Nanopore device and method of manufacturing same
11371981 · 2022-06-28
Assignee
Inventors
Cpc classification
B01D67/0079
PERFORMING OPERATIONS; TRANSPORTING
B82B3/0014
PERFORMING OPERATIONS; TRANSPORTING
B82B1/001
PERFORMING OPERATIONS; TRANSPORTING
G01N33/48721
PHYSICS
B01D67/0034
PERFORMING OPERATIONS; TRANSPORTING
B01D67/00791
PERFORMING OPERATIONS; TRANSPORTING
B01D71/70
PERFORMING OPERATIONS; TRANSPORTING
B01D69/12
PERFORMING OPERATIONS; TRANSPORTING
B01D67/0062
PERFORMING OPERATIONS; TRANSPORTING
B82B3/0019
PERFORMING OPERATIONS; TRANSPORTING
B01D71/0215
PERFORMING OPERATIONS; TRANSPORTING
International classification
B01D67/00
PERFORMING OPERATIONS; TRANSPORTING
B82B3/00
PERFORMING OPERATIONS; TRANSPORTING
B01D69/12
PERFORMING OPERATIONS; TRANSPORTING
B82B1/00
PERFORMING OPERATIONS; TRANSPORTING
Abstract
A 3D nanopore device for characterizing biopolymer molecules includes a first selecting layer having a first axis of selection. The device also includes a second selecting layer disposed adjacent the first selecting layer and having a second axis of selection orthogonal to the first axis of selection. The device further includes an third electrode layer disposed adjacent the second selecting layer, such that the first selecting layer, the second selecting layer, and the third electrode layer form a stack of layers along a Z axis and define a plurality of nanopore pillars.
Claims
1. A 3D nanopore device for characterizing biopolymer molecules, comprising: a first Si.sub.3N.sub.4 layer deposited on a first dielectric layer; a first metal layer deposited on the first Si.sub.3N.sub.4 layer; a second dielectric layer deposited on the first metal layer; a second Si.sub.3N.sub.4 layer deposited on the second dielectric layer; a second metal layer deposited on the second Si.sub.3N.sub.4 layer; a third dielectric layer deposited on the second metal layer; a third Si.sub.3N.sub.4 layer deposited on the third dielectric layer; a third metal layer deposited on the third Si.sub.3N.sub.4 layer; a first plurality of elongate gate electrodes etched and patterned into the second metal layer; and second plurality of elongate gate electrodes etched and patterned into the third metal layer, wherein each of the first plurality of elongate gate electrodes is disposed in the second metal layer, wherein each of the first plurality of elongate gate electrodes is parallel to the other elongate gate electrodes of the first plurality of elongate gate electrodes, wherein each of the second plurality of elongate gate electrodes is parallel to the other elongate gate electrodes of the second plurality of elongate gate electrodes, and wherein the first and second pluralities of elongate gate electrodes are orthogonal to each other along the second and third metal layers respectively.
2. The system of claim 1, further comprising a plurality of nanopore channels etched into the first and second pluralities of parallel elongate gate electrodes, the second and third Si.sub.3N.sub.4 layers, and the second and third dielectric layers.
3. The system of claim 2, further comprising a bottom chamber fluidly coupled to the plurality of nanopore channels.
4. The system of claim 2, further comprising a middle chamber between top and bottom chambers, wherein the first dielectric layer, the first Si.sub.3N.sub.4 layer, the first metal layer, the second dielectric layer, the second Si.sub.3N.sub.4 layer, and the second metal layer are disposed in the middle chamber; and an electrolyte solution disposed in the top, middle, and bottom chambers, such that the top and bottom chambers are fluidly coupled by the plurality of nanopore channels.
5. The system of claim 4, further comprising top and bottom chamber electrodes disposed in the top and bottom chambers respectively, wherein the top and bottom chamber electrodes each comprise Ag/AgCl.sub.2.
6. The device of claim 4, wherein the electrolyte solution comprises KCl or LiCl.sub.2.
7. The system of claim 2, further comprising top and inner surface dielectric coatings deposited on an inner surface of a nanopore channel of the plurality of nanopore channels to functionalize the inner surface of the nanopore channel of the plurality of nanopore channels for a biomolecular interaction.
8. The system of claim 7, wherein the top and inner surface dielectric coatings form a gate electrode dielectric for sensing.
9. The system of claim 7, wherein the top and inner surface dielectric coatings are configured to adjust a width of the nanopore.
