Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/483—Physical analysis of biological material
  • G01N33/487—Physical analysis of biological material of liquid biological material
  • G01N33/48707—Physical analysis of biological material of liquid biological material by electrical means
  • G01N33/48721—Investigating individual macromolecules, e.g. by translocation through nanopores

Definitions

• the present disclosure relates to molecule sensing using nanoscale pores or nanopores. More specifically, the proposed techniques relate to a field effect transistor (FET) device for sensing of target molecules, and systems for use thereof.
• FET field effect transistor
• Nanopore sensing has been used for DNA and RNA detection and sequencing for some time, and the interest of the research community has now also turned to nanopore sensing of biomolecules such as proteins and peptides. Nanopore sensing is attractive as it has the potential to detect multiple distinct types of biomolecules, such as DNA, RNA, and proteins, simultaneously in a complex biological sample, and since it can be integrated into small and portable devices.
• FETs field-effect transistors
• nanopores to develop pore FETs to sense target molecules.
• FETs having a pore are known for use in sensing of particles, such as sensing of single molecules.
• the pore is used for gating the FET such that when a single molecule is passed through the pore, a current modulation of the FET can be achieved.
• a pore FET sensor can be formed, wherein translocation of a single molecule through the pore can affect gating of the FET for allowing detection of the single molecule.
• these devices suffer from noise, especially when applied to larger bandwidths. Accordingly, improved nanopore-FET devices for sensing of target molecules are needed.
• An object of the present disclosure is to provide devices and systems, which provide high translocation signal magnitudes, high bandwidths, while suppressing short channel effects and reducing noise.
• the present invention relates to a pore Field-effect transistor (FET) device for sensing target molecules in an electrolyte.
• the device comprises a pore with at least a first and a second opening, consisting of two contiguous parts: a lumen part and an aperture part.
• the lumen part is connected to the first opening, while the aperture part is connected to the second opening.
• the device also includes at least a first and a second reservoir, with the pore fluidically connected to both reservoirs.
• the first reservoir is connected to the lumen part via the first opening
• the second reservoir is connected to the aperture part via the second opening.
• the device features a sensor region comprising a main electrode that overlaps either the lumen part or the aperture part of the pore, allowing target molecules passing through the pore to pass through the sensor region.
• the geometry of the device is such that: i) the effective cross-section diameter of every transverse cross-section of the pore is less than 1 pm; ii) the aperture part has all its transverse cross-sections having an effective diameter (dA) less than 50 nm; iii) an area of a transverse cross-section in the aperture part (AA) is smaller than an area of a transverse cross-section in the lumen part (AL), with at least 3/4 of the transverse cross-sections of the lumen part having an area at least four times larger than any aperture transverse crosssection (AL ⁇ 4AA); and iv) the main electrode area exposed to the electrolyte is larger than 10000 nm 2 .
• the objective may be obtained by a nanoscale pore Field-effect transistor (FET) device for sensing of target molecules in an electrolyte, the device comprising: a nanoscale pore having at least a first and a second opening and comprising two contiguous parts, a lumen part and an aperture part, such that the lumen part is connected at least to the first opening and the aperture part is connected to the second opening; a pore axis oriented from the first opening to the second opening of the nanoscale pore, wherein the lumen part and the aperture part of the nanoscale pore are oriented along the pore axis; at least a first and a second reservoir, the nanoscale pore being fluidically connected to said first and second reservoir, wherein the first reservoir is in connection with the lumen part of the nanoscale pore via the first opening, and the second reservoir is in connection with the aperture part of the nanoscale pore via the second opening, an electrical center or sensor region comprising a main electrode located between, and potentially overlapping, the lumen part and the aperture part
• the electrode area AE > lOOOOnm 2 .
• the geometry of the device may provide that, on condition that the pore and the at least first and second reservoirs are uniformly filled with a single isotropic and uniformly conducting test material or test liquid, and that the main electrode makes electrical contact with the test material or test liquid with negligible contact resistance and negligible electrode resistance, the resistance between the aperture reservoir and the main electrode (R1) corresponds to the resistance between the lumen reservoir and the main electrode (R2), with R1/R2 ranging from 1/6 to 6.
• the geometry of the device may provide that, on condition that the pore and the at least first and second reservoirs are uniformly filled with a single isotropic and uniformly conducting test material or test liquid, and that the main electrode makes electrical contact with the test material or test liquid with negligible contact resistance and negligible electrode resistance, RA/RL is from 0.27 to 23, preferably from 0.57 to 8.6 , yet more preferably 0.80 to 5.0, even more preferably 1.00 to 3.00, and most preferably 2, wherein RA is the test resistance of the aperture part, which is the electrical resistance between the main electrode and the second reservoir, which is fluidically connected to the aperture, wherein R is the test resistance of the lumen part, which is the resistance between the main electrode and the reservoir or reservoirs fluidically connected to the lumen part of the pore via the first opening.
• Re1 represents the resistivity of the first reservoir
• Re2 represents the resistivity of the second reservoir.
• the lumen part may have a resistance R and the aperture part has a resistance RA, or wherein the pore part located above the electrical center, on the lumen side, has a resistance R c and the pore part located below the electrical center, on the aperture side, has a resistance R p , where the geometry independent of electrolyte conforms to: wherein A(l) is the area of the cross section at position I along the pore, and top, bottom, electrode bottom and electrode top correspond to positions along the pore, where electrode refers to the main electrode, where rtop and rbottom is the effective cross-section radius at the ends of the pore, and wherein F is from 0.27 to 23, F is preferably 0.57 to 8.6.
• R p /R c is from 0.27 to 23.
• the lumen part of the pore may comprise two sub-parts: a first sub-lumen connected to the first opening, and a second sub-lumen connected to a third opening.
• the device may further include a third reservoir, fluidically connected to the second sub-lumen of the pore via the third opening.
• the pore is fluidically connected to the first, second, and third reservoirs.
• the main electrode may be located on the walls of the pore, with at least 3/4 of the electrode area exposed to the lumen part of the pore.
• a thin solid dielectric material may be present between the electrode and the space inside the pore.
• the thin solid dielectric material may have a thickness of 0.5-10 nm and may be made of materials such as AI2O3, TiC>2, ZrC>2 HfC>2, SisN4, or SiC>2.
• the main electrode may be made of an electrically conducting material, such as TiN, Ru, Pt, or silicon.
• the main electrode may be a semiconductor of a metal-oxide- semiconductor field-effect transistor (MOSFET) channel, with a dielectric covering the electrode serving as a gate dielectric.
• MOSFET metal-oxide- semiconductor field-effect transistor
• the main electrode may be electrically connected to a gate of a MOSFET.
• the aperture may have a height (h A ) and an effective diameter (dA), with hA being less than 50 nm and dA being less than 20 nm.
• the lumen may have an effective diameter (di_), ranging from 70 to 1000 nm.
• the device may include a dielectric wall of thickness (w) surrounding the pore, where the total summed capacitance between the electrolyte inside the pore and the outside electrical conductors (including the first and second reservoirs and the main electrode) is smaller than 50 fF.
• the device may further comprise a semiconductor wall of thickness Wsi surrounding the pore, wherein the wall thickness Wsi is 10 nm or less, such as 5 nm or less.
• the wall may comprise at least three different layers consisting of at least two different materials. These layers are arranged on top of each other, with a dielectric material at the top and bottom of the pore.
• the top dielectric layer has a height (h ox _t op )
• the bottom dielectric layer has a height (h ox _bottom)
• a conductive/semiconductive material is arranged in the middle of the pore, with a height (h S j).
• the lumen may have a height (hi.) equal to h ox _to P + h S i, and the aperture may have a height (h A ) equal to h ox _bottom.
• the conductive/semiconductive material may have a height (h S j) ranging from 5 to 500 nm, such as 5 to 100 nm.
• the lumen of the pore may have a uniform shape or a tapered shape.
• the device may include a main electrode and one or more additional electrodes, which may be located in the aperture part or the lumen part of the pore.
• the pore may be embedded in the FET, with the FET being gated by an electrolyte-filled pore running through the channel region of the FET.
• the sensor region may comprise a source-drain axis.
• the semiconductive material may be silicon (Si).
• a fourth layer may be arranged below the bottom dielectric material, with a height (h 4 ).
