1
|
Penkov B, Niedzwiecki D, Lari N, Drndić M, Shepard K. Time-domain event detection using single-instruction, multiple-thread gpGPU architectures in single-molecule biophysical data. COMPUTER PHYSICS COMMUNICATIONS 2024; 300:109191. [PMID: 38737416 PMCID: PMC11086699 DOI: 10.1016/j.cpc.2024.109191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Discrete amplitude levels in ordered, time-domain data often represent different underlying latent states of the system that is being interrogated. Analysis and feature extraction from these data sets generally require considering the order of each individual point; this approach cannot take advantage of contemporary general-purpose graphics processing units (gpGPU) and single-instruction multiple-data (SIMD) instruction set architectures. Two sources of such data from single-molecule biological measurements are nanopores and single-molecule field effect transistor (smFET) nanotube devices; both generate streams of time-ordered current or voltage data, typically sampled near 1 MS/s, with run times of minutes, yielding terabyte-scale datasets. Here, we present three gpGPU-based algorithms to overcome limitations associated with serial event detection in time series data, resulting in a 250× improvement in the rate with which we can detect salient features in nanopore and smFET datasets. The code is freely available.
Collapse
Affiliation(s)
- Boyan Penkov
- Department of Electrical Engineering, Columbia University, New York, NY, 10027
| | - David Niedzwiecki
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Nicolae Lari
- Department of Electrical Engineering, Columbia University, New York, NY, 10027
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kenneth Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, 10027
| |
Collapse
|
2
|
Mehrafrooz B, Yu L, Pandey L, Siwy ZS, Wanunu M, Aksimentiev A. Electro-osmotic Flow Generation via a Sticky Ion Action. ACS NANO 2024. [PMID: 38832758 DOI: 10.1021/acsnano.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Selective transport of ions through nanometer-sized pores is fundamental to cell biology and central to many technological processes such as water desalination and electrical energy storage. Conventional methods for generating ion selectivity include placement of fixed electrical charges at the inner surface of a nanopore through either point mutations in a protein pore or chemical treatment of a solid-state nanopore surface, with each nanopore type requiring a custom approach. Here, we describe a general method for transforming a nanoscale pore into a highly selective, anion-conducting channel capable of generating a giant electro-osmotic effect. Our molecular dynamics simulations and reverse potential measurements show that exposure of a biological nanopore to high concentrations of guanidinium chloride renders the nanopore surface positively charged due to transient binding of guanidinium cations to the protein surface. A comparison of four biological nanopores reveals the relationship between ion selectivity, nanopore shape, composition of the nanopore surface, and electro-osmotic flow. Guanidinium ions are also found to produce anion selectivity and a giant electro-osmotic flow in solid-state nanopores via the same mechanism. Our sticky-ion approach to generate electro-osmotic flow can have numerous applications in controlling molecular transport at the nanoscale and for detection, identification, and sequencing of individual proteins.
Collapse
Affiliation(s)
- Behzad Mehrafrooz
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Luning Yu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Laxmi Pandey
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Zuzanna S Siwy
- Department of Physics, University of California at Irvine, Irvine, California 92697, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
3
|
Seth S, Bhattacharya A. DNA Barcodes Using a Dual Nanopore Device. Methods Mol Biol 2024; 2744:197-211. [PMID: 38683320 DOI: 10.1007/978-1-0716-3581-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.
Collapse
|
4
|
Cai S, Ren R, He J, Wang X, Zhang Z, Luo Z, Tan W, Korchev Y, Edel JB, Ivanov AP. Selective Single-Molecule Nanopore Detection of mpox A29 Protein Directly in Biofluids. NANO LETTERS 2023; 23:11438-11446. [PMID: 38051760 PMCID: PMC10755749 DOI: 10.1021/acs.nanolett.3c02709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
Single-molecule antigen detection using nanopores offers a promising alternative for accurate virus testing to contain their transmission. However, the selective and efficient identification of small viral proteins directly in human biofluids remains a challenge. Here, we report a nanopore sensing strategy based on a customized DNA molecular probe that combines an aptamer and an antibody to enhance the single-molecule detection of mpox virus (MPXV) A29 protein, a small protein with an M.W. of ca. 14 kDa. The formation of the aptamer-target-antibody sandwich structures enables efficient identification of targets when translocating through the nanopore. This technique can accurately detect A29 protein with a limit of detection of ∼11 fM and can distinguish the MPXV A29 from vaccinia virus A27 protein (a difference of only four amino acids) and Varicella Zoster Virus (VZV) protein directly in biofluids. The simplicity, high selectivity, and sensitivity of this approach have the potential to contribute to the diagnosis of viruses in point-of-care settings.
Collapse
Affiliation(s)
- Shenglin Cai
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Ren Ren
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Jiaxuan He
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Xiaoyi Wang
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Zheng Zhang
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Zhaofeng Luo
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Weihong Tan
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Yuri Korchev
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| |
Collapse
|
5
|
Mehrafrooz B, Yu L, Siwy Z, Wanunu M, Aksimentiev A. Electro-Osmotic Flow Generation via a Sticky Ion Action. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571673. [PMID: 38168277 PMCID: PMC10760089 DOI: 10.1101/2023.12.14.571673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Selective transport of ions through nanometer-sized pores is fundamental to cell biology and central to many technological processes such as water desalination and electrical energy storage. Conventional methods for generating ion selectivity include placement of fixed electrical charges at the inner surface of a nanopore through either point mutations in a protein pore or chemical treatment of a solid-state nanopore surface, with each nanopore type requiring a custom approach. Here, we describe a general method for transforming a nanoscale pore into a highly selective, anion-conducting channel capable of generating a giant electro-osmotic effect. Our molecular dynamics simulations and reverse potential measurements show that exposure of a biological nanopore to high concentrations of guanidinium chloride renders the nanopore surface positively charged due to transient binding of guanidinium cations to the protein surface. A comparison of four biological nanopores reveals the relationship between ion selectivity, nanopore shape, composition of the nanopore surface, and electro-osmotic flow. Remarkably, guanidinium ions are also found to produce anion selectivity and a giant electro-osmotic flow in solid-state nanopores via the same mechanism. Our sticky-ion approach to generate electro-osmotic flow can have numerous applications in controlling molecular transport at the nanoscale and for detection, identification, and sequencing of individual proteins.
