor;

Figure 11 is a perspective view of a valve of the flow cell;

Figure 12 is a bottom plan view of a bottom surface of the valve;

Figure 13 is a perspective view of the valve;

Figure 14 is a perspective view of a light shield of the flow cell;

Figure 15 is a top down view of the light shield;

Figure 16 is a perspective view of a base of the example sequencing instrument;

Figure 17 is a top down view of the flow cell in a first configuration; Figure 18 is an enlarged sectioned view of the flow cell along a vertical plane;

Figure 19 is a top down view of the flow cell with the valve located in a closed position and the light shield in a covered position;

Figure 20 is a sectioned view of the flow cell along a plane which is parallel to the vertical plane of the flow cell;

Figure 21 is a top down view of the flow cell with the valve located in an open position and the light shield in an uncovered position;

Figure 22 is a top down view of some of the components of the main body of the flow cell and a sectioned view of the valve, when the valve is in the open position;

Figure 23 is a top down view of some of the components of the main body of the flow cell and a sectioned view of the valve, when the valve is in the closed position;

Figure 24 is a schematic diagram of a lid polariser and a light shield polariser of an alternative example sequencing instrument;

Figure 25 is a flow chart showing steps of an example method for manufacturing the main body of the flow cell;

Figure 26 is a perspective view of an upper part of the main body of the flow cell;

Figure 27 is a perspective view of a lower part of the main body of the flow cell

Figure 28 is a flow chart showing steps of a first method;

Figure 29 is a flow chart showing steps of a second method; and

Figure 30 is a flow chart showing steps of a third method.

DETAILED DESCRIPTION

Figure 1 shows a sequencing instrument 1 (which is an example of a nanopore array device) having a flow cell 3 and a base 5. Figure 1 also shows the relative orientation between the sequencing instrument 1 and a vertical axis 2, a length axis 4, a width axis 6, a horizontal plane 8, which extends along the length axis 4 and the width axis 6, and a vertical plane 10, which extends along the vertical axis 2 and the width axis 6.

The flow cell 3 (shown in isolation in Figure 2 and Figure 3) has a main body 7, a sensor 9 (shown in Figure 5), an Application Specific Integrated Circuit (ASIC) 11 (shown in Figure 10), a common electrode 13 (shown in Figure 5), a bubble sensor 15 (shown in Figure 5), a valve 17, a light shield 19, and an electrical connector 21.

The main body 7 of the flow cell 3 (shown in isolation in Figure 4 and Figure 5) has a top surface 23, a bottom surface 25, a sensing chamber 27, a connection channel 29, a waste collection channel 31, and a waste channel 33. The sensing chamber 27 and the channels 27,29,31,33 are shown in isolation along with the sensor 9, the bubble sensor 15, and the common electrode 13 in Figure 5. The main body 7 of the flow cell 3 has a maximum width 35 of 28.3mm and a maximum length 37 of 93.5mm, measured in a plane parallel to the horizontal plane 8, and a maximum height 39 of 11.5mm, measured in a plane parallel to the vertical plane 10. A maximum width 35 of no greater than 40mm, a maximum length 37 of no greater than 120mm, and a maximum height 39 of no greater than 30 is also envisaged.

The top surface 23 of the main body 7 of the flow cell 3 has a contact surface 41, a first overhang 43, a second overhang 45, a first stop 47, a second stop 49, a guide recess 51, a fin 53, and a clip recess 55. The top surface 23 of the main body 7 of the flow cell 3 is formed from transparent Cyclic Olefin Copolymer (COC).

The contact surface 41 (enlarged views of which is shown in Figure 6 and Figure 7) is defined on the top surface 23 of the main body 7 of the flow cell 3. The contact surface 41 has a periphery 57 which is circular in shape and a ridge 59 (which may be referred to as an additional projection). The ridge 59 projects upwards from the contact surface 41 and is concentric with the periphery 57 of the contact surface 41. The ridge 59 has an annular shape. The ridge 59 is sized and dimensioned to be received within a valve recess 173 of the valve 17 (as will be discussed in more detail below). The first and second overhangs 43,45 are integrally formed with the main body 7 of the flow cell 3, specifically by being injection moulded in a single operation.

The first overhang 43 has a vertical portion 65, a horizontal portion 67, and a mould split line 69. The vertical portion 65 of the first overhang 43 projects upwards from the top surface 23 of the main body 7 of the flow cell 3. The horizontal portion 67 of the first overhang 43 projects parallel to, and over, the contact surface 41 such that the horizontal portion 67 of the first overhang 43 overlies the contact surface 41. A first recess 71 is defined between the vertical portion 65 of the first overhang 43, the horizontal portion 67 of the first overhang 43, and the contact surface 41. The first recess 71 has a width 75, measured radially outwards from the periphery 57 of the contact surface 41 and in a plane which is parallel to the horizontal plane 8, of 1.1mm. The first recess 71 is sized and dimensioned to receive a first projection 165 of the valve (which will be discussed below in more detail). When viewed from the side (as shown in Figure 8), the first overhang 43 has an inverted L shape. When viewed from above (as shown in Figure 7), the first overhang 43 has an arcuate shape.

The vertical portion 65 of the second overhang 45 projects upwards from the top surface 23 of the main body 7 of the flow cell 3 on an opposite side of the contact surface 41 to the first overhang 43. The second overhang 45 is otherwise identical to the first overhang 43 such that the second overhang 45 defines a second recess 77 which is identical to the first recess 71.