• h L h ox _to P + h S j + h ox _bottom
• h A h 4 .
• the fourth layer may be a dielectric multi-layer consisting of multiple different dielectric materials.
• the fourth layer may be a 2D material.
• the device may include a remote extended FET, where an electrode wrapped around the nanopore is connected to a remote gate sensor.
• the wall material and conductive material may be an electrode material, such as titanium nitride (TiN), ruthenium (Ru), or platinum (Pt), which is coupled to a gate of a silicon transistor remote from the pore.
• electrode material such as titanium nitride (TiN), ruthenium (Ru), or platinum (Pt), which is coupled to a gate of a silicon transistor remote from the pore.
• the present invention may relate to a system for sensing target molecules in an electrolyte, the system including a first reservoir comprising target molecules in an electrolyte, a second reservoir, and optionally additional reservoirs.
• the system may also include a pore FET device as described in the previous embodiments, with the pore connecting the first and second reservoirs.
• the sensing of target molecules involves the target molecules exiting the first reservoir, entering the lumen part of the pore via the first opening, passing through the pore along the pore axis, and exiting through the second opening of the aperture part into the second reservoir (or vice versa).
• the electrolyte in the lumen has a resistance R L
• the electrolyte in the aperture has a resistance RA.
• the system may be for sensing of target molecules in an electrolyte, the system comprising: i) a first reservoir comprising target molecules in an electrolyte; ii) a second reservoir; iii) optionally additional reservoirs; iv) a nanoscale pore Field-effect transistor (FET) device as defined above and below, comprising a nanopore connecting the first and second reservoir, wherein the sensing of target molecules comprises the target molecules exiting the first reservoir, entering the lumen part of the nanoscale pore of the FET device via the first opening, passing through the nanoscale pore along the pore axis and exiting through the second opening of the aperture part into the second reservoir or vice versa, and wherein the electrolyte in the lumen has a resistance R and the electrolyte in the aperture has a resistance RA, such
• the resistance of the parts of the pore, RA, RL, RP, and RC may be tuned by adapting the geometry of the device, the concentration of a carrier in the electrolyte, and the surface charge.
• the first reservoir has a resistivity Re1
• the second reservoir has a resistivity Re2.
• the simulation method may be for designing a nanoscale pore Field-effect transistor (FET) device, the method comprising: providing a nanoscale pore (FET) device as defined above and below; uniformly filling the nanoscale pore and the first and second reservoirs with a single isotropic and uniformly conducting test material or test liquid; arranging the main electrode to make electrical contact with the test material or test liquid with negligible contact resistance by removing any thin dielectric on the main electrode, and adapting (S3) the geometry of the device such that: i) the resistance between the second reservoir and the main electrode, R1 corresponds to the resistance between the first reservoir and the main electrode, R2, such that R1 and R2 are not different by more than a factor of 6 or less than a factor of 1/6; or ii) the test resistance of the lumen part, R L ,
• the test resistance is the resistance that results from the simulation or experiment. Adapting in this case means adapting the geometry (size) of the parts of the device, especially the lumen part and aperture part.
• Figure 1 illustrates a schematic overview of the pore sensor, the pore having a lumen part and an aperture part separated by an electrical center, where the resistance above the electrical center (of the lumen part) is approximately half of the resistance below the electrical center (of the aperture part). Furthermore, cross-sections across the width of the pore are illustrated, being oriented substantially orthogonally to the length of the pore, having a pore axis running along the length of the pore.
• Figure 2 illustrates a schematic cross-section of a pore.
• Figure 3A illustrates a schematic cross-section of a pore where the aperture and lumen part are vertically oriented
• Figure 3B shows a lateral design where the lumen is rotated 90° so that it is perpendicular to the aperture.
• Figure 4 illustrates an example of a lateral device design.
• Figure 5 illustrates a further example of a lateral design.
• Figure 6 illustrates a further example of a lateral design comprising multiple sub-lumens.
• Figure 7 illustrates the correlation between the resistances Rc/Rp and the optimal signal modulation.
• Figure 8 illustrates schematic cross-sections of the asymmetric device design for a silicon pore FET (embedded nanopore), where Figure 8 (left) shows a side view (longitudinal crosssection) of the device, while Figure 8 (right) shows a top view (horizontal cross section) of the device.
• Figure 9 illustrates an alternative embodiment of the device in Figure 8, where a fourth layer may be arranged below the bottom dielectric material.
• Figure 9 (left) shows the introduction of a dielectric multi-layer consisting of multiple different dielectric materials, while 9 (right) shows the introduction of a 2D material below the bottom oxide.
• Figure 10 illustrates schematic cross-sections of the asymmetric device design for an extended gate pore FET, where 10 (left) shows a side view (longitudinal cross-section) of the device, while 10 (right) shows a top view (horizontal cross section) of the device.
• Figures 11A-D illustrate alternative designs of the present devices, where the location of the main electrode or conductive layer acting as channel may be varied.
• Figures 12A-B illustrate alternative designs of the present devices, where several conductive layers acting as channel or electrode connected thereto may be used, and that the location of these may vary.
• Figure 13 illustrates the pore bandwidth (BW) and SNR trade-off.
• Figure 13 (left) shows the impact of the design measures on the SNR, while Figure 13 (right) illustrates the impact of the design measures on the BW.
• Figure 15 shows the lumen length versus lumen diameter for different aperture sizes.
• molecule as in “target molecule” is used. This refers to any type of analyte that may be detected, identified, and quantified using the device and system of the invention.
• biomolecule In some embodiments a non-limiting term “biomolecule” is used.
• biopolymer may also be used interchangeably.
• target biomolecule or “target biopolymer” may be used, and thus refers to the biomolecule/biopolymer that the invention tries to sense/detect.
• the target biopolymers or biomolecules herein can be any type of biopolymers, such as polynucleotides, polypeptides, lipids, or polysaccharides, including DNA- or RNA-polymers, peptides, and proteins.
• a semiconductor material such as silicon, has an electrical conductivity value falling between that of a conductor and an insulator, and may conduct electric currents in the solid state.
• a transistor is a semiconductor device used to amplify or switch electrical signals and power.
• a field-effect transistor (FET) is a type of transistor that uses an electric field to control the flow of current in a semiconductor.
• FETs such as junction-gate field-effect transistors (JFETs) or metal-oxide-semiconductor field-effect transistor (MOSFETs) are devices with three terminals: source, gate, and drain. FETs control the flow of current by the application of a voltage to the gate, which in turn alters the conductivity between the drain and source.
• MOSFET is a type of field-effect transistor which is most commonly fabricated by the controlled oxidation of silicon. It has an insulated gate, the voltage of which determines the conductivity of the device. This ability to change conductivity with the amount of applied voltage can be used for amplifying or switching electronic signals.
• the gate material can be a layer of polysilicon (polycrystalline silicon).
• oxide different dielectric materials are used with the aim of obtaining strong channels with smaller applied voltages.
• SiO x Silicon oxide
• SiO2 Silicon dioxide
• cross-section and transverse cross-section when referring to the pore, are used interchangeably and refer to the shape of the pore when cut perpendicular to its axis or central pathway.
• the term 'pore' is used throughout this document to describe a structure characterized by an effective transverse cross-sectional diameter that is consistently less than 1 pm along its entire length. Additionally, the pore possesses at least one region where the effective transverse cross-sectional diameter is less than 50 nm. Given these dimensions, the pore qualifies as both a nanopore and a nanoscale pore.
• the term “pore field-effect transistor” should be construed as a FET, wherein a pore is used for providing a gate voltage to the FET.
• the pore could be separately arranged from the channel region of the FET.
• the pore could be provided with an electrode which is directly connected to a gate electrode of the FET arranged close to the channel region, such that a voltage of the gate electrode could be controlled by the electrode of the pore.
• the pore may be arranged in relation to the channel region, such that the pore may control the gate voltage directly, whereby the gate material is represented by the fluid inside the pore.
• the pore may be configured to extend through the channel region.
• nanopore-FET (NP-FET), “nanopore-FET device” , “nanoscale pore-FET” or “nanoscale pore-FET device” may be used interchangeably herein and refers to a device comprising a nanopore/nanoscale pore and a FET sensor, where the FET may be either embedded in the nanopore, or remote, i.e. where an electrode wrapped around the nanopore is connected to a remote gate sensor.
