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Lin X, Chen H, Wu G, Zhao J, Zhang Y, Sha J, Si W. Selective Capture and Manipulation of DNA through Double Charged Nanopores. J Phys Chem Lett 2024:5120-5129. [PMID: 38709198 DOI: 10.1021/acs.jpclett.4c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
In the past few decades, nanometer-scale pores have been employed as powerful tools for sensing biological molecules. Owing to its unique structure and properties, solid-state nanopores provide interesting opportunities for the development of DNA sequencing technology. Controlling DNA translocation in nanopores is an important means of improving the accuracy of sequencing. Here we present a proof of principle study of accelerating DNA captured across targeted graphene nanopores using surface charge density and find the intrinsic mechanism of the combination of electroosmotic flow induced by charges of nanopore and electrostatic attraction/repulsion between the nanopore and ssDNA. The theoretical study performed here provides a new means for controlling DNA transport dynamics and makes better and cheaper application of graphene in molecular sequencing.
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Affiliation(s)
- Xiaojing Lin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Haonan Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Jiajia Zhao
- Department of Pharmacology, Key Laboratory of Neuropsychiatric Diseases, China Pharmaceutical University, Nanjing 211198, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
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2
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Xiong M, Athreya N, Chakraborty R, Leburton JP. Ion Trapping and Thermionic Emission across Sub-nm Pores. NANO LETTERS 2023; 23:11719-11726. [PMID: 38078825 DOI: 10.1021/acs.nanolett.3c03592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Ionic transport through a graphene biomimetic subnanometer (sub-nm) pore of arbitrary shape and realistically decorated by intrinsic negatively charged sites is investigated by all-atom molecular dynamics (MD) simulations. In the presence of external electric fields, cation trapping-assisted translocation occurs in the vicinity of the 2D subnanometer pore, while the anion current is blocked by the negative charges. The adsorbed cations in such asymmetrically charged nanopores are located on the top of the nanopore instead of blocking the pore, as suggested previously in highly symmetric pores such as crown ethers. Our analysis of the different types of energy involved in ion translocations indicates that electrostatics is the dominant factor controlling ion transfer across these sub-nm pores. A physical model based on the thermionic emission formalism to account for the free energy barriers to ion flow reproduces the I-V characteristics.
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3
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Chen F, Athreya N, Zhao C, Xiong M, Tan H, Leburton JP, Feng J. Ion Density-Dependent Dynamic Conductance Switching in Biomimetic Graphene Nanopores. J Phys Chem Lett 2022; 13:3602-3608. [PMID: 35426690 DOI: 10.1021/acs.jpclett.2c00715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gating in ion transport is at the center of many vital living-substance transmission processes, and understanding how gating works at an atomic level is essential but intricate. However, our understanding and finite experimental findings of subcontinuum ion transport in subnanometer nanopores are still limited, which is out of reach of the classical continuum nanofluidics. Moreover, the influence of ion density on subcontinuum ion transport is poorly understood. Here we report the ion density-dependent dynamic conductance switching process in biomimetic graphene nanopores and explain the phenomenon by a reversible ion absorption mechanism. Our molecular dynamics simulations demonstrate that the cations near the graphene nanopore can interact with the surface charges on the nanopore, thereby realizing the switching of high- and low-conductance states. This work has deepened the understanding of gating in ion transport.
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Affiliation(s)
- Fanfan Chen
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | | | - Chunxiao Zhao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | | | - Haojing Tan
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | | | - Jiandong Feng
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- Zhejiang Lab, Hangzhou 310000, China
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4
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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: 26] [Impact Index Per Article: 8.7] [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.
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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
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5
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Wang Q, Liu Y, Yan J, Liu Y, Gao C, Ge S, Yu J. 3D DNA Walker-Assisted CRISPR/Cas12a Trans-Cleavage for Ultrasensitive Electrochemiluminescence Detection of miRNA-141. Anal Chem 2021; 93:13373-13381. [PMID: 34553925 DOI: 10.1021/acs.analchem.1c03183] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this study, a CRISPR/Cas12a (LbCpf1)-mediated electrochemiluminescence (ECL) paper-based platform on the basis of a three-dimensional (3D) DNA walker was proposed for the ultrasensitive detection of miRNA-141. Initially, 3D-rGO with a tremendous loading space was modified on the paper working electrode (PWE) to construct an excellent conductive substrate and facilitate the growth of AuPd nanoparticles (NPs). Afterward, the AuPd NPs were introduced as the coreaction emitter medium of the 3D-rGO/PWE to provide convenience for the transformation between S2O82- and SO42-, amplifying the ECL emission of g-C3N4 nanosheets (NSs). Meanwhile, with the help of Nt.BsmAI nicking endonuclease, a 3D DNA walker signal amplifier was designed to convert and magnify the target miRNA-141 into a particular trigger sequence, which could act as activator DNA to motivate the trans-acting deoxyribonuclease activity of CRISPR/Cas12a to further achieve efficient annihilation of the ECL signal. Furthermore, the proposed multimechanism-driven biosensor exhibited excellent sensitivity and specificity, with a relatively low detection limit at 0.331 fM (S/N = 3) in the concentration range between 1 fM and 10 nM. Consequently, the designed strategy not only extended the application scope of CRISPR/Cas12a but also devoted a new approach for the clinical diagnosis of modern medicine.