The second overhang 45 is identical to the first overhang 43 except that the second overhang 45 has a different length B to the length A of the first overhang 43 (discussed below). There is a first gap 79 between the first and second overhangs 43, and a second gap 81between the first and second overhangs 43,45. The first gap 79 is located on an opposite side of the contact surface 41 to the second gap 81. The first overhang 43 subtends a central angle 83 of 79.2°, measured in a plane which is parallel to the horizontal plane 8. The second overhang 45 subtends a central angle 87 of 66.7°, measured in the plane which is parallel to the horizontal plane 8.

The first gap 79 subtends a central angle 85 of 112.8°. The second gap 81 subtends a central angle 86 of 101.4°. The first overhang 43 extends around the periphery 57 of the contact surface 41 for a length A of 15.4mm, such that the first recess 71 extends around the periphery 57 of the contact surface 41 for the length A of 15.4mm. The second overhang 45 extends around the periphery 57 of the contact surface 41 for a length B of 13.3mm, such that the second recess 77 extends around the periphery 57 of the contact surface 41 for the length B of 13.3mm.

The mould split line 69 of the first overhang 43 is located on a surface of the horizontal portion 67 of the first overhang 43 which faces away from the contact surface 41. Thereby, the mould split line 69 is spaced from a surface of the first overhang 43 which defines the first recess 71. The mould split line 69 of the second overhang 45 is correspondingly located on a surface of the horizontal portion 67 of the second overhang 45 which faces away from the contact surface 41.

The first and second stops 47,49 (shown in Figure 6) are each cuboidal in shape. The first stop 47 projects upwards from the top surface 23 of the main body 7 of the flow cell 3. The first stop 47 has a first end 89 which is physically connected to the first overhang 43 and a second end 91 which is spaced along the top surface 23 of the main body 7 of the flow cell 3 from the contact surface 41.

The second stop 49 is identical to the first stop 47, except that the second stop 49 is physically connected to the second overhang 43.

The guide recess 51 (an enlarged view of which is shown in Figure 9) is defined by the top surface 23 of the main body 7 of the flow cell 3. The guide recess 51 has a deep portion 91, a shallow portion 93, a base 95, and a wall 97. The deep portion 91 has a greater depth than the depth of the shallow portion 93. The deep portion 91 is adjacent to the shallow portion 93. The deep portion 91 and the shallow portion 93 are each sized and dimensioned to receive a main body portion 201 of the light shield 19 (discussed below in more detail). The deep portion 91 is vertically above the sensing chamber 27. The shallow portion 93 is located towards a periphery of the top surface 23 of the main body 7 of the flow cell 3. The wall 97 projects upwards from the base 95 of the guide recess 51.

The fin 53 projects upwards from the base 95 of the guide recess 51 into the guide recess 51.

The fin 53 extends in a width wise direction (parallel to the width axis 6) to span the entire guide recess 51. The fin 53 is sized and dimensioned to be received within a groove 203 of the light shield 19 (discussed below in more detail).

The clip recess 55 (shown in the enlarged view of Figure 9) is located towards one end 99 of the top surface 23 of the main body 7 of the flow cell 3. The clip recess 55 is sized to receive a clip 227 which is part of the base 5 (discussed in more detail below) to mechanically connect the flow cell 3 to the base 5.

The sensing chamber 27 comprising a sensing chamber inlet 101 and a sensing chamber outlet 103. The sensing chamber 27 has a volume of 130pl. The sensing chamber inlet 101 has a circular cross section and a minimum width 105, measured in a plane which is parallel to the horizontal plane, of 1.2mm. The sensing chamber inlet 101 is located in the contact surface 41. The sensing chamber inlet 101 is located at an opposite end of the sensing chamber 27 to the sensing chamber outlet 103.

A width of the sensing chamber 27, measured parallel to the width axis 6 and in a plane a parallel to the horizontal plane 8, varies such that the width of the sensing chamber 27 increases between the sensing chamber inlet 101 and a portion of constant width 107, and then the width of the sensing chamber 27 decreases between the portion of constant width 107 and the sensing chamber outlet 103. A width 109 of the sensing chamber 27 immediately adjacent (measured within 1mm) to the sensing chamber inlet 101, measured parallel to the width axis 6, is 1.2mm, which is equal to the minimum width 105 of the sensing chamber inlet 101. The width 109 of the sensing chamber 27 immediately adjacent to the sensing chamber inlet 101 being no greater than 1.5 times the minimum width 105 of the sensing chamber inlet 101 is also envisaged. The width 111 of the portion of constant width 107, measured parallel to the width axis 6, is 8.4mm. The width 111 of the portion of constant width 107 being no less than 2mm is also envisaged. The portion of constant width 107 is located vertically below (in a direction parallel to the vertical axis 2) the deep portion 91.

The sensor 9 is located in the portion of constant width 107. A volume of an upstream portion 102 of the sensing chamber 27 which is located between the sensing chamber inlet 101 and the sensor 9 is 34pL. The upstream portion 102 have a volume of between lOpL and lOOpL is also envisaged. The connection channel 29 has a connection channel inlet 113 and a connection channel outlet 115. The connection channel inlet 113 is located at an opposite end of the connection channel 29 to the connection channel outlet 115. The connection channel inlet 113 is physically connected to the sensing chamber outlet 103 such that the sensing chamber 27 is fluidically connected to the connection channel 29. The connection channel outlet 115 is located in the contact surface 41.

The waste collection channel 31 has a waste collection channel inlet 117, an air vent 119, a main portion 122 and a fluid trap 124. The waste collection channel 31 has a volume of 2.1ml, which is approximately 16 times greater than the volume of the sensing chamber 27. The waste collection channel 31 having other volumes, which are no less than the volume of the sensing chamber 27, is also envisaged. The waste collection channel 31 has a serpentine shape. The waste collection channel inlet 117 is located in the contact surface 41 and is spaced from the connection channel outlet 115 by a distance 114 of 1 ,5mm along the contact surface 41. The waste collection channel inlet 117 is located at an opposite end of the waste collection channel 31 to the air vent 119. The air vent 119 has a square cross section. The air vent having a different, non-circular cross section is also envisaged. The air vent 119 is located in the top surface 23 of the main body 7 of the flow cell 3 and is spaced from the contact surface 41. The main portion 122 has a greater volume than the fluid trap 122. The fluid trap 122 is located upstream of the main portion 122 and towards the waste collection channel inlet 117. The fluid trap 122 has a serpentine shape.