• nanoscale FETs gated by an electrolyte-filled nanopore running through the channel of the FET is provided, typically a silicon gate.
• an electrode is wrapped around the nanopore, which is connected to a remote FET, thus having an extended gate.
• Nanopores are pores of nanometer size that may be created by a pore-forming protein or as a hole in synthetic materials, such as silicon, silicon nitride or graphene. Typically, nanopores are quite narrow, with larger nanopores being up to 20 nm in effective diameter. However, in the current disclosure, the pores may be up to 1 micron in effective diameter, and thus, to emphasize the possible size of the pores, the term “nanoscale pore” is used interchangeably to nanopore herein. Nanopores may be organic when formed by pore-forming proteins, or they may be inorganic solid-state nanopores made for example in silicon compound membranes. The lack of large-scale tunability of the diameter of biological nanopore provided a motivation for the development of synthetic nanopores.
• Nanoscale pores or channels in solid state materials are fabricated by various means including ion beam sculpting, focused ion beam fabrication, transmission electron microscopy, electron beam fabrication, track-etching, dielectric break down, laser-assisted dielectric breakdown, laser-assisted etching, and layer- by-layer removal. These techniques make it possible to create nanopores with varying shapes and surface chemistries in a range of materials including silicon nitride, silicon dioxide, hafnium oxide, aluminum oxide, graphene, glass and polymer films.
• Nanopores have been shown to function as a single-molecule detector when present in an electrically insulating membrane, where a voltage is applied across the membrane and an ionic current passing through the nanopore is monitored.
• the membrane, biological or solid-state, comprising the nanopore is surrounded by an electrolyte solution, where the membrane may split the solution into two chambers.
• An electric field is attained by applying a bias voltage across the membrane, inducing an electric field that drives motion of charged particles (ions).
• all the voltage drop concentrates near and inside the nanopore such that charged particles in the solution only feel a force from the electric field when they are near the pore region, also denoted capture region.
• Nano-sized polymers such as DNA or protein having a net charge
• the molecule will then, if placed in one of the chambers, feel a force from the electric field when near the pore region.
• the molecule will be attracted to the pore capture region, enter the nanopore, and inside the nanopore translocate through via a combination of electro-phoretic, electro-osmotic and sometimes thermo-phoretic forces.
• the nanopores/nanoscale pores of the present disclosure are sometimes referred to as “pore”, and the pore may also refer to the inside of the nanopore, the nanopore channel, which has a pore axis running along the pore.
• the target molecules enter the device at the lumen part, but optionally the molecules may enter the pore at any opening.
• the nanoscale pore of the present devices may be a hybrid pore in a solid-state pore, such as comprising a biopore.
• a nanopore of molecular dimensions passage of molecules, such as DNA, cause interruptions of the current level of the open pore, leading to a signal as the molecule translocates through the pore.
• molecules such as DNA
• the molecule occupies a volume that partially restricts the flow of ions, observed as an ionic current drop.
• the characteristics of said interruption or disruption of the current may then be used to determine the sequence or identity of the molecule passing through the pore. Based on various factors such as geometry, size and chemical composition, the change in magnitude of the ionic current and the duration of the translocation will vary. Different molecules can then be sensed and potentially be identified based on this modulation in ionic current, which is referred to as nanopore sensing.
• Methods of using a sensor comprising a FET embedded in a nanopore may for example include placing the sensor in an electrolyte comprising at least one of biomolecules and deoxyribonucleic acid (DNA), placing an electrode in the electrolyte, applying a gate voltage in the sub-threshold regime to the electrode, applying a drain voltage to a drain of the FET, applying a source voltage to a source of the FET, detecting a change in a drain current in the sensor in response to the at least one of biomolecules and DNA passing through the nanopore.
• the nanopore FET is a transistor wrapped around a nanopore connecting two electrolyte reservoirs.
• the nanopore FET can detect target molecules passing through the nanopore as a change in a source-drain current of the nanopore FET.
• Designing dimensions of the nanopore FET involves optimizing geometry for formation of a carrier channel in semiconductor around the pore while avoiding leakage current from source to drain.
• Optimal sensitivity can be expected when potential perturbations by molecules in the nanopore impact electron density in the channel maximally.
• Sensitivity of the nanopore FET can be defined as maximal change in current due to presence of the molecule normalized by magnitude of the current.
• a pore field-effect transistor sensor for sensing target molecules
• the pore field-effect transistor sensor comprises a field-effect transistor having a source, a drain, a dielectric, a gate, and a channel region between the source and the drain, wherein the gate is controlled by a pore filled by an electrically conducting fluid (electrolyte) and the pore is configured to extend from a first side to a second side to provide gating of the field-effect transistor from within the pore, and wherein the pore field-effect transistor sensor further comprises a first electrode for setting a first voltage at the first side of the pore and a second electrode for setting a second voltage at the second side of the pore, wherein the molecule to be sensed passing through the fluid in the pore is configured to modulate the drain-source current for detecting presence of the molecule.
• the pore is configured to allow the target molecule to be detected/sensed to pass through the pore. Further, the pore is configured to have a cross-sectional dimension (effective diameter/area) at least in one location of the pore, such that the molecule to be detected blocks the pore to such an extent that potential perturbations within the pore are generated and the effective gate voltage of the FET is changed. Thus, when the molecule to be detected passes through the pore, the effective gate voltage of the FET will be changed such that the drain-source current of the FET will be modulated. This enables detecting the molecule being passed through the pore.
• the pore may be filled by a fluid during operation such that the molecule to be detected may be transported through the fluid for passing through the pore.
• a sample to be analyzed potentially comprising the target molecule, may be inserted into the fluid which is previously provided in the pore FET sensor. Alternatively, the sample may be introduced with the fluid into the pore FET sensor. The fluid (and the sample) may further be removed from the pore FET sensor and replaced so as to allow the pore FET sensor to analyze further samples.
• the FET may be a metal-oxide-semiconductor field-effect transistor (MOSFET) to provide current through the transistor in the subthreshold region.
• MOSFET metal-oxide-semiconductor field-effect transistor
• a voltage difference between the first voltage and the second voltage additionally drives the particle to be detected through the pore.
• the voltage difference between the first voltage and the second voltage may drive the molecules to be detected through the pore. If they are positively charged, they may be driven from the first side to the second side of the pore towards the lower potential set by the second voltage. If the molecules are negatively charged, they may be driven from the second side to the first side.
• the electrically conducting fluid may be provided with salt ions (or other ions) such that presence of an electric field in the fluid due to the difference between the first voltage and the second voltage may create a force on the fluid to generate a movement in the fluid that may drag along uncharged parts of the fluid, such as uncharged particles to be detected.
• the voltage difference provided for enabling detecting the particle to be detected with a high sensitivity may also control flow of the particle to be detected through the pore.
• the driving of particles to be detected through the pore may be provided by in other manners. This may be particularly useful for driving uncharged particles to be detected. For instance, driving of particles may be provided by a pressure difference between the first side and the second side of the pore and/or by a difference in concentration of the particles to be detected or of ions in the fluid, resulting in a fluid flow through the pore dragging particles to be detected along the fluid flow.
• FETs field effect transistors
• nanopores to develop pore FETs to sense target molecules, such as embedding a FET in the nanopore.
• the physical principles of electrolytical ly gated pore FETs are similar to that of the more conventional semiconductor FETs with the exception that the gate consists of an electrolyte containing ions rather than a solid-state metal or highly doped polysilicon gate.
• a potential advantage of using such platforms is that it could enable improved selectivity and controlled molecular transport; however, challenges remain including fabrication, operational stability, and ease of functionalization.
• nanopore FET nanopore FET
• This nano-scale FET-based approach may enable next-generation single-molecule sensing by offering larger signals and hence higher bandwidth, responding to a key challenge of detecting fast translocating molecules, and by offering denser electronic system packing and therefore more parallel sensing.
• a problem with noise occurs.
• the active area of the FET on the inside of the nanopore should be kept as small as possible, and for picking up an as large as possible signal due to translocating molecules the nanopore should be as small as possible, on the nanoscale, while for keeping the noise down, the size and area of the FET inside the nanopore, more particularly of the sensitive surface of the FET inside the nanopore should be large.
