1
|
Smith A, Larsen TRB, Zimmerman HK, Virolainen SJ, Meyer JJ, Keranen Burden LM, Burden DL. Design and Construction of a Multi-Tiered Minimal Actin Cortex for Structural Support in Lipid Bilayer Applications. ACS APPLIED BIO MATERIALS 2024; 7:1936-1946. [PMID: 38427377 PMCID: PMC10951949 DOI: 10.1021/acsabm.3c01267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Artificial lipid bilayers have revolutionized biochemical and biophysical research by providing a versatile interface to study aspects of cell membranes and membrane-bound processes in a controlled environment. Artificial bilayers also play a central role in numerous biosensing applications, form the foundational interface for liposomal drug delivery, and provide a vital structure for the development of synthetic cells. But unlike the envelope in many living cells, artificial bilayers can be mechanically fragile. Here, we develop prototype scaffolds for artificial bilayers made from multiple chemically linked tiers of actin filaments that can be bonded to lipid headgroups. We call the interlinked and layered assembly a multiple minimal actin cortex (multi-MAC). Construction of multi-MACs has the potential to significantly increase the bilayer's resistance to applied stress while retaining many desirable physical and chemical properties that are characteristic of lipid bilayers. Furthermore, the linking chemistry of multi-MACs is generalizable and can be applied almost anywhere lipid bilayers are important. This work describes a filament-by-filament approach to multi-MAC assembly that produces distinct 2D and 3D architectures. The nature of the structure depends on a combination of the underlying chemical conditions. Using fluorescence imaging techniques in model planar bilayers, we explore how multi-MACs vary with electrostatic charge, assembly time, ionic strength, and type of chemical linker. We also assess how the presence of a multi-MAC alters the underlying lateral diffusion of lipids and investigate the ability of multi-MACs to withstand exposure to shear stress.
Collapse
Affiliation(s)
- Amanda
J. Smith
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Theodore R. B. Larsen
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Harmony K. Zimmerman
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Samuel J. Virolainen
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Joshua J. Meyer
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Lisa M. Keranen Burden
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Daniel L. Burden
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| |
Collapse
|
2
|
Burden DL, Meyer JJ, Michael RD, Anderson SC, Burden HM, Peña SM, Leong-Fern KJ, Van Ye LA, Meyer EC, Keranen-Burden LM. Confirming Silent Translocation through Nanopores with Simultaneous Single-Molecule Fluorescence and Single-Channel Electrical Recordings. Anal Chem 2023; 95:18020-18028. [PMID: 37991877 PMCID: PMC10719886 DOI: 10.1021/acs.analchem.3c02329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023]
Abstract
Most of what is known concerning the luminal passage of materials through nanopores arises from electrical measurements. Whether nanopores are biological, solid-state, synthetic, hybrid, glass-capillary-based, or protein ion channels in cells and tissues, characteristic signatures embedded in the flow of ionic current are foundational to understanding functional behavior. In contrast, this work describes passage through a nanopore that occurs without producing an electrical signature. We refer to the phenomenon as "silent translocation." By definition, silent translocations are invisible to the standard tools of electrophysiology and fundamentally require a simultaneous ancillary measurement technique for positive identification. As a result, this phenomenon has been largely unexplored in the literature. Here, we report on a derivative of Cyanine 5 (sCy5a) that passes through the α-hemolysin (αHL) nanopore silently. Simultaneously acquired single-molecule fluorescence and single-channel electrical recordings from bilayers formed over a closed microcavity demonstrate that translocation does indeed take place, albeit infrequently. We report observations of silent translocation as a function of time, dye concentration, and nanopore population in the bilayer. Lastly, measurement of the translocation rate as a function of applied potential permits estimation of an effective energy barrier for transport through the pore as well as the effective charge on the dye, all in the absence of an information-containing electrical signature.
Collapse
Affiliation(s)
- Daniel L. Burden
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Joshua J. Meyer
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Richard D. Michael
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Sophie C. Anderson
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Hannah M. Burden
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Sophia M. Peña
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | | - Lily Anne Van Ye
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Elizabeth C. Meyer
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | |
Collapse
|
3
|
Afshar Bakshloo M, Kasianowicz JJ, Pastoriza-Gallego M, Mathé J, Daniel R, Piguet F, Oukhaled A. Nanopore-Based Protein Identification. J Am Chem Soc 2022; 144:2716-2725. [PMID: 35120294 DOI: 10.1021/jacs.1c11758] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The implementation of a reliable, rapid, inexpensive, and simple method for whole-proteome identification would greatly benefit cell biology research and clinical medicine. Proteins are currently identified by cleaving them with proteases, detecting the polypeptide fragments with mass spectrometry, and mapping the latter to sequences in genomic/proteomic databases. Here, we demonstrate that the polypeptide fragments can instead be detected and classified at the single-molecule limit using a nanometer-scale pore formed by the protein aerolysin. Specifically, three different water-soluble proteins treated with the same protease, trypsin, produce different polypeptide fragments defined by the degree by which the latter reduce the nanopore's ionic current. The fragments identified with the aerolysin nanopore are consistent with the predicted fragments that trypsin could produce.
Collapse
Affiliation(s)
| | - John J Kasianowicz
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States.,Freiburg Institute for Advanced Studies, Universität Freiburg, 79104 Freiburg, Germany
| | | | - Jérôme Mathé
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, 91000, France
| | - Régis Daniel
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, 91000, France
| | - Fabien Piguet
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, 95000, France
| | | |
Collapse
|
4
|
Xie S, Leung AWS, Zheng Z, Zhang D, Xiao C, Luo R, Luo M, Zhang S. Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. Innovation (N Y) 2021; 2:100153. [PMID: 34901902 PMCID: PMC8640597 DOI: 10.1016/j.xinn.2021.100153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them.