10. The system of claim 7, wherein the inner dielectric coating comprises Al.sub.2O.sub.3, SiO.sub.2, ZnO, or HfO.
11. The system of claim 7, wherein the inner dielectric coating has a thickness of about 10 nm to about 50 nm.
12. The system of claim 7, wherein the top dielectric coating comprises Si.sub.3N.sub.4, Al.sub.2O.sub.3, or SiO.sub.2.
13. The system of claim 7, wherein the top dielectric coating has a thickness of about 5 nm to about 50 nm.
14. The system of claim 2, wherein each of the plurality of nanopore channels has respective diameters from about 2 nm to about 100 nm.
15. The system of claim 1, further comprising a stack of dielectric layers, including the second and third dielectric layers; a stack of Si.sub.3N.sub.4 layers, including the second and third Si.sub.3N.sub.4 layers; a stack of metal layers, including the second and third metal layers; and a nanopore channel etched into the respective stacks of dielectric layers, Si.sub.3N.sub.4 layers, and metal layers.
16. The system of claim 1, wherein the first plurality of elongate gate electrodes are a first plurality of inhibitory electrodes.
17. The system of claim 16, wherein the second plurality of elongate gate electrodes are a second plurality of inhibitory electrodes.
18. The system of claim 17, wherein the first and second pluralities of inhibitory electrodes form an array partially defining the plurality of a plurality of nanopore channels.
19. The system of claim 1, further comprising a sensing electrode layer.
20. The system of claim 19, wherein the sensing electrode layer is configured to operate by ion blockade, tunneling, capacitive sensing, piezoelectric, or microwave-sensing.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
(1) The foregoing and other aspects of embodiments are described in further detail with reference to the accompanying drawings, in which the same elements in different figures are referred to by common reference numerals, wherein:
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(9) In order to better appreciate how to obtain the above-recited and other advantages and objects of various embodiments, a more detailed description of embodiments is provided with reference to the accompanying drawings. It should be noted that the drawings are not drawn to scale and that elements of similar structures or functions are represented by like reference numerals throughout. It will be understood that these drawings depict only certain illustrated embodiments and are not therefore to be considered limiting of scope of embodiments.
DETAILED DESCRIPTION OF ILLUSTRATED EMBODIMENTS
Exemplary Nanopore Devices
(10) As described above, current state-of-art nanopore devices are limited at least in terms of sensitivity and manufacturing cost. The nanopore device embodiments described herein address, inter alia, these limitations of current nanopore devices.
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(12) The top 2D array 202A includes first and second selecting (inhibitory electrode) layers 206, 208 configured to direct movement of charged particles (e.g., biopolymers) through the nanopores 210 (pillars) formed in the first and second selecting layers 206, 208. The first selecting layer 206 is configured to select from a plurality of rows (R1-R3) in the 2D array 202A. The second selecting layer 208 is configured to select from a plurality of columns (C1-C3) in the 2D array 202A. In one embodiment, the first and second selecting layers 206, 208 select from the rows and columns, respectively, by modifying a charge adjacent the selected row and column and/or adjacent to the non-selected rows and columns. The other 2D arrays 202B-202E include rate control/current sensing electrodes. Rate control electrodes may be made of highly conductive metals, such as Au—Cr, TiN, TaN, Pt, Cr, Graphene, Al—Cu, etc. The rate control electrodes may have a thickness of about 2 to about 1000 nm. Rate control electrodes may also be made in the biological layer in hybrid nanopores.
(13) Hybrid nanopores include a stable biological/biochemical component with solid state components to form a semi-synthetic membrane porin to enhance stability of the nanopore. For instance, the biological component may be an αHL molecule. The αHL molecule may be inserted into a SiN based 3D nanopore. The αHL molecule may be induced to take on a structure to ensure alignment of the αHL molecule with the SiN based 3D nanopore by apply a bias to an electrode (e.g., in the top 2D array 202A).
(14) The nanopore device 200 has a 3D vertical pillar stack array structure that provides a much larger surface area for charge detection than that of a conventional nanopore device having a planar structure. As a charged particle (e.g., biopolymer) passes through each 2D array 202A-202E in the device, its charge can be detected with a detector (e.g., electrode) in some of the 2D arrays 202B-202E. Therefore, the 3D array structure of the device 200 facilitates higher sensitivity, which can compensate for a low signal detector/electrode. Further, the highly integrated small form factor 3D structure provides a high density nanopore array while minimizing manufacturing cost.
(15) In use, the nanopore device 200 is disposed in a middle chamber separating top and bottom chambers (not shown) such that the top and bottom chambers are fluidly coupled by the nanopore pillars 210. The top, middle, and bottom chambers include an electrolyte solution (e.g., Ag, AgCl.sub.2, etc.) containing the charged particles (e.g., DNA) to be detected. Different electrolyte solutions can be used for the detection of different charged particles.