Collapse
Affiliation(s)
- Behzad Mehrafrooz
- Center for Biophysics and Quantitative Biology
- Beckman Institute for Advanced Science and Technology
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Luning Yu
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Zuzanna Siwy
- Department of Physics, University of California at Irvine, Irvine, CA 92697, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA 02115 USA
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology
- Beckman Institute for Advanced Science and Technology
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| |
Collapse
|
6
|
Irving OJ, Matthews L, Coulthard S, Neely RK, Grant MM, Albrecht T. Sterically Enhanced Control of Enzyme-Assisted DNA Assembly. Chembiochem 2023; 24:e202300361. [PMID: 37681318 DOI: 10.1002/cbic.202300361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/15/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
Traditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100 bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA that spatially restrict enzymatic activity. This approach, sterically controlled nuclease enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, when using the same starting materials, conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.
Collapse
Affiliation(s)
- Oliver J Irving
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Lauren Matthews
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Steven Coulthard
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Melissa M Grant
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital, Birmingham Community Healthcare Trust), 5 Mill Pool Way, Edgbaston, Birmingham, B5 7EG, UK
| | - Tim Albrecht
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| |
Collapse
|
7
|
Mereuta L, Asandei A, Andricioaei I, Park J, Park Y, Luchian T. Considerable slowdown of short DNA fragment translocation across a protein nanopore using pH-induced generation of enthalpic traps inside the permeation pathway. NANOSCALE 2023; 15:14754-14763. [PMID: 37655668 DOI: 10.1039/d3nr03344a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
A pressing challenge in the realm of nanopore-based sensing technologies for nucleic acid characterization has been the cheap and efficient control of analyte translocation. To address this, a plethora of methods were tested, including mutagenesis, molecular motors, enzymes, or the optimization of experimental conditions. Herein, we present a paradigm exploiting the manipulation of electrostatic interactions between 22-mer single-stranded DNAs (22_ssDNA) and low pH-induced charges in the alpha-hemolysin (α-HL) nanopore, to efficiently control the passage of captured molecules. We discovered that in electrolytes buffered at pH = 5 and pH = 4.5 where the nanopore's vestibule and lumen become oppositely charged as compared to that at neutral pH, the electrostatic anchoring at these regions of a 22_ssDNA fragment leads to a dramatic increase of the translocation time, orders of magnitude larger compared to that at neutral pH. This pH-dependent tethering effect is reversible, side invariant, and sensitive to the ionic strength and ssDNA contour length. In the long run, our discovery has the potential to provide a simple read-out of the sequence of bases pertaining to short nucleotide sequences, thus extending the efficacy of current nanopore-based sequencers.
Collapse
Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Ioan Andricioaei
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, CA 92617, USA
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, 61452, Republic of Korea.
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
| |
Collapse
|
8
|
Ganjalizadeh V, Hawkins AR, Schmidt H. Adaptive time modulation technique for multiplexed on-chip particle detection across scales. OPTICA 2023; 10:812-818. [PMID: 38818330 PMCID: PMC11138143 DOI: 10.1364/optica.489068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Integrated optofluidic biosensors have demonstrated ultrasensitivity down to single particle detection and attomolar target concentrations. However, a wide dynamic range is highly desirable in practice and can usually only be achieved by using multiple detection modalities or sacrificing linearity. Here, we demonstrate an analysis technique that uses temporal excitation at two different time scales to simultaneously enable digital and analog detection of fluorescent targets. We demonstrated the seamless detection of nanobeads across eight orders of magnitude from attomolar to nanomolar concentration. Furthermore, a combination of spectrally varying modulation frequencies and a closed-loop feedback system that provides rapid adjustment of excitation laser powers enables multiplex analysis in the presence of vastly different concentrations. We demonstrated this ability to detect across scales via an analysis of a mixture of fluorescent nanobeads at femtomolar and picomolar concentrations. This technique advances the performance and versatility of integrated biosensors, especially toward point-of-use applications.
Collapse
Affiliation(s)
- Vahid Ganjalizadeh
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California, 95064, USA
| | - Aaron R. Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, Utah, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California, 95064, USA
| |
Collapse
|
9
|
Yanagi I, Akahori R, Takeda KI. Dwell Time Prolongation and Identification of Single Nucleotides Passing through a Solid-State Nanopore by Using Ammonium Sulfate Aqueous Solution. ACS OMEGA 2023; 8:21285-21292. [PMID: 37332803 PMCID: PMC10268630 DOI: 10.1021/acsomega.3c02703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
The ionic current blockades when poly(dT)60 or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)2SO4 were investigated. The dwell time of poly(dT)60 in the nanopores in an aqueous solution containing (NH4)2SO4 was significantly longer compared to that in an aqueous solution that did not contain (NH4)2SO4. This dwell time prolongation effect due to the aqueous solution containing (NH4)2SO4 was also confirmed when dCTP passed through the nanopores. In addition, when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)2SO4, the dwell time prolongation effect for dCTP still occurred even after the aqueous solution was displaced with the aqueous solution without (NH4)2SO4. Furthermore, we measured the ionic current blockades when the four types of dNTPs passed through the same nanopore, and the four types of dNTPs could be statistically identified according to their current blockade values.
Collapse
Affiliation(s)
- Itaru Yanagi
- Center
for Exploratory Research, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Rena Akahori
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Ken-ichi Takeda
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| |
Collapse
|
10
|
Kitta K, Sakamoto M, Hayakawa K, Nukazuka A, Kano K, Yamamoto T. Nanopore Impedance Spectroscopy Reveals Electrical Properties of Single Nanoparticles for Detecting and Identifying Pathogenic Viruses. ACS OMEGA 2023; 8:14684-14693. [PMID: 37125101 PMCID: PMC10134219 DOI: 10.1021/acsomega.3c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
In the conventional nanopore method, direct current (DC) is used to study molecules and nanoparticles; however, it cannot easily discriminate between materials with similarly sized particles. Herein, we developed an alternating current (AC)-based nanopore method to measure the impedance of a single nanoparticle and distinguish between particles of the same size based on their material characteristics. We demonstrated the performance of this method using impedance measurements to determine the size and frequency characteristics of various particles, ranging in diameter from 200 nm to 1 μm. Furthermore, the alternating current method exhibited high accuracy for biosensing applications, identifying viruses with over 85% accuracy using single-particle measurement and machine learning. Therefore, this novel nanopore method is useful for applications in materials science, biology, and medicine.