Collapse
Affiliation(s)
- Shangqian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China
| | - Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Zhenxian Zheng
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Dake Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou 510060, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Ming Luo
- Agriculture and Biotechnology Research Center, Guangdong Provincial Key Laboratory of Applied Botany, Center of Economic Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shoudong Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| |
Collapse
|
5
|
Abstract
Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.
Collapse
|
6
|
Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
Collapse
Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| |
Collapse
|
7
|
Lysenin Channels as Sensors for Ions and Molecules. SENSORS 2020; 20:s20216099. [PMID: 33120957 PMCID: PMC7663491 DOI: 10.3390/s20216099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
Lysenin is a pore-forming protein extracted from the earthworm Eisenia fetida, which inserts large conductance pores in artificial and natural lipid membranes containing sphingomyelin. Its cytolytic and hemolytic activity is rather indicative of a pore-forming toxin; however, lysenin channels present intricate regulatory features manifested as a reduction in conductance upon exposure to multivalent ions. Lysenin pores also present a large unobstructed channel, which enables the translocation of analytes, such as short DNA and peptide molecules, driven by electrochemical gradients. These important features of lysenin channels provide opportunities for using them as sensors for a large variety of applications. In this respect, this literature review is focused on investigations aimed at the potential use of lysenin channels as analytical tools. The described explorations include interactions with multivalent inorganic and organic cations, analyses on the reversibility of such interactions, insights into the regulation mechanisms of lysenin channels, interactions with purines, stochastic sensing of peptides and DNA molecules, and evidence of molecular translocation. Lysenin channels present themselves as versatile sensing platforms that exploit either intrinsic regulatory features or the changes in ionic currents elicited when molecules thread the conducting pathway, which may be further developed into analytical tools of high specificity and sensitivity or exploited for other scientific biotechnological applications.
Collapse
|
8
|
Wang S, Cao J, Jia W, Guo W, Yan S, Wang Y, Zhang P, Chen HY, Huang S. Single molecule observation of hard-soft-acid-base (HSAB) interaction in engineered Mycobacterium smegmatis porin A (MspA) nanopores. Chem Sci 2019; 11:879-887. [PMID: 34123066 PMCID: PMC8146584 DOI: 10.1039/c9sc05260g] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the formation of coordination interactions between metal ions and amino acids in natural metalloproteins, the bound metal ion is critical either for the stabilization of the protein structure or as an enzyme co-factor. Though extremely small in size, metal ions, when bound to the restricted environment of an engineered biological nanopore, result in detectable perturbations during single channel recordings. All reported work of this kind was performed with engineered α-hemolysin nanopores and the observed events appear to be extremely small in amplitude (∼1–3 pA). We speculate that the cylindrical pore restriction of α-hemolysin may not be optimal for probing extremely small analytes. Mycobacterium smegmatis porin A (MspA), a conical shaped nanopore, was engineered to interact with Ca2+, Mn2+, Co2+, Ni2+, Zn2+, Pb2+ and Cd2+ and a systematically larger event amplitude (up to 10 pA) was observed. The measured rate constant suggests that the coordination of a single ion with an amino acid follows hard–soft-acid–base theory, which has never been systematically validated in the case of a single molecule. By adjusting the measurement pH from 6.8 to 8.0, the duration of a single ion binding event could be modified with a ∼46-fold time extension. The phenomena reported suggest MspA to be a superior engineering template for probing a variety of extremely small analytes, such as monatomic and polyatomic ions, small molecules or chemical intermediates, and the principle of hard–soft-acid–base interaction may be instructive in the pore design. The principle of hard–soft-acid–base (HSAB) theory was first validated in single molecule by measurements with engineered Mycobacterium smegmatis porin A (MspA) nanopore reactors.![]()
Collapse
Affiliation(s)
- Sha Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - Jiao Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - Weiming Guo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| |
Collapse
|
9
|
Wang H, Kasianowicz JJ, Robertson JWF, Poster DL, Ettedgui J. A comparison of ion channel current blockades caused by individual poly(ethylene glycol) molecules and polyoxometalate nanoclusters. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:83. [PMID: 31250227 DOI: 10.1140/epje/i2019-11838-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Proteinaceous nanometer-scale pores have been used to detect and physically characterize many different types of analytes at the single-molecule limit. The method is based on the ability to measure the transient reduction in the ionic channel conductance caused by molecules that partition into the pore. The distribution of blockade depth amplitudes and residence times of the analytes in the pore are used to physically and chemically characterize them. Here we compare the current blockade events caused by flexible linear polymers of ethylene glycol (PEGs) and structurally well-defined tungsten polyoxymetallate nanoparticles in the nanopores formed by Staphylococcus aureusα-hemolysin and Aeromonas hydrophila aerolysin. Surprisingly, the variance in the ionic current blockade depth values for the relatively rigid metallic nanoparticles is much greater than that for the flexible PEGs, possibly because of multiple charged states of the polyoxymetallate clusters.
Collapse
Affiliation(s)
- Haiyan Wang
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Shenzhen Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, 508060, Shenzhen, China
| | - John J Kasianowicz
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA.
- Columbia University, Department of Applied Physics Applied Mathematics, 10027, New York, NY, USA.
| | - Joseph W F Robertson
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Dianne L Poster
- National Institute of Standards and Technology, Material Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Jessica Ettedgui
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Columbia University, Department of Chemical Engineering, 10027, New York, NY, USA
| |
Collapse
|
10
|
Tan CS, Fleming AM, Ren H, Burrows CJ, White HS. γ-Hemolysin Nanopore Is Sensitive to Guanine-to-Inosine Substitutions in Double-Stranded DNA at the Single-Molecule Level. J Am Chem Soc 2018; 140:14224-14234. [PMID: 30269492 DOI: 10.1021/jacs.8b08153] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biological nanopores provide a unique single-molecule sensing platform to detect target molecules based on their specific electrical signatures. The γ-hemolysin (γ-HL) protein produced by Staphylococcus aureus is able to assemble into an octamer nanopore with a ∼2.3 nm diameter β-barrel. Herein, we demonstrate the first application of γ-HL nanopore for DNA structural analysis. To optimize conditions for ion-channel recording, the properties of the γ-HL pore (e.g., conductance, voltage-dependent gating, and ion-selectivity) were characterized at different pH, temperature, and electrolyte concentrations. The optimal condition for DNA analysis using γ-HL corresponds to 3 M KCl, pH 5, and T = 20 °C. The γ-HL protein nanopore is able to translocate dsDNA at about ∼20 bp/ms, and the unique current-signature of captured dsDNA can directly distinguish guanine-to-inosine substitutions at the single-molecule level with ∼99% accuracy. The slow dsDNA threading and translocation processes indicate this wild-type γ-HL channel has potential to detect other base modifications in dsDNA.