The waste channel 33 has a waste channel inlet 121 and a waste port 123. The waste port 123 has a circular cross section. The waste channel inlet 121 is located in the contact surface 41. The waste channel inlet 121 is spaced from the waste collection channel inlet 117 by a distance 125 of 1.4mm along the contact surface 41, which is equal to the distance 114 by which the waste collection channel inlet 117 is spaced from the connection channel outlet 115. The waste channel inlet 121 is located on an opposite side of the waste collection channel inlet 117 to the connection channel outlet 115. The waste channel inlet 121 is located at an opposite end of the waste channel 33 to the waste port 123.

The waste port 123 has a minimum width 127 of 1.2mm. The waste port 123 having a minimum width 127 of no less than 1mm is also envisaged. The waste port 123 is located in the top surface 23 of the main body 7 of the flow cell 3 and is spaced from the contact surface 41.

The sensor 9 (shown schematically in Figure 10) has a substrate 131, and an array of nanopore sensing elements 133. The sensor 9 is located vertically below the deep portion. The substrate 131 has an array of wells 135. The substrate 131 and the array of nanopore sensing elements 133 are located in a bottom surface of the sensing chamber 27, in the portion of constant width 107

Each nanopore sensing element 134 of the array of nanopore sensing elements 133 has a membrane 139 and a sensor electrode 141. The membrane 139 is supported across one of the wells 135 of the array of wells 135 with a nanopore 143 inserted in the membrane 139. Each nanopore sensing element 134 of the array of nanopore sensing elements 133 supports a respective nanopore 143. Each nanopore 143 provides a nanopore channel 144 extending through it, a common chamber side 136 and a well side 138. The array of nanopore sensing elements 133 has a total surface area 153, when viewed in a plane which is parallel to the horizontal plane 8, of 72mm². Each sensor electrode 141 is located in a respective well 135 such that each sensor electrode 141 is on the opposite side of their respective membrane 139 to the sensing chamber 27.

The ASIC 11 is electrically connected to the sensor 9 and the electrical connector 21. The ASIC 11 is for controlling the sensor 9 and common electrode 13, and for processing signals output by the sensor 9 and providing the signals to the electrical connector 21.

The common electrode 13 is located in the connection channel 29 and is thereby downstream of the sensing chamber outlet 103 and the sensor 9 which has the array of nanopore sensing elements 133. The common electrode 13 is for providing a common reference potential to each of the nanopore sensing elements 133.

The bubble sensor 15 is for detecting a bubble in the sensing chamber 27. In this example, the bubble sensor 15 is an optical bubble sensor having a light-emitting diode and a phototransistor receiver located opposite one another. If a clear liquid passes between the light-emitting diode and the phototransistor receiver, a maximum current reading is detected, whereas, a dark liquid produces a minimum current reading. A bubble is detected, as it passes between the light-emitting diode and the phototransistor receiver, by a fluctuation in the output current signal, which is intermediate to that of the maximum and minimum current outputs. Other types of bubble sensors are envisaged including ultrasonic bubble sensors.

The valve 17 (shown in isolation in Figures 11 to 13) has a hub 161, a valve handle 163, a first projection 165, a second projection 167, a top surface 162, and a bottom surface 164. The valve 17 is formed from Polyurethane, which is resiliently deformable. The hub 161, the valve handle 163, and the first and second projections 165,167 are integrally formed with one another, specifically by being injection moulded in a single operation.

The hub 161 has a common channel 169, an input port 171, and a valve recess 173. The hub 161 is disc shaped such that a periphery 181 of the hub 161 is circular. The common channel 169 has a common channel inlet 183 and a common channel outlet 185. The common channel inlet 183 and the common channel outlet 185 are located on the bottom surface 162 of the valve 17. The common channel outlet 185 is spaced from the common channel inlet 183 along the bottom surface 164 of the valve 17 by a distance 187 of 3mm, which is equal to the distance 114 between the connection channel outlet 115 and the waste collection channel inlet 117, and the distance 125 between the waste collection channel inlet 117 and the waste channel inlet 121. When viewed from below (as shown in Figure 12) the common channel 169 has an arcuate shape. The input port 171 extends between the top surface 162 of the valve 17 and the bottom surface 164 of the valve 17. The input port 171 has a conical shape. The input port 171 has a circular cross section, a minimum width 189 of 1.8mm and a maximum width of 1.8mm. The input port 171 having a minimum width 189 of no less than 0.5mm is also envisaged.

The valve recess 173 is defined in a bottom side of the hub 161 and has an annular shape. The valve recess 173 is sized and dimensioned to receive the ridge 59.

The valve handle 163 has a slot 191 and is elongate in shape. The valve handle 163 projects outwards from a portion of the periphery 181 of the hub 161 which is located between the first projection 165 and the second projection 167. The slot 191 is defined in the bottom surface 164 of the valve 163 and is sized and dimensioned to receive a light shield projection 207 of the light shield 19 (discussed below in more detail). The first projection 165 has an arcuate shape when viewed from below (as shown in Figure 12). The first projection 165 projects horizontally outwards from the periphery 181 of the hub 161 and extends around the periphery 181 of the hub 161 for a length 193 of 16.9mm, which is 110% of the length A which the first and second overhangs 43,45 extend discontinuously around the periphery 57 of the contact surface 41. The first projection 165 extending around the periphery 181 of the hub 161 for a length 193 of no less than 50% of the length A which the first and second overhangs 43,45 extend around the periphery 57 of the contact surface 41 is also envisaged.

