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Mereuta L, Bhatti H, Asandei A, Cimpanu A, Ying YL, Long YT, Luchian T. Controlling DNA Fragments Translocation across Nanopores with the Synergic Use of Site-Directed Mutagenesis, pH-Dependent Charge Tuning, and Electroosmotic Flow. ACS APPLIED MATERIALS & INTERFACES 2024; 16:40100-40110. [PMID: 39038810 PMCID: PMC11299134 DOI: 10.1021/acsami.4c03848] [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: 03/07/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 07/24/2024]
Abstract
Biological and solid-state nanopores are at the core of transformative techniques and nanodevices, democratizing the examination of matter and biochemical reactions at the single-molecule level, with low cost, portability, and simplicity in operation. One of the crucial hurdles in such endeavors is the fast analyte translocation, which limits characterization, and a rich number of strategies have been explored over the years to overcome this. Here, by site-directed mutagenesis on the α-hemolysin protein nanopore (α-HL), sought to replace selected amino acids with glycine, electrostatic binding sites were induced on the nanopore's vestibule and constriction region and achieved in the most favorable case a 20-fold increase in the translocation time of short single-stranded DNA (ssDNA) at neutral pH, with respect to the wild-type (WT) nanopore. We demonstrated an efficient tool of controlling the ssDNA translocation time, via the interplay between the nanopore-ssDNA surface electrostatic interactions and electroosmotic flow, all mediated by the pH-dependent ionization of amino acids lining the nanopore's translocation pathway. Our data also reveal the nonmonotonic, pH-induced alteration of ssDNA average translocation time. Unlike mildly acidic conditions (pH ∼ 4.7), at a pH ∼ 2.8 maintained symmetrically or asymmetrically across the WT α-HL, we evidenced the manifestation of a dominant electroosmotic flow, determining the speeding up of the ssDNA translocation across the nanopore by counteracting the ssDNA-nanopore attractive electrostatic interactions. We envision potential applications of the presented approach by enabling easy-to-use, real-time detection of short ssDNA sequences, without the need for complex biochemical modifications to the nanopore to mitigate the fast translocation of such sequences.
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Affiliation(s)
- Loredana Mereuta
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Huma Bhatti
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Alina Asandei
- Interdisciplinary
Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Adina Cimpanu
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Yi-Lun Ying
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Tudor Luchian
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
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2
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Rajendran B, Chen X, Li Z, Zhan Z, Goh KB. How molecular interactions tune the characteristic time of nanocomposite colloidal sensors. J Colloid Interface Sci 2022; 616:668-678. [PMID: 35245793 DOI: 10.1016/j.jcis.2022.02.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
HYPOTHESIS Mass transport critically controls the performance of colloidal metal-polymer sensors. We hypothesize that molecular-level pair interactions, such as electric, steric, and specific binding effects, govern the mass transport and, in return, the characteristic time of these sensors. THEORY Here we present a simple theory guided by experimental data to examine the sensing performance of two usually encountered archetypal metal-polymer sensors, namely (1) core-shell and (2) yolk-shell architectures. For this purpose, we use the static reactive density functional theory framework, determining how (i) charge, (ii) size, and (iii) non-covalent binding factors modulate the characteristic time. FINDINGS We show how an interplay between diffusivity and partitioning governs the sensing time of the sensors, where an anti-correlation cancellation between them renders the time non-trivial. Our study demonstrates that the convoluted substrate-hydrogel shell interaction controls the characteristic time of these colloidal sensors, especially when the sensors are in a collapsed state. Notably, the substrates with a high dipole moment tend to equilibrate greatly, but undesirably, at the shell-solution interface. With this, we encourage the formation of a metastable sorption state.
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Affiliation(s)
- Barathan Rajendran
- School of Engineering, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Xiao Chen
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Republic of Singapore
| | - Zhong Li
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Republic of Singapore; Center for Cellular and Molecular Engineering, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Zhixin Zhan
- School of Aeronautic Science and Engineering, Beihang University, Beijing 100191, China
| | - K B Goh
- School of Engineering, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia.
