1
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Lanzavecchia G, Sapunova A, Douaki A, Weng S, Momotenko D, Paulo G, Giacomello A, Krahne R, Garoli D. Tailored Fabrication of 3D Nanopores Made of Dielectric Oxides for Multiple Nanoscale Applications. NANO LETTERS 2024; 24:10098-10105. [PMID: 39121066 PMCID: PMC11342934 DOI: 10.1021/acs.nanolett.4c02117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 08/11/2024]
Abstract
Solid-state nanopores are a key platform for single-molecule detection and analysis that allow engineering of their properties by controlling size, shape, and chemical functionalization. However, approaches relying on polymers have limits for what concerns hardness, robustness, durability, and refractive index. Nanopores made of oxides with high dielectric constant would overcome such limits and have the potential to extend the suitability of solid-state nanopores toward optoelectronic technologies. Here, we present a versatile method to fabricate three-dimensional nanopores made of different dielectric oxides with convex, straight, and concave shapes and demonstrate their functionality in a series of technologies and applications such as ionic nanochannels, ionic current rectification, memristors, and DNA sensing. Our experimental data are supported by numerical simulations that showcase the effect of different shapes and oxide materials. This approach toward robust and tunable solid-state nanopores can be extended to other 3D shapes and a variety of dielectrics.
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Affiliation(s)
- German Lanzavecchia
- Optoelectronics, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
- Dipartimento
di Fisica, Università degli Studi
di Genova, Via Dodecaneso
33, 16146, Genova, Italy
| | - Anastasiia Sapunova
- Optoelectronics, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
- Università
degli Studi di Milano-Bicocca, Piazza dell’Ateneo Nuovo, 1, 20126, Milano, Italy
| | - Ali Douaki
- Optoelectronics, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Shukun Weng
- Optoelectronics, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
- Università
degli Studi di Milano-Bicocca, Piazza dell’Ateneo Nuovo, 1, 20126, Milano, Italy
| | - Dmitry Momotenko
- Institute
of Chemistry, Carl von Ossietzky Universität
Oldenburg, Oldenburg D-26129, Germany
| | - Gonçalo Paulo
- Dipartimento
di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Roma, Italy
| | - Alberto Giacomello
- Dipartimento
di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Roma, Italy
| | - Roman Krahne
- Optoelectronics, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Denis Garoli
- Optoelectronics, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
- Dipartimento
di Scienze e Metodi dell’Ingegneria, Università degli Studi di Modena e Reggio Emilia, Via Amendola 2, 43122, Reggio Emilia, Italy
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2
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Baldelli M, Di Muccio G, Sauciuc A, Morozzo Della Rocca B, Viola F, Balme S, Bonini A, Maglia G, Chinappi M. Controlling Electroosmosis in Nanopores Without Altering the Nanopore Sensing Region. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2401761. [PMID: 38860821 DOI: 10.1002/adma.202401761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Indexed: 06/12/2024]
Abstract
Nanopores are powerful tools for single-molecule sensing of biomolecules and nanoparticles. The signal coming from the molecule to be analyzed strongly depends on its interaction with the narrower section of the nanopore (constriction) that may be tailored to increase sensing accuracy. Modifications of nanopore constriction have also been commonly used to induce electroosmosis, that favors the capture of molecules in the nanopore under a voltage bias and independently of their charge. However, engineering nanopores for increasing both electroosmosis and sensing accuracy is challenging. Here it is shown that large electroosmotic flows can be achieved without altering the nanopore constriction. Using continuum electrohydrodynamic simulations, it is found that an external charged ring generates strong electroosmosis in cylindrical nanopores. Similarly, for conical nanopores it is shown that moving charges away from the cone tip still results in an electroosmotic flow (EOF), whose intensity reduces increasing the diameter of the nanopore section where charges are placed. This paradigm is applied to engineered biological nanopores showing, via atomistic simulations and experiments, that mutations outside the constriction induce a relatively intense electroosmosis. This strategy provides much more flexibility in nanopore design since electroosmosis can be controlled independently from the constriction, which can be optimized to improve sensing accuracy.