The first projection 165 subtends a central angle 195, measured in a plane which is parallel to the horizontal plane 8, of 95°, which is less than the central angles 85 subtended by the first gap 79. Thereby, the first projection 165 is sized to fit through the first gap 79.

The first projection 165 is sized and dimensioned to be received within the first recess 71. The first projection 165 has a width 197, measured in a plane which is parallel to the horizontal plane 8, of 0.7mm, which is 63% of the width 75 of the first recess 71. The first projection 165 having a width 197 which is no less than 20% of the width 75 of the first recess 71 is also envisaged.

A lubricant 198 is located between the first overhang 43 and the first projection 165, and between the contact surface 41 and the first projection 165.

The second projection 167 is identical to the first projection 165, except that the second project projects from an opposite side of the periphery 181 of hub 161 to the first projection 165.

The light shield 19 (shown in isolation in Figure 14 and Figure 15) has a main body 201, a groove 203, a light shield handle 205, and a light shield projection 207. The light shield 19 is formed from opaque Polycarbonate. The light shield 19 has a total surface area 209, measured in a plane which is parallel to the horizontal plane 8, of 91mm², which is 126% of the total surface area 153 of the array of nanopore sensing elements 133. The light shield 19 having a total surface area 209 of no less than 100%, and no greater than 200% of the total surface area 153 of the array of nanopore sensing elements 133 is also envisaged. The main body 201 of the light shield 19 has a top surface 208 and a bottom surface. The main body 201 of the light shield 19 has a planar shape and is formed of opaque Polycarbonate. The main body 201 of the light shield 19 has a length and a width which are sized to be received in either of the shallow portion 93, and the deep portion 91.

The groove 203 extends between the top surface 208 and the bottom surface of the main body 201 of the light shield 19 and extends along a whole width 211 of the main body 201 of the light shield 19 (extends parallel to the width axis 6) such that the groove 203 divides the main body 201 of the light shield 19 into first and second parts 213,215. The groove 203 is sized and dimensioned to receive the fin 53.

The light shield handle 205 extends from the top surface 208 of the main body 201 of the light shield 19 and extends across the groove 203 to join the first and second parts 213,215 of the main body 201 of the light shield 19 together.

The light shield projection 207 projects upwards from the main body 201 of the light shield 19 and is located on an opposite side of the main body 201 of the light shield 19 to the light shield handle 205. The light shield projection 207 is sized and dimensioned to be received within the slot 191 of the valve handle 163.

The electrical connector 21 is located on the bottom surface 25 of the main body 7 of the flow cell 3 and is for connecting to a corresponding electrical connector on the base 5 (discussed in more detail below) to electrically connect the flow cell 3 to the base 5.

The base 5 (shown in isolation in Figure 16) has a main body 221, an electrical connector 223, a processor 225, a clip 227, a lid 229, and a cable 231.

The main body 221 of the base 5 has a top surface 233. The main body 221 of the base 5 has a cuboidal shape. A base recess 235 is defined in the top surface 233 of the main body 221 of the base 5. The base recess 235 is sized and dimensioned to receive the flow cell 3.

The electrical connector 223 is located in the base recess 235 and, as described previously, is for connecting to the electrical connector 21 on the flow cell 3 to electrically connect the flow cell 3 to the base 5. The processor 225 is located within the main body 221 of the base 5 and is electrically connected to the electrical connector 223 of the base 5 such that signals received from the flow cell 3 via the electrical connectors 21,213 can be received and processed by the processor 225.

The clip 227 is located at one end of the base recess 235. As described above, the clip 227 is sized so that a portion of the clip 227 can be received within the clip recess 55 to mechanically connect the flow cell 3 to the base 5.

The lid 229 has a lid recess 237 and a pivot 239. The lid recess 237 is sized and dimensioned to receive the flow cell 3. The base recess 235 and the lid recess 237 are sized and dimensioned such that when the flow cell 3 is located in the base recess 235 and the lid recess 237, the base 5 completely encloses the flow cell 3.

The pivot 239 pivotably connects the lid 229 to the main body 221 of the base 5 such that the lid 229 can be opened and closed.

The cable 231 extends from the main body 221 of the base 5 and is electrically connected to the processor 225. The cable 231 is for electrically connecting the processor 225 to an external computing device, such as a tablet computer, such that signals and power can be transferred between the external computing device and the processor 225.

To connect the valve 17 to the main body 7 of the flow cell 3, the valve 17 is located above the top surface 23 of the main body 7 of the flow cell 3 with the first projection 165 vertically aligned with the first gap 79, the second projection 167 vertically aligned with the second gap 81 (as shown in Figure 17), and the ridge 59 vertically aligned with the valve recess 173. At the is point, the valve 17 may be referred to as being in a first configuration.

The valve 17 is then moved down towards the top surface 23 of the main body 7 of the flow cell 3 such that the first projection 165 passes through the first gap 79 and the second projection 167 passes through the second gap 81. The valve 17 is continued to be moved down until the bottom surface 164 of the valve 17 contacts the contact surface 41 and the ridge 59 is received within the valve recess 173. Once the ridge 59 has been received within the valve recess 173, a minimum clearance 241 (shown in the enlarged section view of Figure 18), measured parallel to the vertical axis 2, between the ridge 59 and the portion of the bottom surface 164 of the valve 17 which defines the valve recess 173 is 0.15mm.