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3
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Angevine CE, Robertson JWF, Dass A, Reiner JE. Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions. SCIENCE ADVANCES 2021; 7:eabf5462. [PMID: 33883140 PMCID: PMC8059931 DOI: 10.1126/sciadv.abf5462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
Abstract
Single-molecule approaches for probing the free energy of confinement for polymers in a nanopore environment are critical for the development of nanopore biosensors. We developed a laser-based nanopore heating approach to monitor the free energy profiles of such a single-molecule sensor. Using this approach, we measure the free energy profiles of two distinct polymers, polyethylene glycol and water-soluble peptides, as they interact with the nanopore sensor. Polyethylene glycol demonstrates a retention mechanism dominated by entropy with little sign of interaction with the pore, while peptides show an enthalpic mechanism, which can be attributed to physisorption to the nanopore (e.g., hydrogen bonding). To manipulate the energetics, we introduced thiolate-capped gold clusters [Au25(SG)18] into the pore, which increases the charge and leads to additional electrostatic interactions that help dissect the contribution that enthalpy and entropy make in this modified environment. These observations provide a benchmark for optimization of single-molecule nanopore sensors.
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Affiliation(s)
| | - Joseph W F Robertson
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
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4
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Willems K, Ruić D, L R Lucas F, Barman U, Verellen N, Hofkens J, Maglia G, Van Dorpe P. Accurate modeling of a biological nanopore with an extended continuum framework. NANOSCALE 2020; 12:16775-16795. [PMID: 32780087 DOI: 10.1039/d0nr03114c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.
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Affiliation(s)
- Kherim Willems
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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5
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Borsley S, Haugland MM, Oldknow S, Cooper JA, Burke MJ, Scott A, Grantham W, Vallejo J, Brechin EK, Lusby PJ, Cockroft SL. Electrostatic Forces in Field-Perturbed Equilibria: Nanopore Analysis of Cage Complexes. Chem 2019. [DOI: 10.1016/j.chempr.2019.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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6
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Potterton A, Husseini FS, Southey MWY, Bodkin MJ, Heifetz A, Coveney PV, Townsend-Nicholson A. Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A 2A Receptor Binders. J Chem Theory Comput 2019; 15:3316-3330. [PMID: 30893556 DOI: 10.1021/acs.jctc.8b01270] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drug-target residence time, the length of time for which a small molecule stays bound to its receptor target, has increasingly become a key property for optimization in drug discovery programs. However, its in silico prediction has proven difficult. Here we describe a method, using atomistic ensemble-based steered molecular dynamics (SMD), to observe the dissociation of ligands from their target G protein-coupled receptor in a time scale suitable for drug discovery. These dissociation simulations accurately, precisely, and reproducibly identify ligand-residue interactions and quantify the change in ligand energy values for both protein and water. The method has been applied to 17 ligands of the A2A adenosine receptor, all with published experimental kinetic binding data. The residues that interact with the ligand as it dissociates are known experimentally to have an effect on binding affinities and residence times. There is a good correlation ( R2 = 0.79) between the computationally calculated change in water-ligand interaction energy and experimentally determined residence time. Our results indicate that ensemble-based SMD is a rapid, novel, and accurate semi-empirical method for the determination of drug-target relative residence time.