Collapse
Affiliation(s)
- Kazuki Kitta
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Maami Sakamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kei Hayakawa
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Akira Nukazuka
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazuhiko Kano
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Takatoki Yamamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| |
Collapse
|
11
|
Aluru NR, Aydin F, Bazant MZ, Blankschtein D, Brozena AH, de Souza JP, Elimelech M, Faucher S, Fourkas JT, Koman VB, Kuehne M, Kulik HJ, Li HK, Li Y, Li Z, Majumdar A, Martis J, Misra RP, Noy A, Pham TA, Qu H, Rayabharam A, Reed MA, Ritt CL, Schwegler E, Siwy Z, Strano MS, Wang Y, Yao YC, Zhan C, Zhang Z. Fluids and Electrolytes under Confinement in Single-Digit Nanopores. Chem Rev 2023; 123:2737-2831. [PMID: 36898130 PMCID: PMC10037271 DOI: 10.1021/acs.chemrev.2c00155] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification to new gas permeable materials for water electrolyzers and energy-storage devices. SDNs also present unique opportunities to achieve ultrasensitive and selective chemical sensing at the single-ion and single-molecule limit. In this review article, we summarize the progress on nanofluidics of SDNs, with a focus on the confinement effects that arise in these extremely narrow nanopores. The recent development of precision model systems, transformative experimental tools, and multiscale theories that have played enabling roles in advancing this frontier are reviewed. We also identify new knowledge gaps in our understanding of nanofluidic transport and provide an outlook for the future challenges and opportunities at this rapidly advancing frontier.
Collapse
Affiliation(s)
- Narayana R Aluru
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Fikret Aydin
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Daniel Blankschtein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Alexandra H Brozena
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Samuel Faucher
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - John T Fourkas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Hao-Kun Li
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Yuhao Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zhongwu Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Arun Majumdar
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Joel Martis
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Rahul Prasanna Misra
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Tuan Anh Pham
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Haoran Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - Archith Rayabharam
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Mark A Reed
- Department of Electrical Engineering, Yale University, 15 Prospect Street, New Haven, Connecticut06520, United States
| | - Cody L Ritt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Eric Schwegler
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zuzanna Siwy
- Department of Physics and Astronomy, Department of Chemistry, Department of Biomedical Engineering, University of California, Irvine, Irvine92697, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Yun-Chiao Yao
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Cheng Zhan
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Ze Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| |
Collapse
|
12
|
Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device. Sci Rep 2022; 12:11305. [PMID: 35787637 PMCID: PMC9253098 DOI: 10.1038/s41598-022-14609-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/09/2022] [Indexed: 11/08/2022] Open
Abstract
We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on a 48 kbp long dsDNA at the left and the right pore. We study the effect of the electric field inside and beyond the pores, critical to discriminate the protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore. The simulation protocols monitor piecewise dynamics at a sub-nanometer length scale and explain the disparate velocity using the concepts of nonequilibrium tension propagation theory. We further justify the model and the chosen simulation parameters by calculating the Péclet number which is in close agreement with the experiment. We demonstrate that our carefully chosen simulation strategies can serve as a powerful tool to discriminate different types of neutral and charged tags of different origins on a dsDNA construct in terms of their physical characteristics and can provide insights to increase both the efficiency and accuracy of an experimental dual-nanopore setup.
Collapse
|
13
|
Rand A, Zimny P, Nagel R, Telang C, Mollison J, Bruns A, Leff E, Reisner WW, Dunbar WB. Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control. ACS NANO 2022; 16:5258-5273. [PMID: 35302746 PMCID: PMC9048701 DOI: 10.1021/acsnano.1c09575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.
Collapse
Affiliation(s)
- Arthur Rand
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Philip Zimny
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Roland Nagel
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Chaitra Telang
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Justin Mollison
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Aaron Bruns
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Emily Leff
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Walter W. Reisner
- Department
of Physics, McGill University, 3600 Rue University, Montreal, QC, Canada H3A 2T8
| | - William B. Dunbar
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| |
Collapse
|
14
|
Tsutsui M, Arima A, Yokota K, Baba Y, Kawai T. Ionic heat dissipation in solid-state pores. SCIENCE ADVANCES 2022; 8:eabl7002. [PMID: 35148181 PMCID: PMC8836805 DOI: 10.1126/sciadv.abl7002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Energy dissipation in solid-state nanopores is an important issue for their use as a sensor for detecting and analyzing individual objects in electrolyte solution by ionic current measurements. Here, we report on evaluations of heating via diffusive ion transport in the nanoscale conduits using thermocouple-embedded SiNx pores. We found a linear rise in the nanopore temperature with the input electrical power suggestive of steady-state ionic heat dissipation in the confined nanospace. Meanwhile, the heating efficiency was elucidated to become higher in a smaller pore due to a rapid decrease in the through-water thermal conduction for cooling the fluidic channel. The scaling law suggested nonnegligible influence of the heating to raise the temperature of single-nanometer two-dimensional nanopores by a few kelvins under the standard cross-membrane voltage and ionic strength conditions. The present findings may be useful in advancing our understanding of ion and mass transport phenomena in nanopores.
Collapse
Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
15
|
Qiu H, Zhou W, Guo W. Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing. ACS NANO 2021; 15:18848-18864. [PMID: 34841865 DOI: 10.1021/acsnano.1c07960] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.
Collapse
Affiliation(s)
- Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| |
Collapse
|
16
|
Wang Y, Sadar J, Tsao CW, Mukherjee S, Qing Q. Nanopore chip with self-aligned transverse tunneling junction for DNA detection. Biosens Bioelectron 2021; 193:113552. [PMID: 34416434 DOI: 10.1016/j.bios.2021.113552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
To achieve better signal quality and resolution in nanopore sequencing, there has been strong interest in quantum tunneling based detection which requires integration of tunneling junctions in nanopores. However, there has been very limited success due to precision and reproducibility issues. Here we report a new strategy based on feedback-controlled electrochemical processes in a confined nanoscale space to construct nanopore devices with self-aligned transverse tunneling junctions, all embedded on a nanofluidic chip. We demonstrate high-yield (>93%) correlated detection of translocating DNAs from both the ionic channel and the tunneling junction with enriched event rate. We also observed events attributed to non-translocating DNA making contact with the transverse electrodes. Existing challenges for precise sequencing are discussed, including fast translocation speed, and interference from transient electrostatic signals from fast-moving DNAs. Our work can serve as a first step to provide an accessible, and reproducible platform enabling further optimizations for tunneling-based DNA detection, and potentially sequencing.
Collapse
Affiliation(s)
- Yuan Wang
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Joshua Sadar
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Ching-Wei Tsao
- School for Engineering of Matter, Transport & Energy, And Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States
| | - Sanjana Mukherjee
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Quan Qing
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States; Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States.
| |
Collapse
|
17
|
Tang Z, Nouri R, Dong M, Yang J, Greene W, Zhu Y, Yon M, Nair MS, Kuchipudi SV, Guan W. Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores. Biosens Bioelectron 2021; 197:113759. [PMID: 34741956 PMCID: PMC8560184 DOI: 10.1016/j.bios.2021.113759] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/25/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022]
Abstract
The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the disease spread. Here, we present an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2. We validated and compared two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes. The nucleocapsid assay was adopted due to its quick time to positive and better copy number sensitivity. For qualitative positive/negative classification of a testing sample, we used the glass nanopore to digitally count the RT-LAMP amplicons and benchmarked the event rate with a threshold. Due to its intrinsic single molecule sensitivity, nanopore sensors could capture the amplification dynamics more rapidly (quick time to positive). We validated our RT-LAMP coupled glass nanopore digital counting method for SARS-CoV-2 detection by using both spiked saliva samples and COVID-19 clinical nasopharyngeal swab samples. The results obtained showed excellent agreement with the gold standard RT-PCR assay. With its integration capability, the electronic nanopore digital counting platform has significant potential to provide a rapid, sensitive, and specific point-of-care assay for SARS-CoV-2.