• FET-based nanopore sensors with sufficient SNR and short channel control, or good coupling to a remote FET, which all demand a larger nanopore, as well as high sensitivity to short molecules, high resolution and high bandwidth, which all demand smaller nanopores.
• the current disclosure relates to solving the problem of these opposite demands on the device.
• we provide a nanopore solution which satisfies these seemingly opposing sets of demands.
• the present disclosure provides a solution of how to combine a nanopore (a nanoscale pore) with FET-based sensing to read out molecules translocating through the nanopore at higher bandwidth than is possible when reading out ionic currents.
• nanopore FET devices which are nanoscale FETs gated by an electrolyte-filled nanopore running through the channel of the FET, or alternatively, an electrode wrapped around the nanopore may be connected to a remote FET, which have been designed to mitigate these drawbacks of the prior art.
• the key problem solved by these new devices is how to maintain low noise sensor characteristics while still obtaining a very strong translocation signal magnitude and while also discriminating or resolving sub- molecular features spaced apart on a nanometer scale on a (bio)polymer translocating the pore, and while also maintaining a bandwidth advantage (> 1-10MHz bandwidth with SNR>1).
• the device of the present disclosure provides a solution of how to combine a nanopore with FET-based sensing to read out molecules translocating through the nanopore at higher bandwidth than is possible when reading out ionic currents, while maintaining low noise characteristics.
• a pore e.g., nanopore
• FETs e.g., nanoscale FET
• electrolyte-filled pore running through the channel of the FET.
• the pore FET may comprise a sensor region, having a source region and a drain region, defining a source-drain axis, with a channel region between the source region and the drain region, where the pore (e.g., nanopore) may be defined as a an opening in the channel region which completely crosses through the channel region, oriented at an angle (such as orthogonally) to the source-drain axis, the nanopore may have multiple openings, such as having a first opening and a second opening, where the first opening is an opening between a lumen part of the pore (e.g., nanopore) and a first reservoir, which may be referred to as a lumen reservoir, and the second opening between an aperture part of the nanopore and a second reservoir, also referred to as an aperture reservoir.
• an electrode wrapped around the pore may be connected to a remote FET.
• the key problem solved by the devices of the present disclosure is how to maintain low noise sensor characteristics while still obtaining a very strong translocation signal magnitude and while also discriminating or resolving sub-molecular features spaced apart on a nanometer scale on a (bio)polymer translocating the pore, and while also maintaining a bandwidth advantage (> 1-10MHz bandwidth with SNR>1).
• a nanopore FET with a nanopore running through the nanoscale FET’s channel or for a nanopore running through a nanoscale electrode connected to a nanoscale FET a sufficiently high bandwidth can be obtained if the active area of the FET or electrode, on the inside of the nanopore, is kept sufficiently small, preferably on a sub-micron scale.
• the nanopore is preferred to be as small as possible, on the nanoscale ( ⁇ 50nm), both in terms of effective diameter and height.
• a low height is preferred for high resolution, where resolution is the ability to resolve closely spaced features on a molecule.
• the nanopore runs through the FET, the nanopore also determines the effective channel length and the area of the FET, as here the FET’s surface is formed by the inside of the nanopore.
• the effective length and area are desired to be as small as possible for the signal and bandwidth. This poses a problem.
• the size and area of the FET, or of an electrode connected to the gate of a remote FET, is important for the noise of the sensor, the larger the area, the less noise, and low noise is critical for sensors.
• nanoscale FETs suffer from short channel effects unless a particular geometric design is used, and these short channel effects will grow worse for smaller channel lengths.
• the nanopore sizes desired for large signal and high-resolution result in poor FET characteristics due to short channel effects.
• Short-channel effects occur when the channel length is the same order of magnitude as the depletion-layer widths of the source and drain junction. In MOSFETs, channel lengths must be greater than the sum of the drain and source depletion widths to avoid edge effects.
• a number of effects may appear, such as “off-state” leakage current, impact ionization, in which a charge carrier can be affected by other charge carriers, velocity saturation/mobility degradation, drain-induced barrier lowering (DIBL), which is caused by encroachment of the drain depletion region into the channel, drain punch through, whereby current flows regardless of gate voltage-a phenomenon that can occur if the drain is at high enough voltage compared to the source and the depletion region around the drain extends to the source, surface scattering, channel length modulation and threshold voltage roll-off.
• DIBL drain-induced barrier lowering
• Other problems arise due to the small size of the FET as well, such as increased variability. For remote gate sensors, the coupling to a remote FET will improve for larger electrode areas in the nanopore as well.
• the key challenge is how to obtain low noise (and suppress short channel effects or improve coupling) making use of such an unconventional nanopore gate, while also still obtaining a strong signal and resolution of molecules translocating through the nanopore, as well as while maintaining a bandwidth advantage.
• new nanopore/pore FET devices having an embedded FET or a remote FET
• the new FET-based pore e.g., nanoscale pore
• the noise characteristics as well as suppressed short channel effects for silicon gate, and better coupling for extended gate
• high translocation signal magnitude high bandwidth.
• the pore (e.g., nanoscale pore) of the FET-based pore (e.g., nanoscale pore) device comprises two main contiguous parts, a lumen part and an aperture part or aperture, wherein each part contains one end (or opening) of the pore.
• One end of the aperture pore part is fluidically connected to an aperture reservoir.
• the pore (e.g., nanoscale pore) further comprises a plurality of openings.
• the pore (e.g., nanoscale pore) comprises two openings, a first and a second opening, such that the lumen part is connected to the first opening and the aperture part is connected to the second opening.
• the lumen part comprises several sub-lumen parts, each in connection (e.g., direct fluidic connection) with an opening of the pore (e.g., nanoscale pore).
• the lumen part may comprise multiple sub-lumens each fluidically connecting the other end of the aperture part (the end not connected to the aperture reservoir) to a (different) reservoir (excluding the aperture reservoir).
• the lumen part comprises two subparts, a first sub-lumen and a second sub-lumen, wherein the first sub-lumen is connected (e.g., directly fluidically connected) to the first opening and the second sub-lumen is connected to a third opening.
• the openings in the pore leads to a plurality of reservoirs, such as one reservoir per opening, wherein the inside of the pore (e.g., nanoscale pore) is fluidically connected to the reservoirs.
• a plurality of reservoirs such as one reservoir per opening, wherein the inside of the pore (e.g., nanoscale pore) is fluidically connected to the reservoirs.
• one reservoir is connected to the aperture parts, and the other to multiple sub-lumen parts.
• the device comprises a third reservoir and the lumen part comprises two sub-parts, a first sub-lumen and a second sub-lumen connected to the first and third openings, respectively, wherein the third reservoir is in connection with the second sub-lumen of the pore (e.g., nanoscale pore) via the third opening, and wherein the pore is fl uidically connected to the first, second and third reservoir.
• the lumen part comprises two sub-parts, a first sub-lumen and a second sub-lumen connected to the first and third openings, respectively, wherein the third reservoir is in connection with the second sub-lumen of the pore (e.g., nanoscale pore) via the third opening, and wherein the pore is fl uidically connected to the first, second and third reservoir.
• pore e.g., nanoscale pore
• the device further comprises a pore axis oriented from the first opening to the second opening of the pore (e.g., nanoscale pore), wherein the one or more lumen parts and the aperture part of the pore (e.g., nanoscale pore) are oriented along the pore axis.
• the device further comprises a pore central pathway running from the first opening to the other openings of the pore, wherein the one or more lumen part and the aperture part of the pore are oriented along the pore central pathway.
• the pore axis is not necessarily linear, but may be bent, and also it may be split if the pore comprises more than two openings, such that the pore axis may head in two different directions towards different openings.
• the pore axis may be seen as a curve running through the center of the pore tubular structure.
• the center is the center of mass of the cross-section, or 2D cross- sectional shape (assuming uniform mass density) in a plane orthogonal to the pore axis.
• Target molecules may translocate through the nanopore along the pore axis, e.g. from a first reservoir into a second (or further) reservoir.
• the target molecules enter the pore (e.g., nanoscale pore) from a first reservoir via a first opening in the lumen part and exit the nanopore via the second opening in the aperture part, where the lumen part and aperture are oriented along the pore axis.