(16) Electrophoretic charged particle translocation can be driven by applying a bias to electrodes disposed in a top chamber (not shown) adjacent the top 2D array 202A of the nanopore device 200 and a bottom chamber (not shown) adjacent the bottom 2D array 202E of the nanopore device 200. In some embodiments, the nanopore device 200 is disposed in a middle chamber (not shown) such that the top and bottom chambers are fluidly and electrically coupled by the nanopore pillars 210 in the nanopore device 200. The top, middle, and bottom chambers may contain the electrolyte solution.
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(18) By applying an inhibitory electrical bias (0V-VCC) to select nanogap nano-electrodes 312CS-312Cn, 312RS-312Rn in the top 2D array 302, biomolecular translocation (e.g., electrophoretic) through one or more nanopores 302 in the top 2D nanopore array 302 can be inhibited to control nanopore array operation according to one embodiment. The electrical bias applied to the nano-electrodes 312CS-312Cn, 312RS-312Rn can generate an electric field sufficient to suppress ionic translocation of charged particles (e.g., nucleic acids) from a top chamber (not shown) to a bottom chamber (not shown) in a direction orthogonal to the nano-electrodes 312CS-312Cn, 312RS-312Rn. Nano-electrode 312 mediated ionic translocation suppression can be substantially complete or the electrical bias can be modulated to only reduce the rate of ionic translocation. In one embodiment, after one or more nanopores 310 are selected (e.g., for DNA biomolecules translocation and sequencing), the electrical biases in a stack of 3D nanopore nano-electrodes 312 can be modulated to control the biomolecular translocation speed. In one embodiment, the inhibitory electrical bias reduces/stops ionic current flow in the vertical direction to thereby select and/or deselect various columns and rows defined by the nanogap nano-electrodes 312CS-312Cn, 312RS-312Rn. At the same time, the nano-electrodes 312 can detect current modulations resulting from passage of charged particles (e.g., DNA biomolecules) through the 3D vertical nanopore 310 pillars. In some embodiments, the nano-electrodes 312 can detect current modulations using a variety of principles, including ion blockade, tunneling, capacitive sensing, piezoelectric, and microwave-sensing.
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(21) 3D nanopore devices (e.g., 200, 300) allow either direct or targeted sequencing in an array while minimizing form-factor overhead, because the 2D arrays 202, 302 in the nanopore devices 200, 300 can be stacked vertically instead of positioned horizontally, thereby allowing for high density applications. Further, 3D nanopore devices (e.g., 200, 300) are scalable, with medium to large 3D nanopore devices having more than 1,000 nanopore 210, 310 pillars. Consequently, a larger number of sequencing sensors can be accommodated within the same form-factor. 3D nanopore devices (e.g., 200, 300) can also incorporate biological nanopore or hybrid nanopore technologies to provide more architectural flexibility to accommodate a user's needs.
(22) In 3D nanopore devices (e.g., 300), each nanopore 310 pillar is composed of a stack of nano-electrodes 312 defining a plurality of nanopores 310. As such, the effective surface area of the sensors in each nanopore 310 column can be orders of magnitude greater than the surface area of a single sensor. In one embodiment, the effective sensor surface area can be 2-3 orders of magnitude greater than the surface area of a single sensor. This increase in effective sensor surface area can significantly improve the sensor signal to noise ratio and sensitivity, while minimizing manufacturing costs.
Exemplary Nanopore Device Manufacturing Methods
(23) 3D nanopore devices (e.g., 200, 300) can be manufactured utilizing many different methods. In one embodiment, a semiconductor technology (e.g., CMOS process, described below) is used to manufacture 3D nanopore devices 200, 300. The CMOS process also allows nanopore 310 width to be tunable using a large nanopore array. In one embodiment, nanopore 310 width can be controlled during manufacturing using software with a look up table, allowing for mass production manufacturing. Using a CMOS process can embed biosensor solutions in CMOS technology. In various embodiments, the CMOS process includes a 2-dim well for electrochemical reactions and/or an ion-sensitive filed effect transistor technology. Microfluidic channels can be integrated into the 3D nanopore devices 200, 300 (e.g., within a die), therefore reducing the cost of the devices 200, 300.