The valve 17 is then rotated in a plane which is parallel to the horizontal plane 8 by approximately 90° in a clockwise direction, which moves the valve handle 163 towards the stops 47,49 (shown in Figure 19). This results in the first projection 165 being received within, and moving along, the first recess 71, and the second projection 167 being received within, and moving along, the second recess 77. When the projections 165,167 are received within the recesses 71,77, a minimum clearance 243 (shown in Figure 20), measured in a plane parallel to the horizontal plane 8, between each of the first and second projections 165,167 and the surface of each overhang 43,45 defining their corresponding recess 71,77 is 0.1mm. When the first and second projections 165,167 are received within the recesses 71,77, the contact surface 41 and the horizontal portion 67 of each of the first and second overhangs 43,45 block the movement of the projections 165,167 in a direction 245 parallel to the vertical axis 2, thereby connecting the valve 17 to the main body 7 of the flow cell. Thereby, the first and second projections 165,167 and the first and second overhangs 43,45 operate in a similar manner to a bayonet fitting.

During the rotation of the valve 17, the valve handle 163 is bent upwards, in the direction 245 parallel to the vertical axis 2, away from the top surface 23 of the main body 7 of the flow cell 3 so that the valve handle 163 can pass over one of the first and second stops 47,49. If this was not performed, the valve handle 163 would abut one of the first and second stops 47,49 and prevent the valve 17 from being rotated further to complete the connection of the valve 17 to the main body 7 of the flow cell 3. Once the valve handle 163 has passed over the stop, the valve handle 163 is released and, due to the valve 17 being resiliently deformable, the valve handle 163 moves back towards the top surface 23 of the main body 7 of the flow cell 3. At this point, the valve 17 may be referred to as being in a second configuration. By providing the valve handle 163 which can be resiliently deformed over the first and second stops 47,49, the user can select when the first and second stops 47,49 inhibit or allow movement of the valve 17 between the first configuration (shown in Figure 17) and the second configuration (shown in Figure 19 and Figure 21).

Once the valve 17 is connected to the main body 7 of the flow cell 3 and in the second configuration, the rotation of the valve 17 is constrained to be a maximum of approximately 45° between an open position (shown in Figure 19) and a closed position (shown in Figure 21) by the valve handle 163 abutting either one of the first and second stops 47,49 at either end of this 45° rotation. It is envisaged that the stops 47,49 may be differently located such that the rotation between the open position and the closed position is no greater than 90° and no less than 10 °. The first and second stops 47,49 prevent the valve handle 163 from projecting outside a footprint of the flow cell 3 during rotation between the open position and the closed position. Thereby, the flow cell 3 is configured such that the valve 17 remains within the footprint of the flow cell 3. This may enable the valve 17 to be operated without interfering with other structures surrounding the flow cell 3, such as the base 5 or other flow cells 3. The above steps can be performed in the reverse order to disconnect the valve 17 from the main body 7 of the flow cell 3.

To connect the flow cell 3 to the base 5, the lid 229 is opened, and the flow cell 3 is inserted into the base 5 and the clip 227 moved such that the portion of the clip 227 is received in the clip recess 55 to mechanically connect the flow cell 3 to the base 5. At this point, the electrical connector 21 of the flow cell 3 overlies, and is thereby connected to, the electrical connector of the base 5 such that the flow cell 3 is electrically connected to the base 5.

Prior to conducting an assay using the sequencing instrument 1, a conditioning ionic liquid 242 (which may be a buffer liquid) is located within the sensing chamber 27 (which may be referred to as a cis chamber) and is in contact with the common chamber side 136 of the nanopore 143. A trans ionic liquid 244 is located within each of the wells 135 and in contact with the well side 138 of each of the nanopores 143. The nanopores 143 separate the trans ionic liquid 244 from the conditioning ionic liquid 242.

To conduct an assay using the sequencing instrument 1, the user puts the valve 17 into the open position (shown in Figure 21 and Figure 22) by moving the valve handle 163 such that it abuts the second stop 49. When the valve 17 is in the open position, the input port 171 is vertically aligned with the sensing chamber inlet 101. The common channel 169 is positioned such that the common channel inlet 183 is connected to the connection channel outlet 115, and the common channel outlet 185 is connected to the waste collection channel inlet 117. The valve 17 blocks the waste channel inlet 121 to fluidically disconnect the waste channel 33 from the waste collection channel 31. The light shield projection 207 is received in the slot 191 of the valve handle 163, and the valve handle 163 abuts the light shield handle 205. The main body 201 of the light shield 19 is received in the shallow portion 93 such that no part of the main body 201 of the light shield 19 is located in the deep portion 91. Thereby, when viewed in a plane parallel to the horizontal plane 8, the light shield 19 does not overlie any part of the array of nanopore sensing elements 133, so the light shield 19 does not block any of the light from outside the flow cell 3 from reaching the array of nanopore sensing elements 133. At this point, the light shield 19 is in an uncovered position, in that the array of nanopore sensing elements 133 is not covered by the light shield 19. The fin 53 is located in the groove 203 in the light shield 19.

The user inserts a sample liquid containing molecular entities (which may be referred to as an analyte) which are to be sensed directly into the sensing chamber inlet 101 via the input port 171. The sample liquid then passes through the sensing chamber inlet 101 into the sensing chamber 27 and travels to the senor 9. The insertion of the sample liquid causes the conditioning ionic liquid 242 (which is then referred to as a waste liquid) to be displaced out of the sensing chamber 27 and into the connection channel 29. The waste liquid flows through the connection channel 29, through the common channel 169, and into the waste collection channel 31, where it is collected. As the waste liquid flows into the waste collection channel 31, air already present in the waste collection channel 31 is displaced and exits the waste collection channel 31 via the air vent 119.