Collapse
Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Jianbo Yang
- Department of Pathology and Laboratory Medicine, Penn State Hershey Medical, Hershey, PA, 17033, United States
| | - Wallace Greene
- Department of Pathology and Laboratory Medicine, Penn State Hershey Medical, Hershey, PA, 17033, United States
| | - Yusheng Zhu
- Department of Pathology and Laboratory Medicine, Penn State Hershey Medical, Hershey, PA, 17033, United States
| | - Michele Yon
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, 16802, United States
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, 16802, United States
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, 16802, United States; Center for Infectious Disease Dynamic, Pennsylvania State University, University Park, PA, 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, United States.
| |
Collapse
|
18
|
Nouri R, Jiang Y, Tang Z, Lian XL, Guan W. Detection of SARS-CoV-2 with Solid-State CRISPR-Cas12a-Assisted Nanopores. NANO LETTERS 2021; 21:8393-8400. [PMID: 34542296 PMCID: PMC8491552 DOI: 10.1021/acs.nanolett.1c02974] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/16/2021] [Indexed: 05/12/2023]
Abstract
The outbreak of the SARS-CoV-2 caused the disease COVID-19 to spread globally. Specific and sensitive detection of SARS-CoV-2 facilitates early intervention and prevents the disease from spreading. Here, we present a solid-state CRISPR-Cas12a-assisted nanopore (SCAN) sensing strategy for the specific detection of SARS-CoV-2. We introduced a nanopore-sized counting method to measure the cleavage ratio of reporters, which is used as a criterion for positive/negative classification. A kinetic cleavage model was developed and validated to predict the reporter size distributions. The model revealed the trade-offs between sensitivity, turnaround time, and false-positive rate of the SARS-CoV-2 SCAN. With preamplification and a 30 min CRISPR Cas12a assay, we achieved excellent specificity against other common human coronaviruses and a limit of detection of 13.5 copies/μL (22.5 aM) of viral RNA at a confidence level of 95%. These results suggested that the SCAN could provide a rapid, sensitive, and specific analysis of SARS-CoV-2.
Collapse
Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Yuqian Jiang
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Zifan Tang
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Department of Biology, Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Weihua Guan
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| |
Collapse
|
19
|
Knowles SF, Weckman NE, Lim VJY, Bonthuis DJ, Keyser UF, Thorneywork AL. Current Fluctuations in Nanopores Reveal the Polymer-Wall Adsorption Potential. PHYSICAL REVIEW LETTERS 2021; 127:137801. [PMID: 34623825 DOI: 10.1103/physrevlett.127.137801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Modification of surface properties by polymer adsorption is a widely used technique to tune interactions in molecular experiments such as nanopore sensing. Here, we investigate how the ionic current noise through solid-state nanopores reflects the adsorption of short, neutral polymers to the pore surface. The power spectral density of the noise shows a characteristic change upon adsorption of polymer, the magnitude of which is strongly dependent on both polymer length and salt concentration. In particular, for short polymers at low salt concentrations no change is observed, despite the verification of comparable adsorption in these systems using quartz crystal microbalance measurements. We propose that the characteristic noise is generated by the movement of polymers on and off the surface and perform simulations to assess the feasibility of this model. Excellent agreement with experimental data is obtained using physically motivated simulation parameters, providing deep insight into the shape of the adsorption potential and underlying processes. This paves the way toward using noise spectral analysis for in situ characterization of functionalized nanopores.
Collapse
Affiliation(s)
- Stuart F Knowles
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Nicole E Weckman
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Vincent J Y Lim
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Douwe J Bonthuis
- Institute of Theoretical and Computational Physics, Graz University of Technology, 8010 Graz, Austria
| | - Ulrich F Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Alice L Thorneywork
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| |
Collapse
|
20
|
Hsu C, Lin CY, Alizadeh A, Daiguji H, Hsu WL. Investigation of entrance effects on particle electrophoretic behavior near a nanopore for resistive pulse sensing. Electrophoresis 2021; 42:2206-2214. [PMID: 34472124 DOI: 10.1002/elps.202100162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022]
Abstract
Resistive pulse sensing using solid-state nanopores provides a unique platform for detecting the structure and concentration of molecules of different types of analytes in an electrolyte solution. The capture of an entity into a nanopore is subject not only to the electrostatic force but also the effect of electroosmotic flow originating from the charged nanopore surface. In this study, we theoretically analyze spherical particle electrophoretic behavior near the entrance of a charged nanopore. By investigating the effects of pore size, particle-pore distance, and salt concentration on particle velocity, we summarize dominant mechanisms governing particle behavior for a range of conditions. In the literature, the Helmholtz-Smoluchowski equation is often adopted to evaluate particle translocation by considering the zeta potential difference between the particle and nanopore surfaces. We point out that, due to the difference of the electric field inside and outside the nanopore and the influence from the existence of the particle itself, the zeta potential of the particle, however, needs to be at least 30% higher than that of the nanopore to allow the particle to enter into the nanopore when its velocity is close to zero. Accordingly, we summarize the effective salt concentrations that enable successful particle capture and detection for different pore sizes, offering direct guidance for nanopore applications.
Collapse
Affiliation(s)
- Chien Hsu
- Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan
| | - Chih-Yuan Lin
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan
| | - Amer Alizadeh
- Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, Canada
| | - Hirofumi Daiguji
- Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan
| | - Wei-Lun Hsu
- Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
21
|
Fried JP, Swett JL, Nadappuram BP, Fedosyuk A, Sousa PM, Briggs DP, Ivanov AP, Edel JB, Mol JA, Yates JR. Understanding Electrical Conduction and Nanopore Formation During Controlled Breakdown. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102543. [PMID: 34337856 DOI: 10.1002/smll.202102543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Controlled breakdown has recently emerged as a highly appealing technique to fabricate solid-state nanopores for a wide range of biosensing applications. This technique relies on applying an electric field of approximately 0.4-1 V nm-1 across the membrane to induce a current, and eventually, breakdown of the dielectric. Although previous studies have performed controlled breakdown under a range of different conditions, the mechanism of conduction and breakdown has not been fully explored. Here, electrical conduction and nanopore formation in SiNx membranes during controlled breakdown is studied. It is demonstrated that for Si-rich SiNx , oxidation reactions that occur at the membrane-electrolyte interface limit conduction across the dielectric. However, for stoichiometric Si3 N4 the effect of oxidation reactions becomes relatively small and conduction is predominately limited by charge transport across the dielectric. Several important implications resulting from understanding this process are provided which will aid in further developing controlled breakdown in the coming years, particularly for extending this technique to integrate nanopores with on-chip nanostructures.
