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Young TW, Kappler MP, Call ED, Brown QJ, Jacobson SC. Integrated In-Plane Nanofluidic Devices for Resistive-Pulse Sensing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:221-242. [PMID: 38608295 DOI: 10.1146/annurev-anchem-061622-030223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Single-particle (or digital) measurements enhance sensitivity (10- to 100-fold improvement) and uncover heterogeneity within a population (one event in 100 to 10,000). Many biological systems are significantly influenced by rare or infrequent events, and determining what species is present, in what quantity, and the role of that species is critically important to unraveling many questions. To develop these measurement systems, resistive-pulse sensing is used as a label-free, single-particle detection technique and can be combined with a range of functional elements, e.g., mixers, reactors, filters, separators, and pores. Virtually, any two-dimensional layout of the micro- and nanofluidic conduits can be envisioned, designed, and fabricated in the plane of the device. Multiple nanopores in series lead to higher-precision measurements of particle size, shape, and charge, and reactions coupled directly with the particle-size measurements improve temporal response. Moreover, other detection techniques, e.g., fluorescence, are highly compatible with the in-plane format. These integrated in-plane nanofluidic devices expand the toolbox of what is possible with single-particle measurements.
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Affiliation(s)
- Tanner W Young
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Michael P Kappler
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Ethan D Call
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Quintin J Brown
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
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Rathnayaka C, Chandrosoma IA, Choi J, Childers K, Chibuike M, Akabirov K, Shiri F, Hall AR, Lee M, McKinney C, Verber M, Park S, Soper SA. Detection and identification of single ribonucleotide monophosphates using a dual in-plane nanopore sensor made in a thermoplastic via replication. LAB ON A CHIP 2024; 24:2721-2735. [PMID: 38656267 PMCID: PMC11091956 DOI: 10.1039/d3lc01062g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
We report the generation of ∼8 nm dual in-plane pores fabricated in a thermoplastic via nanoimprint lithography (NIL). These pores were connected in series with nanochannels, one of which served as a flight tube to allow the identification of single molecules based on their molecular-dependent apparent mobilities (i.e., dual in-plane nanopore sensor). Two different thermoplastics were investigated including poly(methyl methacrylate), PMMA, and cyclic olefin polymer, COP, as the substrate for the sensor both of which were sealed using a low glass transition cover plate (cyclic olefin co-polymer, COC) that could be thermally fusion bonded to the PMMA or COP substrate at a temperature minimizing nanostructure deformation. Unique to these dual in-plane nanopore sensors was two pores flanking each side of the nanometer flight tube (50 × 50 nm, width × depth) that was 10 μm in length. The utility of this dual in-plane nanopore sensor was evaluated to not only detect, but also identify single ribonucleotide monophosphates (rNMPs) by using the travel time (time-of-flight, ToF), the resistive pulse event amplitude, and the dwell time. In spite of the relatively large size of these in-plane pores (∼8 nm effective diameter), we could detect via resistive pulse sensing (RPS) single rNMP molecules at a mass load of 3.9 fg, which was ascribed to the unique structural features of the nanofluidic network and the use of a thermoplastic with low relative dielectric constants, which resulted in a low RMS noise level in the open pore current. Our data indicated that the identification accuracy of individual rNMPs was high, which was ascribed to an improved chromatographic contribution to the nano-electrophoresis apparent mobility. With the ToF data only, the identification accuracy was 98.3%. However, when incorporating the resistive pulse sensing event amplitude and dwell time in conjunction with the ToF and analyzed via principal component analysis (PCA), the identification accuracy reached 100%. These findings pave the way for the realization of a novel chip-based single-molecule RNA sequencing technology.
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Affiliation(s)
- Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Indu A Chandrosoma
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Maximillian Chibuike
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Khurshed Akabirov
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Adam R Hall
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
- Atrium Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston Salem, NC 27157, USA.
| | - Maxwell Lee
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
| | - Collin McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Verber
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Liu P, Kong XY, Jiang L, Wen L. Ion transport in nanofluidics under external fields. Chem Soc Rev 2024; 53:2972-3001. [PMID: 38345093 DOI: 10.1039/d3cs00367a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Nanofluidic channels with tailored ion transport dynamics are usually used as channels for ion transport, to enable high-performance ion regulation behaviors. The rational construction of nanofluidics and the introduction of external fields are of vital significance to the advancement and development of these ion transport properties. Focusing on the recent advances of nanofluidics, in this review, various dimensional nanomaterials and their derived homogeneous/heterogeneous nanofluidics are first briefly introduced. Then we discuss the basic principles and properties of ion transport in nanofluidics. As the major part of this review, we focus on recent progress in ion transport in nanofluidics regulated by external physical fields (electric field, light, heat, pressure, etc.) and chemical fields (pH, concentration gradient, chemical reaction, etc.), and reveal the advantages and ion regulation mechanisms of each type. Moreover, the representative applications of these nanofluidic channels in sensing, ionic devices, energy conversion, and other areas are summarized. Finally, the major challenges that need to be addressed in this research field and the future perspective of nanofluidics development and practical applications are briefly illustrated.