Collapse
Affiliation(s)
- Cherie S Tan
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| |
Collapse
|
11
|
Willems K, Van Meervelt V, Wloka C, Maglia G. Single-molecule nanopore enzymology. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630164 DOI: 10.1098/rstb.2016.0230] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here, we describe the approaches and challenges in nanopore enzymology.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
Collapse
Affiliation(s)
- Kherim Willems
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Department of Life Sciences and Imaging, IMEC, Kapeldreef 75, 3001 Leuven, Belgium
| | - Veerle Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| |
Collapse
|
12
|
Wang H, Ettedgui J, Forstater J, Robertson JWF, Reiner JE, Zhang H, Chen S, Kasianowicz JJ. Determining the Physical Properties of Molecules with Nanometer-Scale Pores. ACS Sens 2018; 3:251-263. [PMID: 29381331 DOI: 10.1021/acssensors.7b00680] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nanometer-scale pores have been developed for the detection, characterization, and quantification of a wide range of analytes (e.g., ions, polymers, proteins, anthrax toxins, neurotransmitters, and synthetic nanoparticles) and for DNA sequencing. We describe the key requirements that made this method possible and how the technique evolved. Finally, we show that, despite sound theoretical work, which advanced both the conceptual framework and quantitative capability of the method, there are still unresolved questions that need to be addressed to further improve the technique.
Collapse
Affiliation(s)
- Haiyan Wang
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Jessica Ettedgui
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Jacob Forstater
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Joseph W. F. Robertson
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Huisheng Zhang
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Siping Chen
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - John J. Kasianowicz
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Applied Physics Applied Mathematics, Columbia University New York, New York 10027, United States
| |
Collapse
|
13
|
|
14
|
Rokitskaya TI, Nazarov PA, Golovin AV, Antonenko YN. Blocking of Single α-Hemolysin Pore by Rhodamine Derivatives. Biophys J 2017; 112:2327-2335. [PMID: 28591605 DOI: 10.1016/j.bpj.2017.04.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/06/2017] [Accepted: 04/25/2017] [Indexed: 11/30/2022] Open
Abstract
Measurements of ion conductance through α-hemolysin pore in a bilayer lipid membrane revealed blocking of the ion channel by a series of rhodamine 19 and rhodamine B esters. The longest dwell closed time of the blocking was observed with rhodamine 19 butyl ester (C4R1), whereas the octyl ester (C8R1) was of poor effect. Voltage asymmetry in the binding kinetics indicated that rhodamine derivatives bound to the stem part of the aqueous pore lumen. The binding frequency was proportional to a quadratic function of rhodamine concentrations, thereby showing that the dominant binding species were rhodamine dimers. Two levels of the pore conductance and two dwell closed times of the pore were found. The dwell closed times lengthened as the voltage increased, suggesting impermeability of the channel for the ligands. Molecular docking analysis revealed two distinct binding sites within the lumen of the stem of the α-hemolysin pore for the C4R1 dimer, but only one binding site for the C8R1 dimer. The blocking of the α-hemolysin nanopore by rhodamines could be utilized in DNA sequencing as additional optical sensing owing to bright fluorescence of rhodamines if used for DNA labeling.
Collapse
Affiliation(s)
- Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Pavel A Nazarov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
15
|
Perera RT, Fleming AM, Peterson AM, Heemstra JM, Burrows CJ, White HS. Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore. Biophys J 2016; 110:306-314. [PMID: 26789754 DOI: 10.1016/j.bpj.2015.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 01/04/2023] Open
Abstract
Unzipping of double-stranded nucleic acids by an electric field applied across a wild-type α-hemolysin (αHL) nanopore provides structural information about different duplex forms. In this work, comparative studies on A-form DNA-RNA duplexes and B-form DNA-DNA duplexes with a single-stranded tail identified significant differences in the blockage current and the unzipping duration between the two helical forms. We observed that the B-form duplex blocks the channel 1.9 ± 0.2 pA more and unzips ∼15-fold more slowly than an A-form duplex at 120 mV. We developed a model to describe the dependence of duplex unzipping on structure. We demonstrate that the wider A-form duplex (d = 2.4 nm) is unable to enter the vestibule opening of αHL on the cis side, leading to unzipping outside of the nanopore with higher residual current and faster unzipping times. In contrast, the smaller B-form duplexes (d = 2.0 nm) enter the vestibule of αHL, resulting in decreased current blockages and slower unzipping. We investigated the effects of varying the length of the single-stranded overhang, and studied A-form DNA-PNA duplexes to provide additional support for the proposed model. This study identifies key differences between A- and B-form duplex unzipping that will be important in the design of future probe-based methods for detecting DNA or RNA.