Collapse
Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | | | | | - Pedro Miguel Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Dayrl P Briggs
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University London, London, E1 4NS, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| |
Collapse
|
22
|
Kishimoto S, Tsutsui M, Yokota K, Taniguchi M. Inertial focusing and zeta potential measurements of single-nanoparticles using octet-nanochannels. LAB ON A CHIP 2021; 21:3076-3085. [PMID: 34195745 DOI: 10.1039/d1lc00239b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Capture-to-translocation dynamics control is an important issue for single-particle and -molecule analyses by resistive pulse waveforms. Here, we report on regulated motions for accurate zeta-potential assessments of single nanoscale objects passing through an octet-nanochannel. We observed ionic spike signals consisting of eight consecutive sub-pulses signifying the ion blockage at the eight sensing zones in series upon electrophoretic translocation of individual nanoparticles. We find an exponential decrease to saturation of the channel-to-channel translocation duration as a nanobead moves forward, reflecting the more restricted radial motion degrees of freedom via inertial effects at the downstream side of the octet channel. This finding enabled a protocol for single-nanoparticle zeta potential estimation impervious to the uncertainty stemming from the stochastic nature of the translocation dynamics. The multi-channel approach presented in this study may be used as a useful tool for analyzing particles and molecules of variable sizes.
Collapse
Affiliation(s)
- Shohei Kishimoto
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| |
Collapse
|
23
|
Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
Collapse
Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
| |
Collapse
|
24
|
Abstract
![]()
Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
Collapse
Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
25
|
Wright JG, Amin MN, Schmidt H, Hawkins AR. Performance Comparison of Flow-Through Optofluidic Biosensor Designs. BIOSENSORS 2021; 11:226. [PMID: 34356697 PMCID: PMC8301811 DOI: 10.3390/bios11070226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 12/04/2022]
Abstract
Optofluidic flow-through biosensors are being developed for single particle detection, particularly as a tool for pathogen diagnosis. The sensitivity of the biosensor chip depends on design parameters, illumination format (side vs. top), and flow configuration (parabolic, two- and three-dimensional hydrodynamic focused (2DHF and 3DHF)). We study the signal differences between various combinations of these design aspects. Our model is validated against a sample of physical devices. We find that side-illumination with 3DHF produces the strongest and consistent signal, but parabolic flow devices process a sample volume more quickly. Practical matters of optical alignment are also discussed, which may affect design choice.
Collapse
Affiliation(s)
- Joel G. Wright
- Electrical and Computer Engineering, Brigham Young University, 450 Engineering Building, Provo, UT 84602, USA;
| | - Md Nafiz Amin
- Electrical and Computer Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA; (M.N.A.); (H.S.)
| | - Holger Schmidt
- Electrical and Computer Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA; (M.N.A.); (H.S.)
| | - Aaron R. Hawkins
- Electrical and Computer Engineering, Brigham Young University, 450 Engineering Building, Provo, UT 84602, USA;
| |
Collapse
|
26
|
Yang H, Saqib M, Hao R. Single-Entity Detection With TEM-Fabricated Nanopores. Front Chem 2021; 9:664820. [PMID: 34026729 PMCID: PMC8138203 DOI: 10.3389/fchem.2021.664820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/13/2021] [Indexed: 12/04/2022] Open
Abstract
Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.
Collapse
Affiliation(s)
| | | | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
27
|
Ren Y, Chen Q, He M, Zhang X, Qi H, Yan Y. Plasmonic Optical Tweezers for Particle Manipulation: Principles, Methods, and Applications. ACS NANO 2021; 15:6105-6128. [PMID: 33834771 DOI: 10.1021/acsnano.1c00466] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Inspired by the idea of combining conventional optical tweezers with plasmonic nanostructures, a technique named plasmonic optical tweezers (POT) has been widely explored from fundamental principles to applications. With the ability to break the diffraction barrier and enhance the localized electromagnetic field, POT techniques are especially effective for high spatial-resolution manipulation of nanoscale or even subnanoscale objects, from small bioparticles to atoms. In addition, POT can be easily integrated with other techniques such as lab-on-chip devices, which results in a very promising alternative technique for high-throughput single-bioparticle sensing or imaging. Despite its label-free, high-precision, and high-spatial-resolution nature, it also suffers from some limitations. One of the main obstacles is that the plasmonic nanostructures are located over the surfaces of a substrate, which makes the manipulation of bioparticles turn from a three-dimensional problem to a nearly two-dimensional problem. Meanwhile, the operation zone is limited to a predefined area. Therefore, the target objects must be delivered to the operation zone near the plasmonic structures. This review summarizes the state-of-the-art target delivery methods for the POT-based particle manipulating technique, along with its applications in single-bioparticle analysis/imaging, high-throughput bioparticle purifying, and single-atom manipulation. Future developmental perspectives of POT techniques are also discussed.
Collapse
Affiliation(s)
- Yatao Ren
- Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P.R. China
| | - Qin Chen
- Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Mingjian He
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P.R. China
| | - Xiangzhi Zhang
- Research Centre for Fluids and Thermal Engineering, University of Nottingham, Ningbo 315100, P.R. China
| | - Hong Qi
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P.R. China
| | - Yuying Yan
- Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- Research Centre for Fluids and Thermal Engineering, University of Nottingham, Ningbo 315100, P.R. China
| |
Collapse
|
28
|
Nanopores: a versatile tool to study protein dynamics. Essays Biochem 2021; 65:93-107. [PMID: 33296461 DOI: 10.1042/ebc20200020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins - involving conformational changes and interactions - remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics - one molecule at a time.
Collapse
|
29
|
Abstract
The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.