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Affiliation(s)
- Matteo Baldelli
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
| | - Giovanni Di Muccio
- Department of Mechanical and Aerospace Engineering, University of Rome Sapienza, Roma, 00184, Italy
| | - Adina Sauciuc
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | | | | | - Sébastien Balme
- Institut Europeen des Membranes, UMR5635, University of Montpellier ENCSM CNRS, Montpellier, 34095, France
| | - Andrea Bonini
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
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3
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Sauciuc A, Morozzo Della Rocca B, Tadema MJ, Chinappi M, Maglia G. Translocation of linearized full-length proteins through an engineered nanopore under opposing electrophoretic force. Nat Biotechnol 2024; 42:1275-1281. [PMID: 37723268 DOI: 10.1038/s41587-023-01954-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023]
Abstract
Nanopores have recently been used to identify and fingerprint proteins. However, because proteins, unlike DNA, do not have a uniform charge, the electrophoretic force cannot in general be used to translocate or linearize them. Here we show that the introduction of sets of charges in the lumen of the CytK nanopore spaced by ~1 nm creates an electroosmotic flow that induces the unidirectional transport of unstructured natural polypeptides against a strong electrophoretic force. Molecular dynamics simulations indicate that this electroosmotic-dominated force has a strength of ~20 pN at -100 mV, which is similar to the electric force on single-stranded DNA. Unfolded polypeptides produce current signatures as they traverse the nanopore, which may be used to identify proteins. This approach can be used to translocate and stretch proteins for enzymatic and non-enzymatic protein identification and sequencing.
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Affiliation(s)
- Adina Sauciuc
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | | | - Matthijs Jonathan Tadema
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Rome, Italy
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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4
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Wen C, Schmid S, Dekker C. Understanding Electrophoresis and Electroosmosis in Nanopore Sensing with the Help of the Nanopore Electro-Osmotic Trap. ACS NANO 2024; 18:20449-20458. [PMID: 39051760 PMCID: PMC11308919 DOI: 10.1021/acsnano.4c04788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Nanopore technology is widely used for sequencing DNA, RNA, and peptides with single-molecule resolution, for fingerprinting single proteins, and for detecting metabolites. However, the molecular driving forces controlling the analyte capture, its residence time, and its escape have remained incompletely understood. The recently developed Nanopore Electro-Osmotic trap (NEOtrap) is well fit to study these basic physical processes in nanopore sensing, as it reveals previously missed events. Here, we use the NEOtrap to quantitate the electro-osmotic and electrophoretic forces that act on proteins inside the nanopore. We establish a physical model to describe the capture and escape processes, including the trapping energy potential. We verified the model with experimental data on CRISPR dCas9-RNA-DNA complexes, where we systematically screened crucial modeling parameters such as the size and net charge of the complex. Tuning the balance between electrophoretic and electro-osmotic forces in this way, we compare the trends in the kinetic parameters with our theoretical models. The result is a comprehensive picture of the major physical processes in nanopore trapping, which helps to guide the experiment design and signal interpretation in nanopore experiments.
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Affiliation(s)
- Chenyu Wen
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Sonja Schmid
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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5
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Mehrafrooz B, Yu L, Pandey L, Siwy ZS, Wanunu M, Aksimentiev A. Electro-osmotic Flow Generation via a Sticky Ion Action. ACS NANO 2024; 18:17521-17533. [PMID: 38832758 PMCID: PMC11233251 DOI: 10.1021/acsnano.4c00829] [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] [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.
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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
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6
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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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7
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Zhang QL, Zhou T, Chang C, Gu SY, Wang YJ, Liu Q, Zhu Z. Ultrahigh-Flux Water Nanopumps Generated by Asymmetric Terahertz Absorption. PHYSICAL REVIEW LETTERS 2024; 132:184003. [PMID: 38759176 DOI: 10.1103/physrevlett.132.184003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/04/2023] [Accepted: 03/21/2024] [Indexed: 05/19/2024]
Abstract
Controlling active transport of water through membrane channels is essential for advanced nanofluidic devices. Despite advancements in water nanopump design using techniques like short-range invasion and subnanometer-level control, challenges remain facilely and remotely realizing massive waters active transport. Herein, using molecular dynamic simulations, we propose an ultrahigh-flux nanopump, powered by frequency-specific terahertz stimulation, capable of unidirectionally transporting massive water through asymmetric-wettability membrane channels at room temperature without any external pressure. The key physics behind this terahertz-powered water nanopump is revealed to be the energy flow resulting from the asymmetric optical absorption of water.