The user then puts the valve 17 into a closed position (shown in Figure 19 and Figure 23) by rotating the valve 17 by 45 degrees in an anticlockwise direction until the valve handle 163 abuts the first stop 47.

When the valve 17 is in the closed position, the input port 171 is vertically misaligned with the sensing chamber inlet 101 and the hub 161 blocks the sensing chamber inlet 101. The common channel 169 is positioned such that the common channel inlet 183 is connected to the waste collection channel inlet 117, and the common channel outlet 185 is connected to the waste channel inlet 121. The valve 17 blocks the connection channel outlet 115 such that the waste collection channel 31 is fluidically disconnected from the connection channel 29. As the light shield projection 207 is received in the slot 191 of the valve handle 163, the valve handle 163 is coupled to the light shield 19 such that as the valve handle 163 moves into the closed position, the light shield 19 also moves. The main body 201 of the light shield 19 slides linearly in a width direction 251 parallel to the width axis 6 until the main body 201 of the light shield 19 is located in the deep portion 91. During this sliding, sliding of the light shield 19 along a length direction 253 parallel to the length axis 4, is restricted by the interaction of the fin 53 and the groove 203, and the main body 201 of the light shield 19 and the top surface 23 of the main body 7 of the flow cell 3 which defines the guide recess 51. Thereby the fin 53 and the groove 203, and the main body 201 of the light shield 19 and the top surface 23 of the main body 7 of the flow cell 3 which defines the guide recess 51 may be considered as a guide which guides the sliding of the light shield 19.

Once the main body 201 of the light shield 19 is located in the deep portion 91, the main body 201 of the light shield 19 completely overlies the total surface area 153 of the array of nanopore sensing elements 133 when viewed in a plane which is parallel to the horizontal plane 8 such that substantially no light from outside the flow cell 3 can reach the array of nanopore sensing elements 133. Thereby, by moving the light shield 19 between being located in the shallow portion 93 and being located in the deep portion 91, the amount of light which can reach the array of nanopore sensing elements 133 is varied. At this point, the light shield 19 is in a covered position.

The ASIC 11 controls the common electrode 13 and the sensor electrodes 141 such that an electrical potential is created between the common electrode 13 and the sensor electrodes 141. This electrical potential causes the molecular entities to translocate trough the nanopores 143 and an ion current to flow through the nanopores 143.

The sensing electrodes 141 output signals dependant on the interactions between the molecular entities and the nanopores 143. For example, translocation of a molecular entity through a nanopore 143 may alter an ion current flowing through the nanopore 143, which may be sensed by the sensing electrodes 141. The signals are output from the sensor 9 to the ASIC 11, which processes the signals. The signals are then sent to the processor 225 for further processing, and then sent to the external computing device where the signals are also processed, for example, to determine the DNA sequence of the molecular entities. When the light shield 19 is in the covered position, the bubble sensor 15 is operable to detect the presence of bubbles in the sensing chamber 27.

When the valve 17 is in the closed position, the user can empty the waste collection channel 31 by inserting a pipette into the waste port 123, and applying suction using the pipette which draws the waste liquid out of the waste collection channel 31, through the common channel 169, through the waste channel 33, and out of the waste port 123.

The user can close the lid 229 to completely enclose the flow cell 3 within the base 5.

The user can then move the valve 17 to the open position to start another assay. This is performed by rotating the valve 17 by 45° in a clockwise direction until the valve handle 163 abuts the first stop 47. During this rotation, the valve handle 163 will also abuts the light shield handle 205 and thereby couple the valve handle 163 to the light shield handle 205 such that as the valve handle 163 moves into the open position, the light shield 19 also slides. The main body 201 of the light shield 19 slides linearly along the direction 251 which is parallel to the width axis 6 of the flow cell 3 until the main body 201 of the light shield 19 is located in the shallow portion 93.

In the previous example, the light shield 19 is formed from an opaque material. An alternative sequencing instrument comprises an alternative light shield and an alternative base. The other features of the alternative sequencing instrument are identical to those of the sequencing instrument 1 described above. A main body of the alternative light shield has a light shield polariser 303 instead of being formed from an opaque material. The light shield polariser 303 has a polarisation axis 305. The main body of the alternative light shield remains stationary in the deep portion 91 during operation rather than moving between the deep portion 91 and the shallow portion 93. Thereby, the light shield polariser 303 remains fixed in a position which overlies the total surface area 153 of the array of nanopore sensing elements 133 when viewed in a plane which is parallel to the horizontal plane 8. Thereby, when the lid is open, the light shield polariser 303 blocks a portion of the light which originates outside the flow cell from reaching the array of nanopore sensing elements 133 but lets the remainder of the light reach the array of nanopore sensing elements 133. A lid of the alternative base has a lid polariser 307. The lid polariser 307 has a polarisation axis 309. When the lid of the alternative base is closed, the lid polariser 307 is vertically above the light shield polariser 303 such that light which passes through the lid polariser 307 is attenuated by the light shield polariser 303. When the lid of the alternative base is closed, the polarisation axis 309 of the lid polariser 307 and the polarisation axis 305 of the light shield polariser 303 are angularly offset from each other when viewed in two parallel reference planes 311,313 (shown in Figure 24). Specifically, the polarisation axes 305,309 are orthogonal to one another. Thereby, the light shield polariser 303 and the lid polariser 307 are crossed such that substantially all of the light is attenuated. Thereby, the user can open and close the lid of the alternative base, which causes the lid polariser 307 to move relative to the light shield polariser 303, to vary the amount of light which can reach the array of nanopore sensing elements 133. In other examples, other angles of angular offset can be used. Equally, in further examples, the light shield polariser 303 and the lid polariser 307 could be a fixed distance from one another, and the polarisation axes 305,309 moved relative to one another to vary the amount of light which can reach the array of nanopore sensing elements 133.