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Affiliation(s)
- Andrew Potterton
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom
| | - Fouad S Husseini
- Centre for Computational Science, Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Michelle W Y Southey
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Mike J Bodkin
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Alexander Heifetz
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom.,Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom.,Computational Science Laboratory, Institute for Informatics, Faculty of Science , University of Amsterdam , Amsterdam 1098XH , The Netherlands
| | - Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom
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7
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Haugland MM, Borsley S, Cairns-Gibson DF, Elmi A, Cockroft SL. Synthetically Diversified Protein Nanopores: Resolving Click Reaction Mechanisms. ACS NANO 2019; 13:4101-4110. [PMID: 30864781 DOI: 10.1021/acsnano.8b08691] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopores are emerging as a powerful tool for the investigation of nanoscale processes at the single-molecule level. Here, we demonstrate the methionine-selective synthetic diversification of α-hemolysin (α-HL) protein nanopores and their exploitation as a platform for investigating reaction mechanisms. A wide range of functionalities, including azides, alkynes, nucleotides, and single-stranded DNA, were incorporated into individual pores in a divergent fashion. The ion currents flowing through the modified pores were used to observe the trajectory of a range of azide-alkyne click reactions and revealed several short-lived intermediates in Cu(I)-catalyzed azide-alkyne [3 + 2] cycloadditions (CuAAC) at the single-molecule level. Analysis of ion-current fluctuations enabled the populations of species involved in rapidly exchanging equilibria to be determined, facilitating the resolution of several transient intermediates in the CuAAC reaction mechanism. The versatile pore-modification chemistry offers a useful approach for enabling future physical organic investigations of reaction mechanisms at the single-molecule level.
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Affiliation(s)
- Marius M Haugland
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Stefan Borsley
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Dominic F Cairns-Gibson
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Alex Elmi
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Scott L Cockroft
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
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8
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Gilpin C, Darmon D, Siwy Z, Martens C. Information Dynamics of a Nonlinear Stochastic Nanopore System. ENTROPY 2018; 20:e20040221. [PMID: 33265312 PMCID: PMC7512734 DOI: 10.3390/e20040221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022]
Abstract
Nanopores have become a subject of interest in the scientific community due to their potential uses in nanometer-scale laboratory and research applications, including infectious disease diagnostics and DNA sequencing. Additionally, they display behavioral similarity to molecular and cellular scale physiological processes. Recent advances in information theory have made it possible to probe the information dynamics of nonlinear stochastic dynamical systems, such as autonomously fluctuating nanopore systems, which has enhanced our understanding of the physical systems they model. We present the results of local (LER) and specific entropy rate (SER) computations from a simulation study of an autonomously fluctuating nanopore system. We learn that both metrics show increases that correspond to fluctuations in the nanopore current, indicating fundamental changes in information generation surrounding these fluctuations.
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Affiliation(s)
- Claire Gilpin
- Department of Physics and Astronomy, University of California-Irvine, Irvine, CA 92697-4575, USA
- Correspondence:
| | - David Darmon
- Department of Military and Emergency Medicine, Uniformed Services University, Bethesda, MD 20814, USA
| | - Zuzanna Siwy
- Department of Physics and Astronomy, University of California-Irvine, Irvine, CA 92697-4575, USA
| | - Craig Martens
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697-2025, USA
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9
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Borsley S, Cooper JA, Lusby PJ, Cockroft SL. Nanopore Detection of Single‐Molecule Binding within a Metallosupramolecular Cage. Chemistry 2018; 24:4542-4546. [DOI: 10.1002/chem.201800760] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Stefan Borsley
- EaStCHEM School of ChemistryUniversity of Edinburgh, Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - James A. Cooper
- EaStCHEM School of ChemistryUniversity of Edinburgh, Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Paul J. Lusby
- EaStCHEM School of ChemistryUniversity of Edinburgh, Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of Edinburgh, Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
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10
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Cooper JA, Borsley S, Lusby PJ, Cockroft SL. Discrimination of supramolecular chirality using a protein nanopore. Chem Sci 2017; 8:5005-5009. [PMID: 28970887 PMCID: PMC5612056 DOI: 10.1039/c7sc01940h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/04/2017] [Indexed: 11/21/2022] Open
Abstract
Supramolecular chirality may emerge from self-assembly processes to yield architectures that differ only in the topological arrangement of their constituent parts. Since the properties of the resulting enantiomeric assemblies are identical, purification and characterisation can be challenging. Here, we have examined the hypothesis that the intrinsic chirality of a protein nanopore can be exploited to detect supramolecular chirality. Transient blockages in the ion current flowing through a single membrane-spanning α-haemolysin nanopore were shown to discriminate between M4L6 tetrahedral coordination cages of opposing chiralities. The single-molecule nature of the approach facilitated direct access to the rates of association and dissociation with the nanopore, which allowed the concentrations of the enantiomeric supramolecular assemblies to be determined in situ. Thus, we have established that a protein nanopore can be used to discriminate the chiral topologies of supramolecular assemblies, even when they are too large to fully enter the nanopore.