Collapse
Affiliation(s)
- Xingyi Ma
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
| |
Collapse
|
30
|
Farajpour N, Lastra LS, Sharma V, Freedman KJ. Measuring trapped DNA at the liquid-air interface for enhanced single molecule sensing. NANOSCALE 2021; 13:5780-5790. [PMID: 33704302 DOI: 10.1039/d0nr07759c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanopore sensing is a promising tool with widespread application in single-molecule detection. Borosilicate glass nanopores are a viable alternative to other solid-state nanopores due to low noise and cost-efficient fabrication. For dielectric materials, including borosilicate glass, the capacitive noise is one of the major contributors to noise, which depends on the wall thickness and the surface area submerged in an ionic solution. Here, we investigated the root mean square (IRMS) noise and ionic conductance for borosilicate nanopores in different depths (i.e., tip submersion depth) ranging from the solution surface (assumed to be zero) to 5000 μm. Our findings demonstrate a decrease in IRMS noise as the pipette moves toward the surface. We further demonstrate that borosilicate nanopores can detect single lambda DNA (λ-DNA) molecules with a high signal-to noise ratio close to the liquid-air interface. Specifically, our results indicate a higher signal to noise ratio as the submersion depth is reduced owing to the reduced surface area and thus capacitive noise. Further, our experimental results show higher DNA capture frequency at the air-water interface due to a combined effect of evaporation and an evaporation-induced thermal gradient at the surface. Therefore, our findings demonstrate that borosilicate glass nanopores are suitable for studying interfacial concentration gradients of molecules, specifically DNA, with a higher signal to noise.
Collapse
Affiliation(s)
- Nasim Farajpour
- Department of Bioengineering, University of California Riverside, Riverside, CA 92521, USA.
| | | | | | | |
Collapse
|
31
|
Xia P, Zuo J, Paudel P, Choi S, Chen X, Rahman Laskar MA, Bai J, Song W, Im J, Wang C. Sapphire-supported nanopores for low-noise DNA sensing. Biosens Bioelectron 2021; 174:112829. [PMID: 33308962 DOI: 10.1016/j.bios.2020.112829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/24/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Solid-state nanopores have broad applications from single-molecule biosensing to diagnostics and sequencing. The high capacitive noise from conventionally used conductive silicon substrates, however, has seriously limited both their sensing accuracy and recording speed. A new approach is proposed here for forming nanopore membranes on insulating sapphire wafers to promote low-noise nanopore sensing. Anisotropic wet etching of sapphire through micro-patterned triangular masks is used to demonstrate the feasibility of scalable formation of small (<25 μm) membranes with a size deviation of less than 7 μm over two 2-inch wafers. For validation, a sapphire-supported (SaS) nanopore chip with a 100 times larger membrane area than conventional nanopores was tested, which showed 130 times smaller capacitance (10 pF) and 2.6 times smaller root-mean-square (RMS) noise current (18-21 pA over 100 kHz bandwidth, with 50-150 mV bias) when compared to a silicon-supported (SiS) nanopore (~1.3 nF, and 46-51 pA RMS noise). Tested with 1k base-pair double-stranded DNA, the SaS nanopore enabled sensing at microsecond speed with a signal-to-noise ratio of 21, compared to 11 from a SiS nanopore. This SaS nanopore presents a manufacturable nanoelectronic platform feasible for high-speed and low-noise sensing of a variety of biomolecules.
Collapse
Affiliation(s)
- Pengkun Xia
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Jiawei Zuo
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Pravin Paudel
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA
| | - Shinhyuk Choi
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Xiahui Chen
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Md Ashiqur Rahman Laskar
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Jing Bai
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA
| | - Weisi Song
- Biodesign Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, USA
| | - JongOne Im
- Biodesign Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, USA; Curent Address: INanoBio Inc, Scottsdale, AZ, USA
| | - Chao Wang
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA.
| |
Collapse
|
32
|
Di Lecce S, Albrecht T, Bresme F. Taming the thermodiffusion of alkali halide solutions in silica nanopores. NANOSCALE 2020; 12:23626-23635. [PMID: 33211052 DOI: 10.1039/d0nr04912c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Thermal fields give rise to thermal coupling phenomena, such as mass and charge fluxes, which are useful in energy recovery applications and nanofluidic devices for pumping, mixing or desalination. Here we use state of the art non-equilibrium molecular simulations to quantify the thermodiffusion of alkali halide solutions, LiCl and NaCl, confined in silica nanopores, targeting diameters of the order of those found in mesoporous silica nanostructures. We show that nanoconfinement modifies the thermodiffusion behaviour of the solution. Under confinement conditions, the solutions become more thermophilic, with a preference to accumulate at hot sources, or thermoneutral, with the thermodiffusion being inhibited. Our work highlights the importance of nanoconfinement in thermodiffusion and outlines strategies to tune mass transport at the nanoscale, using thermal fields.
Collapse
Affiliation(s)
- Silvia Di Lecce
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College, W12 0BZ London, UK.
| | | | | |
Collapse
|
33
|
Abstract
Nanopores hold great potential for the analysis of complex biological molecules at the single-entity level. One particularly interesting macromolecular machine is the ribosome, responsible for translating mRNAs into proteins. In this study, we use a solid-state nanopore to fingerprint 80S ribosomes and polysomes from a human neuronal cell line andDrosophila melanogaster cultured cells and ovaries. Specifically, we show that the peak amplitude and dwell time characteristics of 80S ribosomes are distinct from polysomes and can be used to discriminate ribosomes from polysomes in mixed samples. Moreover, we are able to distinguish large polysomes, containing more than seven ribosomes, from those containing two to three ribosomes, and demonstrate a correlation between polysome size and peak amplitude. This study highlights the application of solid-state nanopores as a rapid analytical tool for the detection and characterization of ribosomal complexes.
Collapse
Affiliation(s)
- Mukhil Raveendran
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K
| | - Anna Rose Leach
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K
| | - Tayah Hopes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- LeedsOmics, University of Leeds, Leeds LS2 9JT, U.K
| | - Julie L. Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- LeedsOmics, University of Leeds, Leeds LS2 9JT, U.K
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K
- LeedsOmics, University of Leeds, Leeds LS2 9JT, U.K
- Bragg Centre for Materials Research, Leeds LS2 9JT, U.K
| |
Collapse
|
34
|
Berkenbrock JA, Grecco-Machado R, Achenbach S. Microfluidic devices for the detection of viruses: aspects of emergency fabrication during the COVID-19 pandemic and other outbreaks. Proc Math Phys Eng Sci 2020; 476:20200398. [PMID: 33363440 PMCID: PMC7735301 DOI: 10.1098/rspa.2020.0398] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Extensive testing of populations against COVID-19 has been suggested as a game-changer quest to control the spread of this contagious disease and to avoid further disruption in our social, healthcare and economical systems. Nonetheless, testing millions of people for a new virus brings about quite a few challenges. The development of effective tests for the new coronavirus has become a worldwide task that relies on recent discoveries and lessons learned from past outbreaks. In this work, we review the most recent publications on microfluidics devices for the detection of viruses. The topics of discussion include different detection approaches, methods of signalling and fabrication techniques. Besides the miniaturization of traditional benchtop detection assays, approaches such as electrochemical analyses, field-effect transistors and resistive pulse sensors are considered. For emergency fabrication of quick test kits, the local capabilities must be evaluated, and the joint work of universities, industries, and governments seems to be an unequivocal necessity.