• the device includes a pore central pathway that extends from the first opening to the second opening of the pore.
• This pathway serves as a reference line for the orientation of the one or more lumen parts and the aperture part of the pore.
• the central pathway through the pore need not be straight and may even divide into branches.
• the central pathway may comprise a straight axis or a plurality of straight axis connected to one another at an angle or via a curved section.
• multiple straight axes may be defined, each extending toward different openings.
• axes can be understood as straight lines that pass through the center of mass of the pore's cross-sectional shape, assuming uniform mass density, in a plane that is perpendicular to each straight axis.
• Target molecules may move along pathways that are generally aligned with these axes, for example, transitioning from a first reservoir to a second or subsequent reservoir.
• the device may further comprise an electrical center (9, see Fig. 1) and at least one sensor region.
• the at least one sensor region is such that a target molecule travelling along the pore axis (i.e., passing through the pore) will pass through the sensor region (sensitive region).
• the sensor region may also be referred to as an electrode region.
• the sensor region of the pore comprises a sensitive gate surface exposed to the electrolyte of the pore.
• the sensor region is in between a source and drain region (source drain axis).
• the sensor region then comprises the semiconductor channel of the FET with the nanopore running through or beside the semiconductor channel.
• the channel has an electrical contact to both the source region and the drain region.
• the FET is instead remote, there are no source and drain regions near the sensor region, but the sensor region comprises a conducting (e.g. metal) electrode with the nanopore running through or beside it, and one contact to the electrode can suffice. This contact is in electrical connection to the gate of a remote FET.
• a conducting (e.g. metal) electrode with the nanopore running through or beside it, and one contact to the electrode can suffice. This contact is in electrical connection to the gate of a remote FET.
• the device comprises an electrical center comprising a sensor region of the device, the sensor region comprising the main electrode located between, and potentially overlapping, the lumen part and the aperture part of the pore (e.g., nanoscale pore).
• the main electrode overlaps at least one of the lumen parts and the aperture part of the pore.
• This sensor region is mostly in the lumen region to allow for a sufficiently large electrode size to enable low noise.
• the main electrode area is exposed for at least three quarters to the lumen part of the pore. The location of the sensor region mostly in the large lumen region importantly allows for a larger sensitive gate surface area then would be possible in the aperture region.
• the larger sensitive gate surface area allows low noise while still being sufficiently small to attain high bandwidths.
• the main electrode is made of an electrically conducting or semi-conducting material, such as but not limited to TiN, Ru, Pt, and silicon.
• a thin solid dielectric material (0.5-1 Onm), such as but not limited to AI2O3, TiC>2, ZrC>2, HfC>2, SisN4, SiC>2, may be present between the electrode and the space inside the pore.
• the main electrode is typically located on the wall of the pore.
• the main electrode is either the semiconductor of a metal-oxide-semiconductor field effect transistor (MOSFET) channel whereby the dielectric covering the electrode is the gate dielectric or it is electrically connected to the gate of a metal-oxide-semiconductor field effect transistor (MOSFET). In this last case, the electrode is electrically conducting. Additional electrodes may be present apart from the main electrode. Thus, in some embodiments the device comprises a main electrode and one or more additional electrodes. The additional electrode may be located in the aperture part or the lumen part of the nanopore.
• MOSFET metal-oxide-semiconductor field effect transistor
• the sensor region design of electrical center in the lumen has been “decoupled” from the aperture.
• the aperture determines the translocation signal.
• the decoupling enables an aperture with a small effective diameter and low height ( ⁇ 50nm) for a strong molecular signal, and a lumen, containing the sensor region, with larger effective diameter and height for low noise.
• the maintenance of a sufficiently small scale ( ⁇ 1um) for the lumen allows for maintaining high bandwidth and high integration density.
• the pore axis runs parallel to ion flow direction, through the center of cross sections of the pore, where the cross-sections are defined as a 2D shape formed by a cross-section of the pore tubular structure and a plane orthogonal to the nanopore axis running through the point on the pore axis. It should be appreciated that the pore axis does not necessarily need to be linear, but can also be bent, as discussed above.
• the lumen part and aperture part meet near the electrical center, which is the main electrode position, such that the aperture part is situated mainly “below” the main electrode, such that less than 25% of the electrode area of the electrical center is in the aperture part, and the lumen part is situated mainly “above” the main electrode, where the electrode may be situated entirely in the lumen part, and there may be a spacer in the lumen part separating the electrode from the aperture part.
• both high bandwidth and low noise may be attained.
• the asymmetric design allows to decouple the FET design in the lumen from the aperture, where the aperture determines the translocation signal. In this way the FET can be made larger to control the short channel effects, while still maintaining an optimal translocation signal, because the aperture can be made very small without affecting FET properties.
• the FET active area determines the bandwidth but can still be kept sufficiently small to realize bandwidths > 1-10MHz for which SNR > 1.
• the devices of the present disclosure allow a high-quality FET with suppressed short channel effects, an optimal signal magnitude and high resolution nanopore detector and high bandwidths (>1-10MHz bandwidth with SNR>1).
• FIG. 1 An embodiment of the invention is illustrated in Figure 1 , showing the lumen part (7) of the nanopore as the wide and long part of the pore, while the aperture part (8) is narrow and short.
• a cross-section may be made at a point on the pore axis; a 2D shape formed by the cross-section of the pore tubular structure and a plane orthogonal to the nanopore axis (i.e., the pore central pathway) (1) running through the point on the pore axis.
• the inside of the pore may not be fully circular, but may for instance be square or have other shapes.
• an effective cross-section diameter of any part of the pore e.g., nanoscale pore
• micron (1 pm micron
• the effective cross-section diameter may be an average diameter at a certain location if the pore is not circular in shape.
• the aperture part inside the pore has an effective cross-section diameter, dA, less than 50 nm, preferably smaller than 50 nm for all its transverse cross-sections.
• the length of the pore is not restricted to nanoscale lengths. Any cross-section of the lumen part is at least 50 nm.
• the area of at least 90% of the cross sections (2) of the lumen part (AL), e.g., all of them, is much larger than the area of any cross section of the aperture part (AA), such that AL>2AA, i.e.
• the area of at least 90% or any cross section of the lumen part is larger than twice the area of the largest aperture cross section. This may also be defined as that the largest cross-sectional area of at least 90% of the aperture part is smaller than half the area of the smallest cross sectional area taken across the 90% of the lumen part of the pore. Typically, the difference in size is even larger, such that the area of the majority, such as 3/4 (i.e. >75%), of the lumen cross sectional areas are at least 4 times larger than minimum pore cross section of the aperture part (AL>4AA), or even 8 or 16 times larger or more than minimum pore cross section of the aperture part (AL>8AAorAL>16AA).
• each sub-lumen of the lumen part has larger dimensions (effective cross-section diameter, along length) than the aperture part, as defined above. For instance, where more than three quarters of the cross-section areas are at least 4x larger than the minimum pore cross section area of the aperture parts, preferably 8x larger, even more preferably 16x larger.
• the area of the cross-section of the first reservoir near (e.g., at) the connection with the lumen part is at least 1pm. This distinguishes the reservoir from the lumen.
• the cross-section of the first reservoir is at least 1 pm along its whole length.
• the area of the cross-section of the first reservoir near (e.g., at) the connection with the aperture part is at least 50 nm. This distinguishes the reservoir from the aperture.
• the cross-section of the first reservoir is at least 50 nm along its whole length.
• the pore e.g., nanoscale pore
• the cross-section area at each opening (5, 6) of the pore (e.g., nanoscale pore), Ao may show an enlargement of the pore compared to an area inside the pore, Ai, such that at least Ao>4Ai.
• FIG. 2 An example of a pore shape is illustrated in Figure 2, a schematic cross-section of a pore (7, 8) having a narrow aperture (8) at the top, and a wide lumen (7) part below, with an electrode area (11) surrounding the top part of the lumen facing the aperture.
• the resistance of the aperture should be approximately double that of the resistance of the lumen because the signal amplitude to noise amplitude ratio (SNR) in that .