In the above example, the valve 17 has a single common channel 169. In an alternative valve, the single common channel 169 may be replaced by two separate channels: a transfer channel and a transport channel. The transfer channel is fluidically connected to the connection channel outlet 115 and the waste collection channel inlet 117 when the valve is in the open position. The transfer channel is fluidically disconnected from the connection channel inlet 113 and the waste collection channel inlet 117 when the valve is in the closed position. The transport channel is fluidically connected to the waste collection channel inlet 117 and the waste channel inlet 121 when the valve is in the closed position. The transport channel is fluidically disconnected from the waste collection channel inlet 117 and the waste channel inlet 121 when the valve is in the closed position.

In the above example, when the valve 17 is moved from the closed position to the open position, the light shield is coupled to the valve 17 by the valve handle 163 abutting the light shield handle 205. In other examples, the light shield is coupled to the valve 17 during the movement from the closed to the open position by the light shield projection 207 being received in the slot 191 of the valve handle 163. In these examples, the light shield handle 205 can be omitted. In the above example, the light shield 19 and the valve 17 are separate components. In other examples, the light shield 19 may be integrally formed with the valve 17 such that the light shield 19 and the valve 17 are not separate components.

In the above example, the light shield 19 has a light shield projection 207, and the valve handle 163 has a slot 191 which receives the light shield projection 207 to couple the valve 17 to the light shield. In other examples, the slot 191 may be provided in the light shield 19, and the projection may be provided on the valve 17.

In the above example, the light shield 19 moves linearly in a direction 251 which is a parallel to the width axis 6, and the valve 17 rotates. In other examples, the light shield 19rotates and/or the valve 17 moves linearly.

In the above example, when in the uncovered position, the light shield 19 does not overlie any part of the array of nanopore sensing elements 133, so the light shield 19 does not block any of the light from outside the flow cell 3 from reaching the array of nanopore sensing elements 133. In other examples, when in the uncovered position, the light shield 19 overlies some of the total surface area 153 of the array of nanopore sensing elements 133, such as no greater than 20% of the total surface area 153 of the array of nanopore sensing elements 133 when viewed in a plane which is parallel to the horizontal plane 8.

In the above example, when in the covered position, the light shield 19 completely overlies the total surface area 153 of the array of nanopore sensing elements 133 when viewed in a plane which is parallel to the horizontal plane 8 such that substantially no light from outside the flow cell 3 can reach the array of nanopore sensing elements 133. In other examples, when in the covered position, the light shield 19 overlies less than 100% of the total surface area 153 of the array of nanopore sensing elements 133, such as no less than 80% of the total surface area 153 of the array of nanopore sensing elements 133 when viewed in a plane which is parallel to the horizontal plane 8. Equally, in other examples, instead of substantially no light from outside the flow cell 3 can reach the array of nanopore sensing elements 133 when the light shield 19 is in the covered position, no greater than 50% of an amount of light which can reach the array of nanopore sensing elements 133 when the light shield 19 is in the uncovered position, can reach the nanopore 143. In the above example, the sequencing instrument 1 has a single flow cell 3. In other examples, the sequencing instrument 1 has multiple flow cells 3.

In the above example, the valve 17 has first and second projections 165,167, and the main body 7 of the flow cell 3 has first and second overhangs 43,45. In other examples, the valve 17 has a different number of projections 165,167, such as one projection 165, and the main body 7 of the flow cell 3 has an equal number of overhangs 43,45, such as one.

Figure 25 shows a flow chart which details a method 501 of manufacturing the main body 7 of the flow cell 3.

The main body 7 of the flow cell 3 is manufactured from two parts: an upper part 601 and a lower part 603 (shown in Figure 26 and Figure 27). The upper part 601 defines an upper portion of the sensing chamber 27, the connection channel 29, the waste collection channel 31, and the waste channel 33. The upper part 601 has a joining surface 605, which is the surface of the upper part 601 intended to abut and join with a corresponding joining surface of the lower part 603. The joining surface 605 of the upper part 601 extends around a periphery of the upper part and the peripheries of the upper portions of the sensing chamber 27, the connection channel 29, the waste collection channel 31, and the waste channel 33.

The lower part 603 of the main body 7 defines a lower portion of the sensing chamber 27, the connection channel 29, the waste collection channel 31, and the waste channel 33. The lower part 603 of the main body 7 has a joining surface 607, which is the surface of the lower part 603 of the main body 7 intended to abut and join with the joining surface 605 of the upper part 601 of the main body 7. The joining surface 607 of the lower part 603 extends around a periphery of the lower part 603 and the peripheries of the lower portions of the sensing chamber 27, the connection channel 29, the waste collection channel 31, and the waste channel 33. The joining surface 607 of the lower part 603 comprises a bead 611 which projects upwards from the joining surface 607 of the lower part 603. The entire lower part 603 is injection moulded in a single operation such that the bead 611 is integrally formed with the joining surface 607 of the lower part 603.

To join the lower part 603 to the upper part 601, the method commences with providing 503 the upper part 601 and the lower part 603. The upper part 601 is placed on the lower part 603 such that the joining surface 607 of the lower part 603 abuts 505 the joining surface 605 of the upper part 601. Then the bead 611 is melted 507 using a laser to weld the joining surface 607 of the lower part 603 to the joining surface 605 of the upper part 601. The laser is aimed through the upper part 601, which is formed of a transparent material.

Figure 28 shows a flow chart which details a first method 701. Firstly, a flow cell for use as part of a nanopore array device is provided 713. The flow cell is the same as the flow cell 3 described above. Secondly, the valve is moved 705 between: a first position in which the valve allows the liquid to flow through the sensing chamber inlet and the liquid to flow through the sample chamber outlet; and a second position in which the valve inhibits the liquid from flowing through the sensing chamber inlet and the liquid from flowing through the sample chamber outlet.