Collapse
Affiliation(s)
- Rukshan T Perera
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | | | | | | | - Henry S White
- Department of Chemistry, University of Utah, Salt Lake City, Utah.
| |
Collapse
|
16
|
Pederson ED, Barbalas J, Drown BS, Culbertson MJ, Keranen Burden LM, Kasianowicz JJ, Burden DL. Proximal Capture Dynamics for a Single Biological Nanopore Sensor. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Jonathan Barbalas
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Bryon S. Drown
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | | | | - John J. Kasianowicz
- Semiconductor
Electronics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Daniel L. Burden
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| |
Collapse
|
17
|
Zhang S, Sun T, Wang E, Wang J. Investigation of self-assembled protein dimers through an artificial ion channel for DNA sensing. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0626-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
| |
Collapse
|
19
|
Kasianowicz JJ, Reiner JE, Robertson JWF, Henrickson SE, Rodrigues C, Krasilnikov OV. Detecting and characterizing individual molecules with single nanopores. Methods Mol Biol 2012; 870:3-20. [PMID: 22528255 DOI: 10.1007/978-1-61779-773-6_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Single-nanometer-scale pores have demonstrated the capability for the detection, identification, and characterization of individual molecules. This measurement method could soon extend the existing commercial instrumentation or provide solutions to niche applications in many fields, including health care and the basic sciences. However, that paradigm shift requires a significantly better understanding of the physics and chemistry that govern the interactions between nanopores and analytes. We describe herein some of our methods and approaches to address this issue.
Collapse
Affiliation(s)
- John J Kasianowicz
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
| | | | | | | | | | | |
Collapse
|
20
|
Potential analytical applications of lysenin channels for detection of multivalent ions. Anal Bioanal Chem 2011; 401:1871-9. [PMID: 21818682 DOI: 10.1007/s00216-011-5277-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 07/13/2011] [Accepted: 07/21/2011] [Indexed: 11/27/2022]
Abstract
Transmembrane protein transporters possessing binding sites for ions, toxins, pharmaceutical drugs, and other molecules constitute excellent candidates for developing sensitive and selective biosensing devices. Their attractiveness for analytical purposes is enhanced by the intrinsic amplification capabilities shown when the binding event leads to major changes in the transportation of ions or molecules other than the analyte itself. The large-scale implementation of such transmembrane proteins in biosensing devices is limited by the difficulties encountered in inserting functional transporters into artificial bilayer lipid membranes and by the limitations in understanding and exploiting the changes induced by the interaction with the analyte for sensing purposes. Here, we show that lysenin, a pore-forming toxin extracted from earthworm Eisenia foetida, which inserts stable and large conductance channels into artificial bilayer lipid membranes, functions as a multivalent ion-sensing device. The analytical response consists of concentration and ionic-species-dependent macroscopic conductance inhibition most probably linked to a ligand-induced gating mechanism. Multivalent ion removal by chelation or precipitation restores, in most cases, the initial conductance and demonstrates reversibility. Changes in lipid bilayer membrane compositions leading to the absence of voltage-induced gating do not affect the analytical response to multivalent ions. Microscopic current analysis performed on individual lysenin channels in the presence of Cu(2+) revealed complex open-closed transitions characterized by unstable intermediate sub-conducting states. Lysenin channels provide an analytical tool with a built-in sensing mechanism for inorganic and organic multivalent ions, and the excellent stability in an artificial environment recommend lysenin as a potential candidate for single-molecule detection and analysis.
Collapse
|
21
|
Asandei A, Apetrei A, Luchian T. Uni-molecular detection and quantification of selected β-lactam antibiotics with a hybrid α-hemolysin protein pore. J Mol Recognit 2011; 24:199-207. [DOI: 10.1002/jmr.1038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
22
|
Mahendran KR, Singh PR, Arning J, Stolte S, Kleinekathöfer U, Winterhalter M. Permeation through nanochannels: revealing fast kinetics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454131. [PMID: 21339617 DOI: 10.1088/0953-8984/22/45/454131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The permeation of water soluble molecules across cell membranes is controlled by channel-forming proteins and, in particular, the channel surface determines the selectivity. An adequate method to study the properties of these channels is electrophysiology and, in particular, analyzing the ion current fluctuation in the presence of permeating solutes. Ion current fluctuation analysis provides information on possible interactions of solutes with the channel surface. Due to the limited time resolution, fast permeation events are not visible using standard techniques. Here, we demonstrate that miniaturization of the lipid bilayer; varying the temperature or changing the solvent may enhance the resolution. Although electrophysiology is considered as a single molecule technique, it does not provide atomic resolution. Molecular details of solute permeation can be revealed by combining electrophysiology and all-atom computer modeling; these methods include ion conductance, selectivity, ion pair formation, and rate limiting interactions of the solute with the channel walls during permeation.
Collapse
|
23
|
Mussi V, Fanzio P, Repetto L, Firpo G, Scaruffi P, Stigliani S, Menotta M, Magnani M, Tonini GP, Valbusa U. Electrical characterization of DNA-functionalized solid state nanopores for bio-sensing. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454104. [PMID: 21339592 DOI: 10.1088/0953-8984/22/45/454104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present data concerning the electrical properties of a class of biosensor devices based on bio-functionalized solid state nanopores able to detect different kinds of interactions between probe molecules, chemically attached to the pore surface, and target molecules present in solution and electrophoretically drawn through the nanometric channel. The great potentiality of this approach resides in the fact that the functionalization of a quite large pore (up to 50-60 nm) allows a sufficient diameter reduction for the attainment of a single molecule sensing dimension and selective activation, without the need for further material deposition, such as metal or oxides, or localized surface modification. The results indicate that it will be possible, in the near future, to conceive and design devices for parallel analysis of biological samples made of arrays of nanopores differently functionalized, fabricated by standard lithographic techniques, with important applications in the field of molecular diagnosis.
Collapse
Affiliation(s)
- V Mussi
- Nanomed Labs, Physics Department, University of Genova, and Nanobiotechnologies, National Institute of Cancer Research (IST), Largo R Benzi, 10 Genova, 16132, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Fologea D, Krueger E, Al Faori R, Lee R, Mazur YI, Henry R, Arnold M, Salamo GJ. Multivalent ions control the transport through lysenin channels. Biophys Chem 2010; 152:40-5. [PMID: 20724059 DOI: 10.1016/j.bpc.2010.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/27/2010] [Accepted: 07/28/2010] [Indexed: 11/30/2022]
Abstract
We report the effect of different ions on the conducting properties of lysenin channels inserted into planar lipid bilayer membranes. Our observations indicated that multivalent ions inhibited the lysenin channels conductance in a concentration dependent manner. The analysis performed on single channels revealed that multivalent ions induced reversible sub-conducting or closed states depending on the ionic charge and size. Good agreement is reported between experimental results and a theoretical model that is proposed to describe the interaction between divalent ions and lysenin channels as a simple isothermal absorption process.