• SNR signal amplitude to noise amplitude ratio
• AG P is the modulation of the Gp aperture resistance when a target molecule passes by
• V is the total voltage applied across the total pore
• k is Boltzman’s constant
• T temperature and B bandwidth The reason to have an asymmetry between the aperture and the lumen is that a small aperture gives rise to a high translocation signal and high resolution, while a large lumen gives no disturbing translocation signal and can fit a large electrode. Larger electrodes mean less noise, and large electrode capacitance makes a device less sensitive to parasitic interconnect capacitance, providing better coupling to a remote FET, but it should not be too large to maintain bandwidth.
• FIG. 3A Example of schematic cross-sections of pore shapes are further illustrated in Figure 3.
• a pore (e.g., nanoscale pore) (7, 8) is illustrated having an aperture (8) at the top, and a lumen (7) part below, with an electrode area (11) surrounding the top part of the lumen facing the aperture.
• the layer thickness determines electrode size, and the layer thickness cannot typically be varied on the same wafer.
• the electrode size is fixed by the effective lumen diameter, and to keep lumen resistance half of aperture resistance, the lumen depth is set by the lumen effective diameter. Varying effective diameter on the same wafer is hence difficult, as one cannot change thicknesses easily.
• the maximum electrode size is limited by the achievable vertical etch aspect ratio.
• FIG. 4 A further example of a lateral device design is illustrated in Figure 4, showing the aperture (8), the lumen (7), a planar electrode (11) an insulator, a FET (3), a base of foundry Si (bottom layer), add-on processing on the foundry wafer (the whole structure minus the fluidics wall), and fluidics (top black rectangle) and a cis and trans reservoir and a pore (7, 8).
• Figure 5 illustrates a further example of a lateral design, in a zoomed-out view of the cross section.
• the device comprising a foundry wafer (two first bottom layers), a cis reservoir in connection with an aperture (8), a sensing electrode (11), a bias electrode (shown on the right side of the sensing electrode), and a large channel (e.g. height > 30 pm) to a trans reservoir, wherein the cis reservoir and the trans reservoir are separated by bonded glass or Si (black structure).
• Figure 6 illustrates a further example of a lateral design similar to Figure 5, but comprising multiple sub-lumens (7a, 7b).
• the device typically comprises a wall/walls having a width/thickness w surrounding the nanopore.
• the area and the thicknesses of the insulating walls surrounding the pore are such that the total summed capacitances between the electrolyte inside the pore and the outside electrical conductors, such as the first and second reservoirs and including the electrode, is smaller than 50fF, preferably smaller than 10fF even more preferably smaller than 1fF.
• the geometry of the nanoscale pore is such that 1) if the pore and reservoirs are uniformly filled (in simulation) with a single isotropic and uniformly conducting test material or test liquid and 2) if it is made sure (in experiment or theory) that the main electrode makes electrical contact with this test material or liquid with negligible contact resistance (by removing any thin dielectric on the electrode) and negligible electrode resistance, then the (test) resistance between the aperture reservoir as electrically contacted by that reservoir’s electrode and the main electrode (R1) approximately equals the (test) resistance between the lumen reservoir as electrically contacted by that reservoir’s electrode and the main electrode (R2). Approximately equal resistance here refers to equal within a factor of 1/6 to 6 or more preferably within a factor of 1/3 to 3. In other words, R1/R2 may be from 1/6 to 6 or 1/3 to 3.
• the geometry of the pore is such that 1) if the pore and reservoirs are uniformly filled (in simulation) with a single isotropic and uniformly conducting test material or test liquid and 2) if it is made sure (in experiment or theory) that the main electrode makes electrical contact with this test material or liquid with negligible contact resistance (by removing any thin dielectric on the electrode) and negligible electrode resistance, then the (test) resistance between the aperture reservoir as electrically contacted by that reservoir’s electrode and the main electrode (RA) approximately equals double the (test) resistance between the lumen reservoir as electrically contacted by that reservoir’s electrode and the main electrode (R ). Approximately double resistance here refers to equal within a factor of 0.27 to 23 or more preferably within a factor of 0.57 to 8.6. In other words, RA/RL may be from 0.27 to 23 or 0.57 to 8.6.
• the geometry of the pore is such that if the pore and reservoirs are uniformly filled (in experiment or theory) with a single isotropic and uniformly conducting test material or test liquid and 2) if it is made sure in experiment or theory that the main electrode makes electrical contact with this test material or liquid with negligible contact resistance (by removing any thin dielectric on the electrode) and negligible electrode resistance, then the lumen test resistance (R ) approximately equals theta/2 (0/2) times the aperture test resistance (RA), i.e. 0/2* RA . Approximately here refers to 0* R A / RL being within the range of 0.27 to 23 or more preferably within a range of 0.57 to 8.6.
• Theta (0) is the resistivity of the electrolyte of the aperture reservoir/second reservoir (the nanopore device is meant to be used with) Re1 , divided by the resistivity of the electrolyte of the lumen reservoir (the
• Equation 2
• the resistance of the lumen part, RL is approximately half the resistance of the aperture part, RA, when no molecule is translocating through the pore, such that RA® 2 RL.
• RL may be described approximately a
• Equation 5 i.e. the optimal resistive divider condition of the geometry independent of electrolyte.
• the total resistance may be approximately defined as: .. Equation 6 , where p is the resistivity.
• A(l) is the area of the cross section at position along pore axis /, and top, bottom, electrode bottom and electrode top correspond to positions along the pore axis, where electrode refers to the main electrode.
• Rtop and rbottom is the effective cross-section radius at the ends of the pore.
• F is the demanded proportion between resistances, F ranges from 0.27 to 23, more preferably from 0.57 to 8.6.
• the pore part above the main electrode will have approximately half the resistance of the pore part below the main electrode, where the pore above and below the electrical center (9) may correspond to the lumen (7) and aperture (8) part, or may be partially overlapping as the main electrode may be partially situated in the different parts as discussed above, thus the pore above and below the main electrode is not necessarily the same as pore lumen part and pore aperture part, in which the resistance of pore below the electrode may be referred to as Rp (which may be identical to RA, and the resistance of the pore above the electrode may be referred to as Rc (which may be identical to R ).
• Rp resistance of pore below the electrode
• Rc resistance of the pore above the electrode
• the largest part (>75%) of the area of the main electrode is exposed to the lumen part of the pore (the wide part of the pore).
• a pore where the pore part above and pore part below the (main) electrode have approximately double resistance may be realized in different ways. It can for example be translated in purely geometric criterium independent of electrolyte.
• the electrode satisfying this equal resistance criterium most closely is the main electrode, others are optional auxiliary electrodes. It should be noted that an electrode does not need to entirely wrap around pore.
• the electrode is typically made of a conductive material, which may be selected from (but not limited to) the of following materials; titanium nitride, TiN, ruthenium, Ru or platinum, Pt, or silicon, Si.
• the electrode can for example be covered with a thin dielectric.
• R c /Rp can be in a range of 0.04 - 650, this would imply a reduction by at most a factor of 1/10 versus the optimal signal to noise ratio (SNR > 10% of the optimal value).
• R C /R P can be in a range of 0.27 - 23 which would imply a reduction by at most a factor of 1/2 versus the optimal signal to noise ratio (SNR > 50% of the optimal value), or in a third example, R C /R P can be in a range of 0.57 - 8.6 which would imply a reduction by at most a factor of 3/4 of the optimal signal to noise ratio (SNR > 75% of optimal SNR).
• Approximately double the resistance may refer here to being in a range of 0.27 - 23 or more preferably within a range of 0.57 - 8.6. This is illustrated in Figure 7, where the relation between the ratio of resistances and the optimal signal to noise ratio is shown, such that x1/2 of optimal signal modulation corresponds to 0.27 - 23 leeway in R C /R P , and similarly that x3/4 of optimal signal modulation corresponds to 0.57 - 8.6 leeway in R C /R P .
• the lumen part is so large, the height or length of the lumen part of the nanopore can be larger than 1 micron, such as multiple microns, or multiple 10s of microns, or larger, and the cross sections is so large, but typically smaller than 1 micron in effective diameter, that when a target molecule passes through, no significant modulation of the resistance (R ) occurs, while the aperture part is so narrow, the height being 50 nm or smaller and the effective diameter being 20 nm or smaller, that when a target molecule passes through, a significant modulation of the resistance (RA) occurs.