Collapse
Affiliation(s)
- José Alvim Berkenbrock
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rafaela Grecco-Machado
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sven Achenbach
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
35
|
Navikas V, Leitão SM, Marion S, Davis SJ, Drake B, Fantner GE, Radenovic A. High-Throughput Nanocapillary Filling Enabled by Microwave Radiation for Scanning Ion Conductance Microscopy Imaging. ACS APPLIED NANO MATERIALS 2020; 3:7829-7834. [PMID: 33458601 PMCID: PMC7809705 DOI: 10.1021/acsanm.0c01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/02/2020] [Indexed: 05/17/2023]
Abstract
Solid-state nanopores provide a highly sensitive tool for single-molecule sensing and probing nanofluidic effects in solutions. Glass nanopipettes are a cheap and robust type of solid-state nanopore produced from pulling glass capillaries with opening orifice diameters down to below tens of nanometers. Sub-50 nm nanocapillaries allow an unprecedented resolution for translocating single molecules or for scanning ion conductance microscopy imaging. Due to the small opening orifice diameters, such nanocapillaries are difficult to fill with solutions, compromising their advantages of low cost, availability, and experimental simplicity. We present a simple and cheap method to reliably fill nanocapillaries down to sub-10 nm diameters by microwave radiation heating. Using a large statistic of filled nanocapillaries, we determine the filling efficiency and physical principle of the filling process using sub-50 nm quartz nanocapillaries. Finally, we have used multiple nanocapillaries filled by our method for high-resolution scanning ion conductance microscopy imaging.
Collapse
Affiliation(s)
- Vytautas Navikas
- Laboratory
of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Samuel M. Leitão
- Laboratory
for Bio- and Nano-Instrumentation, EPFL, 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Laboratory
of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Sebastian James Davis
- Laboratory
of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Barney Drake
- Laboratory
for Bio- and Nano-Instrumentation, EPFL, 1015 Lausanne, Switzerland
| | - Georg E. Fantner
- Laboratory
for Bio- and Nano-Instrumentation, EPFL, 1015 Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory
of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| |
Collapse
|
36
|
Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
Collapse
Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| |
Collapse
|
37
|
Liang S, Xiang F, Tang Z, Nouri R, He X, Dong M, Guan W. Noise in nanopore sensors: Sources, models, reduction, and benchmarking. NANOTECHNOLOGY AND PRECISION ENGINEERING 2020. [DOI: 10.1016/j.npe.2019.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
38
|
Chang M, Morgan G, Bedier F, Chieng A, Gomez P, Raminani S, Wang Y. Review-Recent Advances in Nanosensors Built with Pre-Pulled Glass Nanopipettes and Their Applications in Chemical and Biological Sensing. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2020; 167:037533. [PMID: 34326553 PMCID: PMC8317590 DOI: 10.1149/1945-7111/ab64be] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nanosensors built with pre-pulled glass nanopipettes, including bare or chemically modified nanopipettes and fully or partially filled solid nanoelectrodes, have found applications in chemical and biological sensing via resistive-pulse, current rectification, and electrochemical sensing. These nanosensors are easily fabricated and provide advantages through their needle-like geometry with nanometer-sized tips, making them highly sensitive and suitable for local measurements in extremely small samples. The variety in the geometry and layout have extended sensing capabilities. In this review, we will outline the fundamentals in fabrication, modification, and characterization of those pre-pulled glass nanopipette based nanosensors and highlight the most recent progress in their development and applications in real-time monitoring of biological processes, chemical ion sensing, and single entity analysis.
Collapse
|
39
|
Liu X, Zimny P, Zhang Y, Rana A, Nagel R, Reisner W, Dunbar WB. Flossing DNA in a Dual Nanopore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905379. [PMID: 31858745 DOI: 10.1002/smll.201905379] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/12/2019] [Indexed: 05/16/2023]
Abstract
Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data. Here, an active control technique termed "flossing" that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back-and-forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ-DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.
Collapse
Affiliation(s)
- Xu Liu
- Ontera Inc., Santa Cruz, CA, 95060, USA
| | | | - Yuning Zhang
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
| | | | | | - Walter Reisner
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
| | | |
Collapse
|
40
|
Ali M, Ramirez P, Nasir S, Cervera J, Mafe S, Ensinger W. Ionic circuitry with nanofluidic diodes. SOFT MATTER 2019; 15:9682-9689. [PMID: 31720668 DOI: 10.1039/c9sm01654f] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ionic circuits composed of nanopores functionalized with polyelectrolyte chains can operate in aqueous solutions, thus allowing the control of electrical signals and information processing in physiological environments. We demonstrate experimentally and theoretically that different orientations of single-pore membranes with the same and opposite surface charges can operate reliably in series, parallel, and mixed series-parallel arrangements of two, three, and four nanofluidic diodes using schemes similar to those of solid-state electronics. We consider also different experimental procedures to externally tune the fixed charges of the molecular chains functionalized on the pore surface, showing that single-pore membranes can be used efficiently in ionic circuitry with distinct ionic environments.
Collapse
Affiliation(s)
- Mubarak Ali
- Dept. of Material- and Geo-Sciences, Materials Analysis, Technische Universität Darmstadt, Petersenstr. 23, D-64287 Darmstadt, Germany.
| | | | | | | | | | | |
Collapse
|
41
|
Knowles SF, Keyser UF, Thorneywork AL. Noise properties of rectifying and non-rectifying nanopores. NANOTECHNOLOGY 2019; 31:10LT01. [PMID: 31770739 DOI: 10.1088/1361-6528/ab5be3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Achieving a full understanding of the noise in resistive pulse sensing experiments is central to the development of this important single molecule technique. Here, we present a comprehensive study of the noise properties of conical glass nanopores as components in an ionic circuit by studying the power spectral density of the system in salt solutions at a range of concentrations. We begin by investigating the ionic current rectification of the pores, showing that it is only observed above a critical Dukhin number in agreement with theoretical predictions. We then investigate the noise properties of the pores and demonstrate that the fluctuations in the ionic current at no applied potential difference can be well modelled over four decades of frequency as thermal fluctuations over a complex impedance. Finally, we show that-when an ionic current flows-1/f noise dominates the power spectrum below ∼100 Hz. Fluctuations in the surface current govern the low-frequency 1/f noise, with the asymmetric shape of the pore leading the magnitude to scale with [Formula: see text], faster than predicted by Hooge's empirical relation.