Figure 29 shows a flow chart which details a second method 711. Firstly, a flow cell for use as part of a nanopore array device is provided 713. The flow cell is the same as the flow cell 3 described above.

The flow cell has a main body defining a sensing chamber, the main body comprising a surface through which light can pass into the sensing chamber, an array of nanopore sensing elements located within the sensing chamber; and a light shield for inhibiting passage of light through the surface. The light shield is moved 715 relative to the sensing chamber to vary an amount of light that can reach the array of nanopore sensing elements.

Figure 30 shows a flow chart which details a third method 801. A flow cell for use as part of a nanopore array device is provided 713. The flow cell is the same as the flow cell 3 described above.

Next, the valve is connected 805 to the main body by aligning 807 the projection with the gap; with the projection aligned with the gap, moving 809 the projection through the gap, and moving 811 the valve such that the projection is aligned with the overhang and received within the recess.

When the valve is connected to the main body, the valve is moved 813 between an open position and a closed position. When the valve is in the open position, the valve allows at least one of the sample liquid to enter the sensing chamber inlet and the waste liquid to exit the sensing chamber outlet. When the valve is in the closed position, the valve inhibits at least one of the sample liquid from entering the sensing chamber inlet and the waste liquid from exiting the sensing chamber outlet.

Whilst particular examples have been described, it should be understood that these are illustrative examples only and that various modifications may be made without departing from the scope of the invention as defined by the claims.

Claims

1. A flow cell for use as part of a nanopore array device, the flow cell comprising: a main body defining a sensing chamber, the main body comprising a surface through which light can pass into the sensing chamber; an array of nanopore sensing elements located within the sensing chamber; and a light shield for inhibiting passage of light through the surface, wherein the light shield is moveable relative to the sensing chamber to vary an amount of light that can reach the array of nanopore sensing elements.

2. A flow cell as claimed in claim 1, wherein the flow cell comprises a guide configured to guide the movement of the light shield relative to the sensing chamber to vary the amount of light which can reach the array of nanopore sensing elements.

3. A flow cell as claimed in claim 2, wherein: the guide comprises a recess configured to receive the light shield; and the light shield is located within the recess.

4. A flow cell as claimed in any one of claims 2 or 3, wherein: the light shield is moveable relative to the sensing chamber along a first axis to vary the amount of light which can reach the array of nanopore sensing elements; the guide comprises a fin and a groove; the fin is comprised by one of the main body and the light shield; the groove is comprised by the other of the main body and the light shield; and the fin is located within the groove such that movement of the light shield relative to the sensing chamber along a second axis, perpendicular to the first axis, is inhibited.

5. A flow cell as claimed in any one of the preceding claims, wherein the light shield is slidable relative to the sensing chamber.

6. A flow cell as claimed in any one of the preceding claims, wherein: the flow cell comprises a valve moveable between: an open position and a closed position; and the light shield is coupled to the valve such that movement of the valve causes movement of the light shield relative to the sensing chamber.

7. A flow cell as claimed in claim 6, wherein the light shield and the valve are separate components.

8. A flow cell as claimed in claim 7, wherein: one of the light shield and the valve comprises a projection; the other of the light shield and the valve comprises a slot configured to receive the projection and couple the light shield to the valve such that the movement of the valve causes the movement of the light shield relative to the sensing chamber to vary the amount of light which can reach the array of nanopore sensing elements.

9. A flow cell as claimed in claim 8, wherein: one of the light shield and the valve is configured to move linearly; and the other of the light shield and the valve is configured to rotate.

10. A flow cell as claimed in any one of claims 6 to 9, wherein the light shield is configured to abut the valve to couple the light shield to the valve such that movement of the valve causes movement of the light shield relative to the sensing chamber to vary the amount of light which can reach the array of nanopore sensing elements.

11. A flow cell as claimed in any one of the preceding claims, wherein: the light shield is moveable between: an uncovered position in which a first amount of light can reach the array of nanopore sensing elements; and a covered position in which a second amount of light can reach the array of nanopore sensing elements; and the second amount of light is no greater than 50% of the first amount of light.

12. A flow cell as claimed in claim 11, wherein, when the light shield is in the uncovered position, the light shield overlies no greater than 20% of a total surface area of the array of nanopore sensing elements when viewed in a horizontal plane.

13. A flow cell as claimed in any one of claims 11 or 12, wherein, when the light shield is in the covered position, the light shield overlies no less than 80% of a total surface area of the array of nanopore sensing elements when viewed in a horizontal plane.

14. A flow cell as claimed in any one of the preceding claims, wherein: the array of nanopore sensing elements has a total surface area measured in a horizontal plane; and the light shield has a total surface area measured in the horizontal plane which is no greater than 200% of the total surface area of the array of nanopore sensing elements

15. A flow cell as claimed in any one of the preceding claims, wherein the nanopore array device comprises a bubble sensor configured to detect a bubble in the sensing chamber.

16. A nanopore array device comprising the flow cell as claimed in any one of the preceding claims.

17. A nanopore array device as claimed in claim 16, wherein: the light shield comprises a polariser; and a further light shield comprising a further polariser, wherein the light shield and the further light shield are configured such that light which passes through the further polariser is attenuated by the polariser.

18. A nanopore array device as claimed in claim 17, wherein the polariser and the further polariser are crossed.

19. A method comprising: providing a flow cell for use as part of a nanopore array device as claimed in any one of the preceding claims; and moving the light shield relative to the sensing chamber to vary an amount of light that can reach the array of nanopore sensing elements.