Collapse
Affiliation(s)
- Daniel Fologea
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Abstract
When a voltage is imposed across a thin membrane containing a nanoscopic pore, the electric field generated within the pore captures linear ionized polymers, such as nucleic acids, that are present in the solution bathing the pore. The nucleic acid molecule transiently blocks ionic current as it is translocated through the pore, and modulations of the current provide information about the structure and dynamic motion of the molecule. Altering the imposed voltage allows movement of the DNA molecule in the pore to be controlled. If a DNA-processing enzyme such as an exonuclease or polymerase is present, the enzyme-DNA complex is also drawn to the pore, and further modulations of the ionic current reflect enzyme function at the single-molecule level on millisecond timescales. The combined enzymatic and voltage control of a DNA molecule in the nanopore can be used to sequence the DNA.
Collapse
Affiliation(s)
- David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
| |
Collapse
|
26
|
Sexton LT, Mukaibo H, Katira P, Hess H, Sherrill SA, Horne LP, Martin CR. An Adsorption-Based Model for Pulse Duration in Resistive-Pulse Protein Sensing. J Am Chem Soc 2010; 132:6755-63. [DOI: 10.1021/ja100693x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lindsay T. Sexton
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Hitomi Mukaibo
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Parag Katira
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Henry Hess
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Stefanie A. Sherrill
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Lloyd P. Horne
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| | - Charles R. Martin
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400, Department of Biomedical Engineering, Columbia University, New York, New York 10027, and Department of Chemistry, University of Maryland, College Park, Maryland 20742
| |
Collapse
|
27
|
Henrickson SE, DiMarzio EA, Wang Q, Stanford VM, Kasianowicz JJ. Probing single nanometer-scale pores with polymeric molecular rulers. J Chem Phys 2010; 132:135101. [PMID: 20387958 PMCID: PMC4108643 DOI: 10.1063/1.3328875] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 01/04/2010] [Indexed: 11/14/2022] Open
Abstract
We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus alpha-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the alpha-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.
Collapse
Affiliation(s)
- Sarah E Henrickson
- Semiconductor Electronics Division, NIST, Bldg. 225, Room B326, Gaithersburg, Maryland 20899-8120, USA
| | | | | | | | | |
Collapse
|
28
|
Progress of Research on Nanopore-macromolecule Detection. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.3724/sp.j.1096.2010.00280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
29
|
DING KJ, ZHANG HY, HU HG, ZHAO HM, Guan WJ, Ma YH. Progress of Research on Nanopore-macromolecule Detection. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60022-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
30
|
Nanotechnology for early cancer detection. SENSORS 2010; 10:428-55. [PMID: 22315549 PMCID: PMC3270850 DOI: 10.3390/s100100428] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/14/2009] [Accepted: 12/29/2009] [Indexed: 12/19/2022]
Abstract
Vast numbers of studies and developments in the nanotechnology area have been conducted and many nanomaterials have been utilized to detect cancers at early stages. Nanomaterials have unique physical, optical and electrical properties that have proven to be very useful in sensing. Quantum dots, gold nanoparticles, magnetic nanoparticles, carbon nanotubes, gold nanowires and many other materials have been developed over the years, alongside the discovery of a wide range of biomarkers to lower the detection limit of cancer biomarkers. Proteins, antibody fragments, DNA fragments, and RNA fragments are the base of cancer biomarkers and have been used as targets in cancer detection and monitoring. It is highly anticipated that in the near future, we might be able to detect cancer at a very early stage, providing a much higher chance of treatment.
Collapse
|
31
|
|
32
|
Kececi K, Sexton LT, Buyukserin F, Martin CR. Resistive-pulse detection of short dsDNAs using a chemically functionalized conical nanopore sensor. Nanomedicine (Lond) 2008; 3:787-96. [DOI: 10.2217/17435889.3.6.787] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To develop nanopore resistive-pulse sensors for the detection of short (50 base-pair [bp] and 100 bp) DNAs. Materials & methods: Conically shaped nanopores were chemical etched into polyethylene terphthalate membranes. The as-etched membrane had anionic carboxylate sites on the pore walls. Neutral and hydrophilic ethanolamine functional groups were attached to these carboxylate sites using well-established EDC (1-ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride) chemistry. Results & discussion: The ethanolamine-functionalized pores were used to detect 50 and 100 bp DNAs via the resistive-pulse method. The resistive-pulse signature produced by the 50 bp DNA could be distinguished from that of the 100 bp DNA with these sensors. Conclusions: Attachment of ethanolamine to the carboxylate groups on the pore wall lowered the anionic charge density on the wall. This mitigated the problem of electrostatic rejection of the anionic DNAs from the pore and enabled the detection of these DNA analytes.
Collapse
Affiliation(s)
- Kaan Kececi
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | - Lindsay T Sexton
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | - Fatih Buyukserin
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | - Charles R Martin
- Departments of Chemistry & Anesthesiology, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| |
Collapse
|
33
|
Abstract
The mechanisms of KCl-induced enhancement in identification of individual molecules of poly(ethylene glycol) using solitary alpha-hemolysin nanoscale pores are described. The interaction of single molecules with the nanopore causes changes in the ionic current flowing through the pore. We show that the on-rate constant of the process is several hundred times larger and that the off-rate is several hundred times smaller in 4 M KCl than in 1 M KCl. These shifts dramatically improve detection and make single molecule identification feasible. KCl also changes the solubility of poly(ethylene glycol) by the same order of magnitude as it changes the rate constants. In addition, the polymer-nanopore interaction is determined to be a strong non-monotonic function of voltage, indicating that the flexible, nonionic poly(ethylene glycol) acts as a charged molecule. Therefore, salting-out and Coulombic interactions are responsible for the KCl-induced enhancement. These results will advance the development of devices with sensor elements based on single nanopores.