Collapse
Affiliation(s)
- S F Knowles
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | | | | |
Collapse
|
42
|
Nouri R, Tang Z, Guan W. Quantitative Analysis of Factors Affecting the Event Rate in Glass Nanopore Sensors. ACS Sens 2019; 4:3007-3013. [PMID: 31612705 DOI: 10.1021/acssensors.9b01540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
While the solid-state nanopore sensors have shown exceptional promise with their single-molecule sensitivity and label-free operations, one of the most significant challenges in the nanopore sensor is the limited analyte translocation event rate that leads to prolonged sensor response time. This issue is more pronounced when the analyte concentration is below the nanomolar (nM) range, owing to the diffusion-limited mass transport. In this work, we systematically studied the experimental factors beyond the intrinsic analyte concentration and electrophoretic mobility that affect the event rate in glass nanopore sensors. We developed a quantitative model to capture the impact of nanopore surface charge density, ionic strength, nanopore geometry, and translocation direction on the event rate. The synergistic effects of these factors on the event rates were investigated with the aim to find the optimized experimental conditions for operating the glass nanopore sensor from the response time standpoint. The findings in the study would provide useful and practical insight to enhance the device response time and achieve a lower detection limit for various glass nanopore-sensing experiments.
Collapse
|
43
|
Tang Z, Choi G, Nouri R, Guan W. Loop-Mediated Isothermal Amplification-Coupled Glass Nanopore Counting Toward Sensitive and Specific Nucleic Acid Testing. NANO LETTERS 2019; 19:7927-7934. [PMID: 31657939 DOI: 10.1021/acs.nanolett.9b03040] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores have shown great promise and achieved tremendous success in label-free single-molecule analysis. However, there are three common challenges in solid-state nanopore sensors, including the nanopore size variations from batch to batch that makes the interpretation of the sensing results difficult, the incorporation of sensor specificity, and the impractical analysis time at low analyte concentration due to diffusion-limited mass transport. Here, we demonstrate a novel loop-mediated isothermal amplification (LAMP)-coupled glass nanopore counting strategy that could effectively address these challenges. By using the glass nanopore in the counting mode (versus the sizing mode), the device fabrication challenge is considerably eased since it allows a certain degree of pore size variations and no surface functionalization is needed. The specific molecule replication effectively breaks the diffusion-limited mass transport thanks to the exponential growth of the target molecules. We show the LAMP-coupled glass nanopore counting has the potential to be used in a qualitative test as well as in a quantitative nucleic acid test. This approach lends itself to most amplification strategies as long as the target template is specifically replicated in numbers. The highly sensitive and specific sensing strategy would open a new avenue for solid-state nanopore sensors toward a new form of compact, rapid, low-cost nucleic acid testing at the point of care.
Collapse
Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Gihoon Choi
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Reza Nouri
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Weihua Guan
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biomedical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| |
Collapse
|
44
|
Weckman NE, Ermann N, Gutierrez R, Chen K, Graham J, Tivony R, Heron A, Keyser UF. Multiplexed DNA Identification Using Site Specific dCas9 Barcodes and Nanopore Sensing. ACS Sens 2019; 4:2065-2072. [PMID: 31340637 DOI: 10.1021/acssensors.9b00686] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Decorating double-stranded DNA with dCas9 barcodes to identify characteristic short sequences provides an alternative to fully sequencing DNA samples for rapid and highly specific analysis of a DNA sample. Solid state nanopore sensors are especially promising for this type of single-molecule sensing because of the ability to analyze patterns in the ionic current signatures of DNA molecules. Here, we systematically demonstrate the use of highly specific dCas9 probes to create unique barcodes on the DNA that can be read out using nanopore sensors. Single dCas9 probes are targeted to various positions on DNA strands up to 48 kbp long and are effectively measured in high salt conditions typical of nanopore sensing. Multiple probes bound to the same DNA strand at characteristic target sequences create distinct barcodes of double and triple peaks. Finally, double and triple barcodes are used to simultaneously identify two different DNA targets in a background mixture of bacterial DNA. Our method forms the basis of a fast and versatile assay for multiplexed DNA sensing applications in complex samples.
Collapse
Affiliation(s)
- Nicole E. Weckman
- Cavendish Laboratory, JJ Thomson Ave, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Niklas Ermann
- Cavendish Laboratory, JJ Thomson Ave, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Richard Gutierrez
- Oxford Nanopore Technologies, Gosling Building, Edmund Halley Road, Oxford Science Park OX4 4DQ, United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory, JJ Thomson Ave, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - James Graham
- Oxford Nanopore Technologies, Gosling Building, Edmund Halley Road, Oxford Science Park OX4 4DQ, United Kingdom
| | - Ran Tivony
- Cavendish Laboratory, JJ Thomson Ave, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Andrew Heron
- Oxford Nanopore Technologies, Gosling Building, Edmund Halley Road, Oxford Science Park OX4 4DQ, United Kingdom
| | - Ulrich F. Keyser
- Cavendish Laboratory, JJ Thomson Ave, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| |
Collapse
|
45
|
Choi G, Murphy E, Guan W. Microfluidic Time-Division Multiplexing Accessing Resistive Pulse Sensor for Particle Analysis. ACS Sens 2019; 4:1957-1963. [PMID: 31264411 DOI: 10.1021/acssensors.9b01067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to its simplicity and robustness, pore-based resistive pulse sensors have been widely used to detect, measure, and analyze particles at length scales ranging from nanometers to micrometers. While multiple pore-based resistive pulse sensors are preferred to increase the analysis throughput and to overcome the clogging issues, the scalability is often limited. In response, by combining the time-division multiple access technique in the telecommunication field with the microfluidics, we reported a microfluidic time-division multiplexing accessing (TDMA) single-end resistive pulse sensor, in which particles can be analyzed through a scalable number of microfluidic channels. With an eight-channel microfluidic device and polystyrene particles as proof-of-principle, we successfully demonstrated this multiplexed technology is effective in measuring the particle size and concentration, in analyzing the particle arriving dynamics, and in discriminating mixed populations. Importantly, the availability of multiple sensing pores provides a robust mechanism to overcome the clogging issue, allowing the analysis to continue even when some of the pores are clogged. We anticipate this TDMA approach could find wide applications and facilitate future development of multiplexed resistive pulse sensing from the microscale to nanoscale.
Collapse
Affiliation(s)
- Gihoon Choi
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Erica Murphy
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
46
|
Nouri R, Tang Z, Guan W. Calibration-Free Nanopore Digital Counting of Single Molecules. Anal Chem 2019; 91:11178-11184. [DOI: 10.1021/acs.analchem.9b01924] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|