• the lumen part may have a uniform shape (typically of equal width) or may be tapered, becoming smaller and smaller when approaching the aperture, to relax requirements on the top part.
• the lumen part of the pore need not necessarily have a uniform crosssection, but the pore may have a shape of a truncated cone, such that the pore provides a minimum cross-section at one end of the pore and a maximum cross-section at an opposite end of the pore.
• a nanopore-FET device is illustrated according to an embodiment, wherein the nanopore (4) is embedded in the FET, such that the FET is gated by an electrolyte-filled nanopore running through the channel region of the FET, where Figure 8 (left) illustrates a side view of the device/pore, and Figure 8 (right) illustrates a top view.
• the device comprises a semiconductor wall having a width/thickness w surrounding the nanopore, where the wall thickness w is 10 nm or less, such as 5nm or less, which wall thickness is illustrated as Si wall thickness in Figure 8 (right).
• Wall width/thickness is the width of the electrode/channel between lumen and opposing channel edge.
• the Si wall thickness is the width of the silicon channel formed at the narrowest constriction between the pore and sidewall passivation.
• the wall comprises at least three different layers comprising at least two different materials, the layers being arranged on top of each other such that a dielectric material is arranged at the top and bottom of the pore, the top dielectric layer having a height /7 ox _to P and the bottom dielectric layer having a height /lox bottom, and a conductive/semi-conductive material (11) is arranged in the middle of the pore and having a height h S i, the semiconductor material typically being silicon (Si) and having a height defined as hsi of 5-100nm, or more.
• the effective diameters of the lumen part and aperture part i.e.
• the effective diameter of the lumen part, d ⁇ _ is in the range of 50-300 nm, and the effective diameter of the aperture part, is less than 20 nm.
• the semiconductor wall width and the FET width from a top view of the device/pore are illustrated in Figure 8 (right).
• the demands on the device for realizing a high signal readout with low noise include that it should attain a negligible signal from the lumen part of the pore, which is attained by the majority of the lumen part of the pore being wide, and that the area of cross sections of the lumen part should be much larger than the aperture part, such as typically 4 or even 8 times larger, as described above.
• a second demand, to attain the high signal and high resolution is that the aperture part of the pore should be small, such as being short (a low height h A ) and narrow (a small effective diameter dA and thus a small area AA of a cross section of the aperture part).
• the signal strength may be independent of the resolution as defined by
• Equation 7 where hAis the height (length) of the aperture part, and AA is the area of an aperture cross section.
• the size of the aperture may be adapted based on the application of the nanopore FET device, such that desired resolution and limits are met, where the size of the aperture opening (6), i.e. the effective diameter of the aperture, is typically sub 50 nm, such as sub 20 nm.
• a third demand on the device is the resistive divider criterion, to obtain the highest signal or signal to noise ratio for the overall pore, such that the resistance of the lumen part is approximately the same as the aperture part for maximal signal and such that the resistance of the lumen part is approximately half that of the aperture part for maximal signal-to-noise ratio.
• the demands above are structural demands, wide pore in lumen part (or part above electrical center) and narrow and short pore in the aperture part (or part below electrical center), which are independent of electrolyte. Assuming a uniform electrolyte, and as we aim 1
• resistivity drops out of the equation, resulting in a purely geometric definition.
• the criterion would be the same if the empty space is filled with any material of uniform conductivity.
• the surface charge is not accounted for.
• the definition can be altered, where a parameter can be introduced which depends on electrolyte conditions. It could be noted that surface charge is non-ideal, which is sought to be avoided. Surface charge matters less at the typical high salinities used for nanopores.
• the nanopore of the FET-based nanopore device consists of two parts, an aperture with a small effective diameter and low height as well as a lumen with larger effective diameter and height.
• the aperture with smaller effective diameter is defined in a dielectric layer below the silicon semiconductor layer.
• the thickness of the aperture dielectric layer is reduced in order to increase the resolution with which features can be resolved on a translocating molecule.
• the thickness of the bottom insulator is preferred to be of a similar thickness (or somewhat smaller) as the molecular feature to be detected.
• the aperture effective diameter is preferred as small as possible.
• the lumen with larger diameter is defined in the silicon layer and an insulator layer on top of the silicon.
• the silicon layer is preferably between 5 and 100nm thick.
• the top oxide thickness is chosen to obtain an optimal signal magnitude, which is obtained for an optimal resistive divider condition, where the electrolyte in the top insulator part or lumen part (including access and spreading resistances) should have equal resistance as the electrolyte in the aperture part (including access and spreading resistances).
• the effective diameter of the lumen is chosen larger than the effective diameter of the aperture resulting in an “asymmetric device” (large lumen, small aperture), in order to still allow for an optimal signal magnitude while allowing a thicker silicon or electrode layer (5-100nm).
• the lumen part of the nanopore may have a uniform shape (substantially equal effective diameter throughout) or a tapered shape.
• the relation between the sizes of the lumen and aperture parts are essential to the invention, as this enables the larger bandwidth and low noise.
• the present design allows to decouple the FET design in the lumen from the aperture which determines the translocation signal. In this way the FET can be made larger to control the short channel effects, while still maintaining an optimal translocation signal, because the aperture can be made very small without affecting FET properties.
• the FET active area determines the bandwidth but can still be kept sufficiently small to realize bandwidths > 1- 10MHz.
• the present devices allow a high-quality FET with suppressed short channel effects, an optimal signal magnitude and resolution nanopore detector and high bandwidths (>1-10MHz.).
• the devices of the present preferably operated with bandwidths over 100kHz, even more preferably with bandwidths higher than 1MHz due to nanoscale crosssections of fluidic passage.
• the nanopore effective diameter in the lumen part should not be made too small, such that it may be beneficial to maintain a pore effective diameter larger than 10nm, preferably larger than 20nm.
• a pore effective diameter larger than 10nm preferably larger than 20nm.
• increasing nanopore effective diameter decreases signal strength. This is avoided here by providing the narrower ‘aperture’ pore in the bottom insulator. This aperture will determine signal strength.
• the wall thickness is the width of the silicon channel formed at the narrowest constriction between pore and sidewall passivation.
• This semiconductor wall thickness could be reduced below 10nm, preferably below 5nm.
• thinning down the silicon of the FET further suppresses short channel effects.
• short channel effects depend on the channel length of the FET device (the distance between source and drain junctions) and the effects become worse for decreasing gate length. Hence, the distance of the source and drain junctions may be adjusted to regulate the short channel effects.
• the FET may be embedded in the nanopore, and the aperture has a height corresponding to the height of the bottom layer.
• different designs may be possible.
• One variation allows for a thicker dielectric on the bottom of the silicon to prevent shunting currents running in the bottom of the silicon.
• Another variation makes use of a 2D material (e.g., boron nitride, graphene, dichalcogenide) as the aperture material to realize the thinnest possible aperture membrane for very high molecular resolution, as illustrated in Figure 9.
• a 2D material e.g., boron nitride, graphene, dichalcogenide
• introduction of a dielectric multi-layer consisting of multiple different dielectric materials allows for a thicker dielectric on the bottom of the (silicon) wall while still having a thin aperture height (haperture, 11A). This may be advantageous for suppressing shunt currents on the bottom of the Si, which grow larger with thinner oxides on the bottom of the silicon.
• the thin aperture height allows a higher resolution for resolving closely spaced features on target molecules.
• introducing a 2D material (as discussed above) below the bottom oxide allows for an atomically thin aperture layer (low h A ) for which a very high resolution to resolve closely spaced features on molecules is attained.
• an extended gate variation of the present device is presented, where the silicon in the pore is replaced with an electrode material, wherein the device comprises a remote, extended gate FET, where an electrode wrapped around the nanopore is connected to a remote FET.
• the electrode material is typically a metal, such as titanium nitride, TiN, ruthenium, Ru or platinum, Pt, which is coupled to the gate of a silicon transistor remote from the pore.
• the design allows a sufficiently large metalelectrolyte surface area of the electrode material in the lumen and hence a larger capacitance of the electrode. This allows to limit the signal reduction due to the coupling to a readout transistor, which may be implemented in relatively standard CMOS technology.