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Affiliation(s)
- Pei Liu
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450052, P. R. China
- College of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Xiang-Yu Kong
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, P. R. China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, P. R. China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
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Shiri F, Choi J, Vietz C, Rathnayaka C, Manoharan A, Shivanka S, Li G, Yu C, Murphy MC, Soper SA, Park S. Nano-injection molding with resin mold inserts for prototyping of nanofluidic devices for single molecular detection. LAB ON A CHIP 2023; 23:4876-4887. [PMID: 37870483 PMCID: PMC10995647 DOI: 10.1039/d3lc00543g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
While injection molding is becoming the fabrication modality of choice for high-scale production of microfluidic devices, especially those used for in vitro diagnostics, its translation into the growing area of nanofluidics (structures with at least one dimension <100 nm) has not been well established. Another prevailing issue with injection molding is the high startup costs and the relatively long time between device iterations making it in many cases impractical for device prototyping. We report, for the first time, functional nanofluidic devices with dimensions of critical structures below 30 nm fabricated by injection molding for the manipulation, identification, and detection of single molecules. UV-resin molds replicated from Si masters served as mold inserts, negating the need for generating Ni-mold inserts via electroplating. Using assembled devices with a cover plate via hybrid thermal fusion bonding, we demonstrated two functional thermoplastic nanofluidic devices. The first device consisted of dual in-plane nanopores placed at either end of a nanochannel and was used to detect and identify single ribonucleotide monophosphate molecules via resistive pulse sensing and obtain the effective mobility of the molecule through nanoscale electrophoresis to allow its identification. The second device demonstrated selective binding of a single RNA molecule to a solid phase bioreactor decorated with a processive exoribonuclease, XRN1. Our results provide a simple path towards the use of injection molding for device prototyping in the development stage of any nanofluidic or even microfluidic application, through which rapid scale-up is made possible by transitioning from prototyping to high throughput production using conventional Ni mold inserts.
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Affiliation(s)
- Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Chad Vietz
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Anishkumar Manoharan
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Suresh Shivanka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Guoqiang Li
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Chengbin Yu
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Michael C Murphy
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
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Vaidyanathan S, Wijerathne H, Gamage SST, Shiri F, Zhao Z, Choi J, Park S, Witek MA, McKinney C, Verber M, Hall AR, Childers K, McNickle T, Mog S, Yeh E, Godwin AK, Soper SA. High Sensitivity Extended Nano-Coulter Counter for Detection of Viral Particles and Extracellular Vesicles. Anal Chem 2023; 95:9892-9900. [PMID: 37336762 PMCID: PMC11015478 DOI: 10.1021/acs.analchem.3c00855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
We present a chip-based extended nano-Coulter counter (XnCC) that can detect nanoparticles affinity-selected from biological samples with low concentration limit-of-detection that surpasses existing resistive pulse sensors by 2-3 orders of magnitude. The XnCC was engineered to contain 5 in-plane pores each with an effective diameter of 350 nm placed in parallel and can provide high detection efficiency for single particles translocating both hydrodynamically and electrokinetically through these pores. The XnCC was fabricated in cyclic olefin polymer (COP) via nanoinjection molding to allow for high-scale production. The concentration limit-of-detection of the XnCC was 5.5 × 103 particles/mL, which was a 1,100-fold improvement compared to a single in-plane pore device. The application examples of the XnCC included counting affinity selected SARS-CoV-2 viral particles from saliva samples using an aptamer and pillared microchip; the selection/XnCC assay could distinguish the COVID-19(+) saliva samples from those that were COVID-19(-). In the second example, ovarian cancer extracellular vesicles (EVs) were affinity selected using a pillared chip modified with a MUC16 monoclonal antibody. The affinity selection chip coupled with the XnCC was successful in discriminating between patients with high grade serous ovarian cancer and healthy donors using blood plasma as the input sample.
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Affiliation(s)
- Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harshani Wijerathne
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Sachindra S T Gamage
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Zheng Zhao
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Małgorzata A Witek
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Collin McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Matthew Verber
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Adam R Hall
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and Comprehensive Cancer Center, Wake Forest School of Medicine, Winston Salem, North Carolina 27101, United States
| | - Katie Childers
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Taryn McNickle
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Shalee Mog
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Elaine Yeh
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew K Godwin
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- KU Comprehensive Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Steven A Soper
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- KU Comprehensive Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
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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.
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