Collapse
|
34
|
Ali M, Schiedt B, Healy K, Neumann R, Ensinger W. Modifying the surface charge of single track-etched conical nanopores in polyimide. NANOTECHNOLOGY 2008; 19:085713. [PMID: 21730744 DOI: 10.1088/0957-4484/19/8/085713] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chemical modification of nanopore surfaces is of great interest as it means that the surface composition is no longer fixed by the choice of substrate material, even to the point where large biomolecules can be attached to the pore walls. Controlling nanopore transport characteristics is one important application of surface modification which is very relevant given the significant interest in sensors based on the transport of ions and molecules through nanopores. Reported here is a method to change the surface charge polarity of single track-etched conical nanopores in polyimide, which also has the potential to attach more complex molecules to the carboxyl groups on the nanopore walls. These carboxyl groups were converted into terminal amino groups, first by activation with N-(3-dimethylaminopropyl)-N-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS) followed by the covalent coupling of ethylenediamine. This results in a changed surface charge polarity. Regeneration of a carboxyl-terminated surface was also possible, by reaction of the amino groups with succinic anhydride. The success of these reactions was confirmed by measurements of the pore's pH sensitive current-voltage (I-V) characteristics before and after the chemical modification, which depend on surface charge. The permselectivity of the pores also changed accordingly with the modification.
Collapse
Affiliation(s)
- M Ali
- Department of Materials Science, Darmstadt University of Technology, Petersenstraße 23, D-64287 Darmstadt, Germany
| | | | | | | | | |
Collapse
|
35
|
Ervin EN, Kawano R, White RJ, White HS. Simultaneous Alternating and Direct Current Readout of Protein Ion Channel Blocking Events Using Glass Nanopore Membranes. Anal Chem 2008; 80:2069-76. [DOI: 10.1021/ac7021103] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Eric N. Ervin
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| | - Ryuji Kawano
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| | - Ryan J. White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| | - Henry S. White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112
| |
Collapse
|
36
|
Wang J, Martin CR. A new drug-sensing paradigm based on ion-current rectification in a conically shaped nanopore. Nanomedicine (Lond) 2008; 3:13-20. [DOI: 10.2217/17435889.3.1.13] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To utilize the ion-current rectification phenomenon observed for conically shaped nanopores as the basis for designing sensors for drug molecules that adsorb to the walls of the nanopore. Methods: The conically shaped nanopore was prepared by the well-known track-etch method in a polyimide (Kapton) membrane. The ion current flowing through the nanopore was measured as a function of applied transmembrane potential in the presence of the analyte drug molecule, Hoechst 33258. Results: The pore walls in the Kapton membrane are hydrophobic yet have fixed carboxylate groups that give the walls a net negative charge. This fixed anionic surface charge causes the nanopore to rectify the ion current flowing through it. The analyte drug molecule, Hoechst 33258, is cationic yet also hydrophobic. When the membrane is exposed to this molecule, it adsorbs to the pore walls and neutralizes the anionic surface charge, thus lowering the extent of ion-current rectification. The change in rectification is proportional to the concentration of the drug. Conclusions: This nanopore sensor is selective for hydrophobic cations relative to anions, neutral molecules and less hydrophobic cations. Future work will explore ways of augmenting this hydrophobic effect-based selectivity so that more highly selective sensors can be obtained.
Collapse
Affiliation(s)
- JiaHai Wang
- University of Florida, Department of Chemistry & Center for Research at the Bio/Nano Interface, Gainesville, FL 32605, USA
| | - Charles R Martin
- University of Florida, Department of Chemistry & Center for Research at the Bio/Nano Interface, Gainesville, FL 32605, USA
| |
Collapse
|
37
|
Kasianowicz JJ, Robertson JWF, Chan ER, Reiner JE, Stanford VM. Nanoscopic porous sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:737-766. [PMID: 20636096 DOI: 10.1146/annurev.anchem.1.031207.112818] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
There are thousands of different nanometer-scale pores in biology, many of which act as sensors for specific chemical agents. Recent work suggests that protein and solid-state nanopores have many potential uses in a wide variety of analytical applications. In this review we survey this field of research and discuss the prospects for advances that could be made in the near future.
Collapse
Affiliation(s)
- John J Kasianowicz
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, USA.
| | | | | | | | | |
Collapse
|
38
|
Lambrianou A, Demin S, Hall EAH. Protein engineering and electrochemical biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 109:65-96. [PMID: 17960341 DOI: 10.1007/10_2007_080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Protein engineered biosensors provide the next best step in the advancement of protein-based sensors that can specifically identify chemical substrates. The use of native proteins for this purpose cannot adequately embrace the limits of detection and level of stability required for a usable sensor, due to globular structure restraints. This review chapter attempts to give an accurate representation of the three main strategies employed in the engineering of more suitable biological components for use in biosensor construction. The three main strategies in protein engineering for electrochemical biosensor implementation are: rational protein design, directed evolution and de novo protein design. Each design strategy has limitations to its use in a biosensor format and has advantages and disadvantages with respect to each. The three design techniques are used to modify aspects of stability, sensitivity, selectivity, surface tethering, and signal transduction within the biological environment. Furthermore with the advent of new nanomaterials the implementation of these design strategies, with the attomolar promise of nanostructures, imparts important generational leaps in research for biosensor construction, based on highly specific, very robust, and electrically wired protein engineered biosensors.