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Affiliation(s)
- Qi-Lin Zhang
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Tong Zhou
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Chao Chang
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics, Peking University, Beijing 100871, China
| | - Shi-Yu Gu
- College of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yun-Jie Wang
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Qi Liu
- School of Mathematics-Physics and Finance and School of Materials Science and Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Zhi Zhu
- College of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
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8
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Li M, Muthukumar M. Electro-osmotic flow in nanoconfinement: Solid-state and protein nanopores. J Chem Phys 2024; 160:084905. [PMID: 38411234 DOI: 10.1063/5.0185574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024] Open
Abstract
Electro-osmotic flow (EOF) is a phenomenon where fluid motion occurs in porous materials or micro/nano-channels when an external electric field is applied. In the particular example of single-molecule electrophoresis using single nanopores, the role of EOF on the translocation velocity of the analyte molecule through the nanopore is not fully understood. The complexity arises from a combination of effects from hydrodynamics in restricted environments, electrostatics emanating from charge decorations and geometry of the pores. We address this fundamental issue using the Poisson-Nernst-Planck and Navier-Stokes (PNP-NS) equations for cylindrical solid-state nanopores and three representative protein nanopores (α-hemolysin, MspA, and CsgG). We present the velocity profiles inside the nanopores as a function of charge decoration and geometry of the pore and applied electric field. We report several unexpected results: (a) The apparent charges of the protein nanopores are different from their net charge and the surface charge of the whole protein geometry, and the net charge of inner surface is consistent with the apparent charge. (b) The fluid velocity depends non-monotonically on voltage. The three protein nanopores exhibit unique EOF and velocity-voltage relations, which cannot be simply deduced from their net charge. Furthermore, effective point mutations can significantly change both the direction and the magnitude of EOF. The present computational analysis offers an opportunity to further understand the origins of the speed of transport of charged macromolecules in restricted space and to design desirable nanopores for tuning the speed of macromolecules through nanopores.
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Affiliation(s)
- Minglun Li
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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9
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Paulo G, Sun K, Di Muccio G, Gubbiotti A, Morozzo Della Rocca B, Geng J, Maglia G, Chinappi M, Giacomello A. Hydrophobically gated memristive nanopores for neuromorphic applications. Nat Commun 2023; 14:8390. [PMID: 38110352 PMCID: PMC10728163 DOI: 10.1038/s41467-023-44019-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Signal transmission in the brain relies on voltage-gated ion channels, which exhibit the electrical behaviour of memristors, resistors with memory. State-of-the-art technologies currently employ semiconductor-based neuromorphic approaches, which have already demonstrated their efficacy in machine learning systems. However, these approaches still cannot match performance achieved by biological neurons in terms of energy efficiency and size. In this study, we utilise molecular dynamics simulations, continuum models, and electrophysiological experiments to propose and realise a bioinspired hydrophobically gated memristive nanopore. Our findings indicate that hydrophobic gating enables memory through an electrowetting mechanism, and we establish simple design rules accordingly. Through the engineering of a biological nanopore, we successfully replicate the characteristic hysteresis cycles of a memristor and construct a synaptic device capable of learning and forgetting. This advancement offers a promising pathway for the realization of nanoscale, cost- and energy-effective, and adaptable bioinspired memristors.
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Affiliation(s)
- Gonçalo Paulo
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Ke Sun
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Di Muccio
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Alberto Gubbiotti
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | | | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Maglia
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, Tor Vergata University of Rome, Rome, 00133, Italy
| | - Alberto Giacomello
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy.
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10
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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.
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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
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11
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Heydari A, Khatibi M, Ashrafizadeh SN. Smart nanochannels: tailoring ion transport properties through variation in nanochannel geometry. Phys Chem Chem Phys 2023; 25:26716-26736. [PMID: 37779455 DOI: 10.1039/d3cp03768a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
This research explores ion transport behavior and functionality in a hybrid nanochannel that consists of two conical and cylindrical parts. The numerical investigation focuses on analyzing the length of each part in the nanochannel. The nanochannels are hybrid cavities embedded in a membrane, where the size of the conical part varies as equal to, larger than, or smaller than the cylindrical part. The nanochannel is coated with a polyelectrolyte layer that exhibits a dense charge density distribution. The charge density of the soft layer is described using the soft step distribution function. We study the electroosmotic flow, ionic current, rectification, and selectivity of the nanochannel versus bulk electrolyte concentration, the charge density of the polyelectrolyte layer, and decay length, while considering the effect of ionic partitioning. The steady-state Poisson-Nernst-Planck and Navier-Stokes equations are solved using the finite element method. The findings reveal that the nanochannel with a more extensive conical section demonstrates increased rectification, with the rectification factor rising from 1.4 to 2 at a bulk concentration of 100 mM. Additionally, the nanochannel with a longer cylindrical part exhibits improved selectivity under negative voltage conditions, while positive voltage introduces a different situation. The nanochannel with equal cylindrical and conical parts significantly affects conductivity by modifying the charge density in the soft layer, resulting in a 3.125-fold increase in conductivity under positive voltage when the charge density in the polyelectrolyte layer is raised from 25 to 100 mol m-3. This research focuses on creating intelligent nanochannels by controlling mass concentration, charge density, and collapse length, improving system performance, and optimizing properties. It also offers valuable insights into ion transport mechanisms in nanochannel systems, advancing our understanding in this field.