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Affiliation(s)
- James A Cooper
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , UK .
| | - Stefan Borsley
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , UK .
| | - Paul J Lusby
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , UK .
| | - Scott L Cockroft
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , UK .
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11
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McCurry DA, Bailey RC. Electrolyte Gradient-Based Modulation of Molecular Transport through Nanoporous Gold Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1552-1562. [PMID: 28107634 DOI: 10.1021/acs.langmuir.6b04128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanopores, and nanoporous materials in general, are interesting for applications in chemical and biomolecular transport as pore sizes are on the same scale as the dimension of many (bio)chemical species. Many studies have focused on either single pores or small arrays of cylindrical pores, which are convenient in terms of their amenability toward computational modeling of transport phenomenon. However, the limited overall porosity may inhibit transport flux as well as the eventual implementation of these materials as active separation elements. Inspired by its relatively high porosity, we have explored nanoporous gold (NPG) as a membrane across which small molecular species can be transported. NPG offers a random, bicontinuous pore geometry, while also being inherently conductive and readily amenable to surface modification-attributes that may be enabling in the pursuit of size- and charge-based approaches to molecular separations. NPG was fabricated via a free-corrosion process whereby immersion of Au-containing alloys in concentrated nitric acid preferentially dissolves the less noble metals (e.g., Ni, Cu). Average pore diameters of 50 ± 20 nm were obtained as verified under scanning electron microscopy. NPG membranes were sandwiched between two reservoirs, and the selective transport of chemical species across the membrane in the presence of an ionic strength gradient was investigated. The flux of small molecules were monitored by UV-vis absorption spectrometry and found to be dependent upon the direction and magnitude of the ionic strength gradient. Moreover, transport trends underscored the effects of surface charge in a confined environment, considering that the pore diameters were on the same scale as the electrical double layer experienced by molecules transiting the membrane. Under such conditions, the transport of anions and cations through NPG was found to depend on an induced electric field as well as ion advection. Further electrical and surface chemical modulations of transport are expected to engender increased membrane functionality.
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Affiliation(s)
- Daniel A McCurry
- Department of Chemistry, University of Illinois , 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Ryan C Bailey
- Department of Chemistry, University of Illinois , 600 S. Mathews Ave., Urbana, Illinois 61801, United States
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12
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Payet L, Martinho M, Merstorf C, Pastoriza-Gallego M, Pelta J, Viasnoff V, Auvray L, Muthukumar M, Mathé J. Temperature Effect on Ionic Current and ssDNA Transport through Nanopores. Biophys J 2015; 109:1600-7. [PMID: 26488651 PMCID: PMC4624348 DOI: 10.1016/j.bpj.2015.08.043] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/11/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022] Open
Abstract
We have investigated the role of electrostatic interactions in the transport of nucleic acids and ions through nanopores. The passage of DNA through nanopores has so far been conjectured to involve a free-energy barrier for entry, followed by a downhill translocation where the driving voltage accelerates the polymer. We have tested the validity of this conjecture by using two toxins, α-hemolysin and aerolysin, which differ in their shape, size, and charge. The characteristic timescales in each toxin as a function of temperature show that the entry barrier is ∼15 kBT and the translocation barrier is ∼35 kBT, although the electrical force in the latter step is much stronger. Resolution of this fact, using a theoretical model, reveals that the attraction between DNA and the charges inside the barrel of the pore is the most dominant factor in determining the translocation speed and not merely the driving electrochemical potential gradient.