• a standard CMOS FET typically has a larger capacitance than an aggressively scaled device. Having an increased electrode capacitance leads to a reduced signal decrease due to the capacitive divider which determines signal transfer between electrode and remote FET. A larger electrode with larger capacitance also leads to less signal reduction due to the interconnect capacitance due to the electrode-to-FET interconnect. More standard CMOS technology may be preferred due to cost reasons, and also because analog design prefers larger FETs to suppress noise and variability.
• Figure 10 illustrates an example of the remote gate sensor embodiment, Figure 10 (left) illustrating a side view of the device/pore, and 10 (right) illustrating a top view.
• the metal electrode is connected to the gate of a nearby FET (3) implemented in standard CMOS technology.
• the middle layer, hj S in this embodiment is made from a metal is illustrated in Figure 10 (right, short vertical double arrows at the top and bottom of the circle).
• the embedded FET silicon pore-FET
• the remote FET extended gate pore-FET
• the larger lumen does not affect the signal (which is caused by the molecule in the aperture).
• the lumen resistance approximately equals half the aperture resistance.
• the resistance of the lumen should be approximately half the resistance of the aperture region. Or the resistance of the region above the electrical center should be half that of the resistance of the region below the electrical center.
• the aperture effective diameter and height are kept low to enhance signal magnitude and resolution, respectively.
• noise reduction with maintained signal means the Signal-to-Noise Ratio (SNR) is improved when enlarging the lumen.
• the capacitance associated with the active area determines the bandwidth limit due to the electrode-to-electrolyte capacitance. When enlarging the lumen to enhance SNR, the lumen can still be kept sufficiently small to allow the SNR gains but also realize bandwidths above 1-10MHz.
• the FET can be made larger to control the short channel effects of the silicon nanopore-FET.
• the larger nanopore FET also entails lower FET noise, and hence higher SNR.
• the extended gate nanopore-FET embodiment due to the design one can have a large metal-electrolyte surface area of the electrode material in the lumen and this means a larger capacitance of the electrode.
• the larger capacitance allows to strongly limit the signal reduction due to the capacitive coupling to the readout FET. Moreover, this also allows to choose a larger readout transistor as typically preferred in analog technology, and for cost reasons.
• Figure 11 illustrates some possible alternative designs of the present devices.
• Figure 11A illustrates the general concept having a first part of the pore, a lumen part (7), and a second part of the pore, an aperture part (8), where a conductive material, acting as channel or having an electrode connected thereto, is present in the lower part of the lumen part.
• Figure 11 B a first variation of the concept is illustrated, where parts of the pore are the same, but the main electrode is located both in the lumen (first) part and aperture (second) part of the pore.
• FIG 11 C a second variation of the main concept is illustrated, where the conductive material, acting as channel or having an electrode connected thereto, is present in the lower part of the lumen part, but with a spacer between the main electrode and the aperture part of the pore.
• Figure 11 D a third variation of the main concept is illustrated, where a slanted/sloped main electrode is used. Besides the main electrode, a plurality of additional electrodes may be used, such as one or two additional electrodes besides the main electrode, thus the apparatus may have multiple sensor regions.
• FIG 12A depicting a first cavity (lumen) (7), and a second cavity (aperture) (8), where a conductive layer, acting as channel or having an electrode connected thereto, is present in the lower part of the first cavity, and in addition, a second electrode in present in the second cavity.
• a conductive layer acting as channel or having an electrode connected thereto
• a second electrode in present in the second cavity.
• both the main electrode and the additional electrode is located in the first cavity, thus enabling direct charge sensing.
• a nanopore Field-effect transistor (FET) device comprising a nanopore/nanopore sensor and a FET.
• the nanopore sensor of the present disclosure preferably comprises a solid state nanopore.
• the nanopore is embedded in the FET, such that the FET is gated by an electrolyte-filled nanopore running through the channel region of the FET.
• the device comprises a remote FET, where an electrode wrapped around the nanopore is connected to the remote FET.
• a system comprising said device may also be provided.
• the system may comprise a first and second reservoir, optionally comprising an electrically conducting fluid, such as an electrolyte, a nanopore sensor device, as described above and below, comprising a nanopore connecting the two reservoirs.
• the target molecules/sample to be analyzed may be present in the first reservoir, and may during operation of the device exit the first reservoir, enter the lumen of the nanopore of the device, translocate through the nanopore along the pore axis and exit through the aperture into the second reservoir, wherein the lumen/ electrolyte in the lumen has a resistance R and the aperture/electrolyte in the aperture has a resistance RA, and the aperture has a size such that a significant modulation of the resistance RA occurs when a target molecule translocates through the aperture, while the lumen has a size such that no significant modulation of the resistance R occurs when a target molecule translocates through the lumen.
• the pore (e.g., nanopore) sensor may comprise a first and second electrolyte reservoir, respectively, being separated by a barrier comprising a nanopore.
• the sensor/system may further comprise electrodes for translocating molecules through the nanopore from the first electrolyte reservoir to the second electrolyte reservoir, wherein at least one of the first and second electrolyte reservoirs comprises the target molecule.
• the pore (e.g., nanopore) may have an aperture through which the molecule is translocated.
• the term "effective diameter" of the pore (e.g., nanopore) at a particular location refers to the average diameter of the pore at that location. According to an embodiment, the resistance of the pore parts may be tuned.
• the aperture and lumen resistance can be tuned by having a low surface charge shallow pore (aperture part) combined with a high surface charge high pore (lumen part).
• a concentration of the surface charges is in a range of 1x10 12 - 1x10 15 cm -2 .
• Tuning surface charges can be used to tune the resistance of the pore or parts of it.
• the surface charge concentration is very high, the surface charges could cause a high ion concentration in the fluid in the pore, such that an impact of the charge of the particle to be detected on the effective gate voltage may be reduced and, hence, the modulation of the electrical potential distribution in the pore by the particle to be detected may be reduced. Therefore, the surface charge concentration should preferably not be too high.
• simulation methods are further provided for designing a pore Field-effect transistor (FET) device according to the invention, where the measurements of the device are tuned/adapted to attain desired resistance properties.
• FET Field-effect transistor
• Example 1 siqnal-to-noise ratio (SNR) of different designs As discussed above, a smaller lumen with smaller electrode surface allows higher bandwidth, and a certain bandwidth target determines a ceiling for lumen radius and silicon or electrode area. However, SNR favors increasing lumen size.
• the lumen radius was 40nm and the Si thickness which is identical to the electrode height in this case is 100nm as in the device illustrated in figure 9 or 10. It was observed upon simulation that the bandwidth is still above 100MHz. It was thus concluded that the lumen can still be considerably large while still allowing high bandwidth.
• a smaller lumen radius reduces the height-to-diameter aspect ratio of the lumen - AR becomes smaller for smaller radius, and higher aspect ratios are more difficult to realize/process.
• the SNR grows with the square root of the Si (or electrode) thickness. This is due to a decrease in noise. The dependence of signal on Si thickness is weak. There is no SNR advantage when making silicon thin.
• a nanopore design where the lumen radius is large vs. the aperture radius, results in high resolution because of the thin aperture. There is no strong lumen geometry dependence of the resolution for said asymmetric design, as the resolution depends on the aperture.
• Figure 13 illustrating the pore bandwidth (BW) and SNR trade-off.
• Figure 13 (left) shows the impact of the design measures on the SNR
• Figure 13 (right) illustrates the impact of the design measures on the BW.
• nanoscaling is driven by bandwidth, with SNR gains for larger devices becoming limited. Processing considerations also favor smaller effective lumen diameter in this particular design, and lumen aspect ratio becomes difficult for larger radius.
• the main electrode area is key to obtain the desired SNR and bandwidth properties.
• figure 15 plots the lumen length versus lumen diameter for large lumen diameters in the order of microns.
• the lumen length for a flow-through lumen as illustrated in figure 6 the lumen reaches lengths in the order of millimeters, particularly for highly resistive, small apertures.
• Such lengths will not allow to integrate such pores in high numbers in the order of tens of thousands, preferably hundreds of thousands or millions on a single chip and are hence not desirable.
• a single-ended horizontal lumen would be four times shorter, but the lumen length increases when scaling diameter above 1 micron would still be undesirable for scaling up the number of pore components per chip.
• vertical lumens of such length are undesirable to integrate on chip.

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• 2023
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