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Affiliation(s)
- Qian Wang
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, P.R. China.,School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Yaqi Liu
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, P.R. China
| | - Jixian Yan
- Shandong Provincial Center for Prevention and Control of Solid Waste and Hazardous Chemical Pollution, Jinan 250000, P.R. China
| | - Yunqing Liu
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, P.R. China
| | - Chaomin Gao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, P.R. China
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
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Athreya N, Sarathya A, Xiong M, Leburton JP. 2D Solid-State Nanopore Field-Effect Transistors: Comprehensive Computational Methodology for Biosensing Applications. IEEE NANOTECHNOLOGY MAGAZINE 2020. [DOI: 10.1109/mnano.2020.3024388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tsutsui M, Yamazaki T, Tatematsu K, Yokota K, Esaki Y, Kubo Y, Deguchi H, Arima A, Kuroda S, Kawai T. High-throughput single nanoparticle detection using a feed-through channel-integrated nanopore. NANOSCALE 2019; 11:20475-20484. [PMID: 31647092 DOI: 10.1039/c9nr07039g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The outstanding sensitivity of solid-state nanopore sensors comes at a price of low detection efficiency due to the lack of active means to transfer objects into the nanoscale sensing zone. Here we report on a key technology for high-throughput single-nanoparticle detection which exploits mutual effects of microfluidics control and multipore electrophoresis in nanopore-in-channel units integrated on a thin Si3N4 membrane. Using this novel nanostructure, we demonstrated a proof-of-concept for influenza viruses via hydropressure regulation of mass transport in the fluidic channel for continuous feeding of biosamples into the effective electric field extending out from the nanopores, wherein the feed-through mechanism allowed us to selectively detect charged objects in physiological media such as human saliva. With the versatility of nanopore sensing technologies applicable to analytes of virtually any size from cells to polynucleotides, the present integration strategy may open new avenues for practical ultrasensitive bioanalytical tools.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Tomoko Yamazaki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kenji Tatematsu
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan. and National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Yuko Esaki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Yukari Kubo
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Hiroko Deguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Shun'ichi Kuroda
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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Lin Z, Wu G, Zhao L, Lai KWC. Carbon Nanomaterial-Based Biosensors: A Review of Design and Applications. IEEE NANOTECHNOLOGY MAGAZINE 2019. [DOI: 10.1109/mnano.2019.2927774] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Tsutsui M, Yokota K, Nakada T, Arima A, Tonomura W, Taniguchi M, Washio T, Kawai T. Particle Capture in Solid-State Multipores. ACS Sens 2018; 3:2693-2701. [PMID: 30421923 DOI: 10.1021/acssensors.8b01214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Utilization of multiple-channel structure is a promising way of accomplishing high-throughput detections of analytes in solid-state pore sensors. Here we report on systematic investigation of particle capture efficiency in Si3N4 multipore systems of various array configurations. We demonstrated enhanced detection throughput with increasing numbers of pore channels in a membrane. Meanwhile, we also observed significant contributions of the interchannel crosstalk in closely integrated multipores that tended to deteriorate throughput performance by causing shrinkage of the absorption zone via the interference-derived weakening of the electric field around the pore orifice. At the same time, the interference-derived electric field distributions were also found to diminish the electroosmotic contributions to the particle capture efficiency. The present findings can be useful in designing pore arrays with optimal throughput performance.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Tomoko Nakada
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Wataru Tonomura
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
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10
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Arima A, Tsutsui M, Harlisa IH, Yoshida T, Tanaka M, Yokota K, Tonomura W, Taniguchi M, Okochi M, Washio T, Kawai T. Selective detections of single-viruses using solid-state nanopores. Sci Rep 2018; 8:16305. [PMID: 30390013 PMCID: PMC6214978 DOI: 10.1038/s41598-018-34665-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/23/2018] [Indexed: 01/31/2023] Open
Abstract
Rapid diagnosis of flu before symptom onsets can revolutionize our health through diminishing a risk for serious complication as well as preventing infectious disease outbreak. Sensor sensitivity and selectivity are key to accomplish this goal as the number of virus is quite small at the early stage of infection. Here we report on label-free electrical diagnostics of influenza based on nanopore analytics that distinguishes individual virions by their distinct physical features. We accomplish selective resistive-pulse sensing of single flu virus having negative surface charges in a physiological media by exploiting electroosmotic flow to filter contaminants at the Si3N4 pore orifice. We demonstrate identifications of allotypes with 68% accuracy at the single-virus level via pattern classifications of the ionic current signatures. We also show that this discriminability becomes >95% under a binomial distribution theorem by ensembling the pulse data of >20 virions. This simple mechanism is versatile for point-of-care tests of a wide range of flu types.
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Affiliation(s)
- Akihide Arima
- 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.
| | - Ilva Hanun Harlisa
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo, 152-8552, Japan
| | - Takeshi Yoshida
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo, 152-8552, Japan
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Wataru Tonomura
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo, 152-8552, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.
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Sarathy A, Athreya NB, Varshney LR, Leburton JP. Classification of Epigenetic Biomarkers with Atomically Thin Nanopores. J Phys Chem Lett 2018; 9:5718-5725. [PMID: 30226383 DOI: 10.1021/acs.jpclett.8b02200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We use the electronic properties of 2D solid-state nanopore materials to propose a versatile and generally applicable biosensor technology by using a combination of molecular dynamics, nanoscale device simulations, and statistical signal processing algorithms. As a case study, we explore the classification of three epigenetic biomarkers, the methyl-CpG binding domain 1 (MBD-1), MeCP2, and γ-cyclodextrin, attached to double-stranded DNA to identify regions of hyper- or hypomethylations by utilizing a matched filter. We assess the sensing ability of the nanopore device to identify the biomarkers based on their characteristic electronic current signatures. Such a matched filter-based classifier enables real-time identification of the biomarkers that can be easily implemented on chip. This integration of a sensor with signal processing architectures could pave the way toward the development of a multipurpose technology for early disease detection.
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