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Affiliation(s)
- Amirhossein Heydari
- Research Lab for Advanced Separation Processes, Department of Chemical Engineering, Iran University of Science and Technology, Narmak, Tehran 16846-13114, Iran.
| | - Mahdi Khatibi
- Research Lab for Advanced Separation Processes, Department of Chemical Engineering, Iran University of Science and Technology, Narmak, Tehran 16846-13114, Iran.
| | - Seyed Nezameddin Ashrafizadeh
- Research Lab for Advanced Separation Processes, Department of Chemical Engineering, Iran University of Science and Technology, Narmak, Tehran 16846-13114, Iran.
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12
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Straathof S, Di Muccio G, Yelleswarapu M, Alzate Banguero M, Wloka C, van der Heide NJ, Chinappi M, Maglia G. Protein Sizing with 15 nm Conical Biological Nanopore YaxAB. ACS NANO 2023; 17:13685-13699. [PMID: 37458334 PMCID: PMC10373527 DOI: 10.1021/acsnano.3c02847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.
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Affiliation(s)
- Sabine Straathof
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Di Muccio
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Maaruthy Yelleswarapu
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melissa Alzate Banguero
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin 10178, Germany
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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13
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Yadav SK, D M, Singh C, Kumar M, G A, Ramaprabhu S, Nandigana VVR, Nayak PK. Laser-Assisted Scalable Pore Fabrication in Graphene Membranes for Blue-Energy Generation. Chemphyschem 2022; 24:e202200598. [PMID: 36510477 DOI: 10.1002/cphc.202200598] [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: 08/11/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
The osmotic energy from a salinity gradient (i. e. blue energy) is identified as a promising non-intermittent renewable energy source for a sustainable technology. However, this membrane-based technology is facing major limitations for large-scale viability, primarily due to the poor membrane performance. An atomically thin 2D nanoporous material with high surface charge density resolves the bottleneck and leads to a new class of membrane material the salinity gradient energy. Although 2D nanoporous membranes show extremely high performance in terms of energy generation through the single pore, the fabrication and technical challenges such as ion concentration polarization make the nanoporous membrane a non-viable solution. On the other hand, the mesoporous and micro porous structures in the 2D membrane result in improved energy generation with very low fabrication complexity. In the present work, we report femtosecond (fs) laser-assisted scalable fabrication of μm to mm size pores on Graphene membrane for blue energy generation for the first time. A remarkable osmotic power in the order of μW has been achieved using mm size pores, which is about six orders of magnitudes higher compared to nanoporous membranes, which is mainly due to the diffusion-osmosis driven large ionic flux. Our work paves the way towards fs laser-assisted scalable pore creation in the 2D membrane for large-scale osmotic power generation.
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Affiliation(s)
- Sharad Kumar Yadav
- Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai, 600036, India.,Department of Physics, Indian Institute of Technology Madras, Chennai, 600 036, India.,Micro Nano and Bio-Fluidics Group, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Manikandan D
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Chob Singh
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Mukesh Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Aswathy G
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Sundara Ramaprabhu
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600 036, India.,Alternative Energy and Nanotechnology Laboratory (AENL), Nano Functional Materials Technology Centre (NFMTC), Indian Institute of Technology Madras, Chennai, India
| | - Vishal V R Nandigana
- Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Pramoda K Nayak
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600 036, India.,Micro Nano and Bio-Fluidics Group, Indian Institute of Technology Madras, Chennai, 600036, India.,2D Materials Research and Innovation Group, Indian Institute of Technology Madras, Chennai, 600036, India.,Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Kanakapura, Bangalore, 562112, India
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