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Affiliation(s)
- Linda Payet
- LAMBE, équipe MPI, CNRS-UMR 8587, Université d'Évry, Évry, France
| | - Marlène Martinho
- LAMBE, équipe MPI, CNRS-UMR 8587, Université d'Évry, Évry, France
| | - Céline Merstorf
- LAMBE, équipe MPI, CNRS-UMR 8587, Université d'Évry, Évry, France
| | | | - Juan Pelta
- LAMBE, équipe MPI, CNRS-UMR 8587, Université d'Évry, Évry, France
| | - Virgile Viasnoff
- Laboratoire Gulliver équipe NBP, CNRS-UMR 7083, ESPCI, Paris, France; CNRS UMI 3639, MechanoBiology Institute at National University of Singapore, Singapore, Singapore
| | - Loïc Auvray
- Laboratoire MSC, CNRS-UMR 7057, Université Denis Diderot, Paris, France
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts
| | - Jérôme Mathé
- LAMBE, équipe MPI, CNRS-UMR 8587, Université d'Évry, Évry, France.
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Kukwikila M, Howorka S. Nanopore-Based Electrical and Label-Free Sensing of Enzyme Activity in Blood Serum. Anal Chem 2015; 87:9149-54. [DOI: 10.1021/acs.analchem.5b01764] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Mikiembo Kukwikila
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London, England, United Kingdom
- School
of Chemistry, University of Southampton, Southampton, England, United Kingdom
| | - Stefan Howorka
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London, England, United Kingdom
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14
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Watson MA, Cockroft SL. DNA modulates solvent isotope effects in a nanopore. Chem Commun (Camb) 2015; 51:12243-6. [PMID: 26135014 DOI: 10.1039/c5cc01563d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we investigate the modulation of solvent isotope effects by the entry of DNA molecules into individual α-haemolysin nanopores. Solvent isotope effects in D2O versus H2O were enhanced (kH/kD ≈ 1.6) compared to the bulk (kH/kD ≈ 1.2), except when the pore was most blocked (kH/kD ≤ 1.1).
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Affiliation(s)
- Matthew A Watson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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15
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Barsbay M, Güven O. Grafting in confined spaces: Functionalization of nanochannels of track-etched membranes. Radiat Phys Chem Oxf Engl 1993 2014. [DOI: 10.1016/j.radphyschem.2014.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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16
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Martin HSC, Jha S, Coveney PV. Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. J Comput Chem 2014; 35:692-702. [PMID: 24403093 PMCID: PMC4274958 DOI: 10.1002/jcc.23525] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/13/2013] [Accepted: 12/07/2013] [Indexed: 12/17/2022]
Abstract
The translocation of nucleotide molecules across biological and synthetic nanopores has attracted attention as a next generation technique for sequencing DNA. Computer simulations have the ability to provide atomistic-level insight into important states and processes, delivering a means to develop a fundamental understanding of the translocation event, for example, by extracting the free energy of the process. Even with current supercomputing facilities, the simulation of many-atom systems in fine detail is limited to shorter timescales than the real events they attempt to recreate. This imposes the need for enhanced simulation techniques that expand the scope of investigation in a given timeframe. There are numerous free energy calculation and translocation methodologies available, and it is by no means clear which method is best applied to a particular problem. This article explores the use of two popular free energy calculation methodologies in a nucleotide-nanopore translocation system, using the α-hemolysin nanopore. The first uses constant velocity-steered molecular dynamics (cv-SMD) in conjunction with Jarzynski's equality. The second applies an adaptive biasing force (ABF), which has not previously been applied to the nucleotide-nanpore system. The purpose of this study is to provide a comprehensive comparison of these methodologies, allowing for a detailed comparative assessment of the scientific merits, the computational cost, and the statistical quality of the data obtained from each technique. We find that the ABF method produces results that are closer to experimental measurements than those from cv-SMD, whereas the net errors are smaller for the same computational cost.
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Affiliation(s)
- Hugh S C Martin
- Department of Chemistry, Centre for Computational ScienceUCL, 20 Gordon Street, London, United Kingdom
| | - Shantenu Jha
- Department of Electrical Engineering BuildingRutgers, 94 Brett Road, Piscataway, New Jersey
| | - Peter V Coveney
- Department of Chemistry, Centre for Computational ScienceUCL, 20 Gordon Street, London, United Kingdom
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