Collapse
Affiliation(s)
- Andreas Lambrianou
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | | | | |
Collapse
|
39
|
Sexton LT, Horne LP, Sherrill SA, Bishop GW, Baker LA, Martin CR. Resistive-Pulse Studies of Proteins and Protein/Antibody Complexes Using a Conical Nanotube Sensor. J Am Chem Soc 2007; 129:13144-52. [DOI: 10.1021/ja0739943] [Citation(s) in RCA: 193] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lindsay T. Sexton
- Contribution from the Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200
| | - Lloyd P. Horne
- Contribution from the Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200
| | - Stefanie A. Sherrill
- Contribution from the Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200
| | - Gregory W. Bishop
- Contribution from the Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200
| | - Lane A. Baker
- Contribution from the Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200
| | - Charles R. Martin
- Contribution from the Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200
| |
Collapse
|
40
|
Wharton JE, Jin P, Sexton LT, Horne LP, Sherrill SA, Mino WK, Martin CR. A method for reproducibly preparing synthetic nanopores for resistive-pulse biosensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2007; 3:1424-30. [PMID: 17615589 DOI: 10.1002/smll.200700106] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
There is increasing interest in using nanopores in synthetic membranes as resistive-pulse sensors for biomedical analytes. Analytes detected with prototype artificial-nanopore biosensors include drugs, DNA, proteins, and viruses. This field is, however, currently in its infancy. A key question that must be addressed in order for such sensors to progress from an interesting laboratory experiment to practical devices is: Can the artificial-nanopore sensing element be reproducibly prepared? We have been evaluating sensors that employ a conically shaped nanopore prepared by the track-etch method as the sensor element. We describe here a new two-step pore-etching procedure that allows for good reproducibility in nanopore fabrication. In addition, we describe a simple mathematical model that allows us to predict the characteristics of the pore produced given the experimental parameters of the two-step etch. This method and model constitute important steps toward developing practical, real-world, artificial-nanopore biosensors.
Collapse
Affiliation(s)
- John E Wharton
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | | | | | | | | | | | | |
Collapse
|
41
|
Mamonova T, Kurnikova M. Structure and energetics of channel-forming protein-polysaccharide complexes inferred via computational statistical thermodynamics. J Phys Chem B 2007; 110:25091-100. [PMID: 17149934 PMCID: PMC1941698 DOI: 10.1021/jp065009n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ion channel protein alpha-hemolysin (alphaHL) forms supramolecular complexes with the polysaccharide beta-cyclodextrin (betaCD). This system has potential uses in nanoscale device engineering. It has been found recently that betaCD formed longer- or shorter-lived complexes with some engineered alphaHL mutants then with a wild type protein (Gu et al. J. Gen. Physiol. 2001, 118, 481-493). However, how changes in the protein sequence affect complex lifetime was not completely understood in part due to the lack of knowledge of structures of these metastable complexes. In this paper, we present an extensive molecular modeling study of the betaCD-alphaHL and selected mutant complexes to gain insights into the betaCD-alphaHL interaction mechanisms and to predict possible structures and energetics of the complexes. Thermodynamic integration (TI) and umbrella sampling (US) techniques (with the weighted histogram analysis method (WHAM)) were used to calculate the relative binding affinities of the complexes formed with the wild type alphaHL and the M113N, M113E, M113A, and M113V mutants. Our results are in excellent agreement with experiment. While betaCD-M113N and betaCD-M113A complexes were stable in the configuration of the wild type complex, the equilibrium configuration of the betaCD-M113V and betaCD-M113E complexes was significantly different. In these cases, TI alone was insufficient to accurately calculate the corresponding free energy differences. By utilizing a TI/US combination in a novel manner, we were able to accurately calculate free energy changes in these flexible systems. The betaCD-M113A and betaCD-M113E complexes, which exhibited shorter lifetimes than other complexes in an experiment, in simulations exhibited greater flexibility and higher water solvation of the betaCD adapter. MD simulations of the betaCD-M113N complex with betaCD in a downward orientation were also performed.
Collapse
|
42
|
Sexton LT, Horne LP, Martin CR. Developing synthetic conical nanopores for biosensing applications. MOLECULAR BIOSYSTEMS 2007; 3:667-85. [PMID: 17882330 DOI: 10.1039/b708725j] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this review we bring together recent results from our group focused towards the development of biosensors from single conically-shaped artificial nanopores. The nanopores, used in the work presented here, were prepared using the track-etch process. The fabrication of track-etched conical nanopores has been optimized to allow for single nanopores with reproducible dimensions to be prepared. We have also demonstrated techniques that allow for easy and controllable manipulation of nanopore geometry (e.g., cone angle). We will consider the ion transport properties of the conical nanopores and factors that affect these properties. Methods for introducing functions that mimic biological ion channels, such as voltage-gating, into these nanopores will also be addressed. Three prototype sensors developed from single conical nanopores will be presented. In the first two sensors, the single conical nanopores function as resistive-pulse sensors and detect the presence of analytes as current-blockade events in the ion current. The third sensor functions in an on/off mode, much like a ligand-gated ion channel. In the presence of a target analyte, the ion current permanently shuts off.
Collapse
Affiliation(s)
- Lindsay T Sexton
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
| | | | | |
Collapse
|
43
|
Harrell CC, Choi Y, Horne LP, Baker LA, Siwy ZS, Martin CR. Resistive-pulse DNA detection with a conical nanopore sensor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:10837-43. [PMID: 17129068 DOI: 10.1021/la061234k] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In this paper, we describe resistive-pulse sensing of two large DNAs, a single-stranded phage DNA (7250 bases) and a double-stranded plasmid DNA (6600 base pairs), using a conically shaped nanopore in a track-etched polycarbonate membrane as the sensing element. The conically shaped nanopore had a small-diameter (tip) opening of 40 nm and a large-diameter (base) opening of 1.5 microm. The DNAs were detected using the resistive-pulse, sometimes called stochastic sensing, method. This entails applying a transmembrane potential difference and monitoring the resulting ion current flowing through the nanopore. The phage DNA was driven electrophoretically through the nanopore (from tip to base), and these translocation events were observed as transient blocks in the ion current. We found that the frequency of these current-block events scales linearly with the concentration of the DNA and with the magnitude of the applied transmembrane potential. Increasing the applied transmembrane potential also led to a decrease in the duration of the current-block events. We also analyzed current-block events for the double-stranded plasmid DNA. However, because this DNA is too large to enter the tip opening of the nanopore, it could not translocate the pore. As a result, much shorter duration current-block events were observed, which we postulate are associated with bumping of the double-stranded DNA against the tip opening.