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(34) The 3D nanopore device may facilitate multiplex sequencing applications using high density low cost nanopore channels. A number of electrodes in the 3D nanopore device may be selected depending on the required sequencing applications to provide a Time of Flight (“TOF”) technique to control the translocation speed by controlled biasing. Controlling the translocation speed may improve reading of DNA molecules and improves a sensitivity of the sensor. The 3D nanopore device may also facilitate an electro-chemical, thermal, or electro-optical reaction to take place in an enlarged, separated nanopore well with a multi-electrode system to enhance electrochemical and/or sequencing reactions. The 3D nanopore device may further facilitate multiplex sequencing using a multi-array configuration wherein individual nanopore channel pillars are addressable. Moreover, the 3D nanopore device may further facilitate standard qPCR within a nanopore channel pillar and/or probe-mediated targeted sequencing. In addition, the 3D nanopore channel opening width is tunable for different applications. In one embodiment, the nanopore channel opening width is tunable from about 1 nm to about 100 nm. The nanopore channel opening width may be electronically tunable during manufacturing. The 3D nanopore devices described herein can be used in the detection of various charged particles, including but not limited to biomolecules such as nucleotides, nucleic acids, and proteins (direct detection). The 3D nanopore devices can also be used in DNA sequencing and detection of protein-DNA interactions.
(35) Manufacturing metal or polysilicon plane based nanopore arrays using lithographic processes (e.g., Through-Silicon Via (“TSV”) fabrication) minimizes manufacturing cost and line resistance (which significantly reduces IR drop and RC delay limitations to scaling).
(36) The corresponding structures, materials, acts and equivalents of all means or step plus function elements in the claims below are intended to include any structures, materials, acts and equivalents for performing the function in combination with other claimed elements as specifically claimed. It is to be understood that while the invention has been described in conjunction with the above embodiments, the foregoing description and claims are not to limit the scope of the invention. Other aspects, advantages and modifications within the scope to the invention will be apparent to those skilled in the art to which the invention pertains.
(37) Various exemplary embodiments of the invention are described herein. Reference is made to these examples in a non-limiting sense. They are provided to illustrate more broadly applicable aspects of the invention. Various changes may be made to the invention described and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process act(s) or step(s) to the objective(s), spirit or scope of the present invention. Further, as will be appreciated by those with skill in the art that each of the individual variations described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present inventions. All such modifications are intended to be within the scope of claims associated with this disclosure.
(38) Any of the devices described for carrying out the subject diagnostic or interventional procedures may be provided in packaged combination for use in executing such interventions. These supply “kits” may further include instructions for use and be packaged in sterile trays or containers as commonly employed for such purposes.
(39) The invention includes methods that may be performed using the subject devices. The methods may comprise the act of providing such a suitable device. Such provision may be performed by the end user. In other words, the “providing” act merely requires the end user obtain, access, approach, position, set-up, activate, power-up or otherwise act to provide the requisite device in the subject method. Methods recited herein may be carried out in any order of the recited events which is logically possible, as well as in the recited order of events.
(40) Exemplary aspects of the invention, together with details regarding material selection and manufacture have been set forth above. Other details of the present invention, these may be appreciated in connection with the above-referenced patents and publications as well as generally known or appreciated by those with skill in the art. The same may hold true with respect to method-based aspects of the invention in terms of additional acts as commonly or logically employed.
(41) In addition, though the invention has been described in reference to several examples optionally incorporating various features, the invention is not to be limited to that which is described or indicated as contemplated with respect to each variation of the invention. Various changes may be made to the invention described and equivalents (whether recited herein or not included for the sake of some brevity) may be substituted without departing from the true spirit and scope of the invention. In addition, where a range of values is provided, it is understood that every intervening value, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention.
(42) Also, it is contemplated that any optional feature of the inventive variations described may be set forth and claimed independently, or in combination with any one or more of the features described herein. Reference to a singular item, includes the possibility that there are plural of the same items present. More specifically, as used herein and in claims associated hereto, the singular forms “a,” “an,” “said,” and “the” include plural referents unless the specifically stated otherwise. In other words, use of the articles allow for “at least one” of the subject item in the description above as well as claims associated with this disclosure. It is further noted that such claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.
(43) Without the use of such exclusive terminology, the term “comprising” in claims associated with this disclosure shall allow for the inclusion of any additional element—irrespective of whether a given number of elements are enumerated in such claims, or the addition of a feature could be regarded as transforming the nature of an element set forth in such claims. Except as specifically defined herein, all technical and scientific terms used herein are to be given as broad a commonly understood meaning as possible while maintaining claim validity.
(44) The breadth of the present invention is not to be limited to the examples provided and/or the subject specification, but rather only by the scope of claim language associated with this disclosure.