Collapse
Affiliation(s)
- C Chad Harrell
- Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, USA
| | | | | | | | | | | |
Collapse
|
44
|
Rhee M, Burns MA. Nanopore sequencing technology: research trends and applications. Trends Biotechnol 2006; 24:580-6. [PMID: 17055093 DOI: 10.1016/j.tibtech.2006.10.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 08/04/2006] [Accepted: 10/11/2006] [Indexed: 11/15/2022]
Abstract
Nanopore sequencing is one of the most promising technologies being developed as a cheap and fast alternative to the conventional Sanger sequencing method. Protein or synthetic nanopores have been used to detect DNA or RNA molecules. Although none of the technologies to date has shown single-base resolution for de novo DNA sequencing, there have been several reports of alpha-hemolysin protein nanopores being used for basic DNA analyses, and various synthetic nanopores have been fabricated. This review will examine current nanopore sequencing technologies, including recent developments of new applications.
Collapse
Affiliation(s)
- Minsoung Rhee
- Departments of Chemical Engineering and Biomedical Engineering, Ann Arbor, MI, 48109, USA
| | | |
Collapse
|
45
|
Abstract
We present an example of the use of self-assembly of biomolecules to create nanostructured building blocks. The resulting individual compartments can be tailored to fulfil specific functions: catalysis of a chemical reaction in a confined environment, detection on a molecular level and feedback with the outside. For example, such individually designed components can be assembled to build up macroscopic chemically active filters. The main component is membrane channels acting as molecular sieves, able to control the permeation across the capsule wall. We introduce briefly a new microdevice to characterise membrane channels with a future potential for high-throughput screening of channel properties based on automation, parallelisation and the use of microfluidics. Subsequently, we outline a possible application for channel-forming proteins: encapsulation of charged polymers or proteins into liposomes and restriction of diffusion through transmembrane channels to small ions, creating a Donnan potential. This Donnan potential can be used for external manipulation of nanocontainers by coupling of the capsule to an external electric field, or for the selective uptake of small charged molecules into the capsule.
Collapse
Affiliation(s)
- M Lindemann
- International University Bremen, 28725 Bremen, Germany
| | | |
Collapse
|
46
|
Merzlyak PG, Capistrano MFP, Valeva A, Kasianowicz JJ, Krasilnikov OV. Conductance and ion selectivity of a mesoscopic protein nanopore probed with cysteine scanning mutagenesis. Biophys J 2005; 89:3059-70. [PMID: 16085767 PMCID: PMC1366803 DOI: 10.1529/biophysj.105.066472] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nanometer-scale proteinaceous pores are the basis of ion and macromolecular transport in cells and organelles. Recent studies suggest that ion channels and synthetic nanopores may prove useful in biotechnological applications. To better understand the structure-function relationship of nanopores, we are studying the ion-conducting properties of channels formed by wild-type and genetically engineered versions of Staphylococcus aureus alpha-hemolysin (alphaHL) reconstituted into planar lipid bilayer membranes. Specifically, we measured the ion selectivities and current-voltage relationships of channels formed with 24 different alphaHL point cysteine mutants before and after derivatizing the cysteines with positively and negatively charged sulfhydryl-specific reagents. Novel negative charges convert the selectivity of the channel from weakly anionic to strongly cationic, and new positive charges increase the anionic selectivity. However, the extent of these changes depends on the channel radius at the position of the novel charge (predominantly affects ion selectivity) or on the location of these charges along the longitudinal axis of the channel (mainly alters the conductance-voltage curve). The results suggest that the net charge of the pore wall is responsible for cation-anion selectivity of the alphaHL channel and that the charge at the pore entrances is the main factor that determines the shape of the conductance-voltage curves.
Collapse
Affiliation(s)
- Petr G Merzlyak
- Laboratory of Membrane Biophysics, Department of Biophysics and Radiobiology, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | | | | | | |
Collapse
|
47
|
Danelon C, Lindemann M, Borin C, Fournier D, Winterhalter M. Channel-forming membrane proteins as molecular sensors. IEEE Trans Nanobioscience 2005; 3:46-8. [PMID: 15382643 DOI: 10.1109/tnb.2004.824271] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Membrane channels are typically around or less than 1 nm in diameter and a description of the flow through them requires a molecular approach called nanofluidic. The ion current through channels is extremely sensitive to pore sizes. It is tempting to use the ion current to probe conformational changes of the channel or, for a fixed channel conformation, the current can be used to follow binding of molecules to the pore surfaces. Here we show the sensitivity of this method. It is possible to observe the passage of single isolated molecules through the channel and it is possible to discriminate between different passing molecules. Bioengineering allows us to modify channel surfaces and the affinity to different host molecules. Combining engineered proteins with the appropriated detection technique will allow a new type of molecular sensor.
Collapse
|
48
|
Berkane E, Orlik F, Charbit A, Danelon C, Fournier D, Benz R, Winterhalter M. Nanopores: maltoporin channel as a sensor for maltodextrin and lambda-phage. J Nanobiotechnology 2005; 3:3. [PMID: 15743521 PMCID: PMC555588 DOI: 10.1186/1477-3155-3-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Accepted: 03/02/2005] [Indexed: 11/12/2022] Open
Abstract
Background To harvest nutrition from the outside bacteria e.g. E. coli developed in the outer cell wall a number of sophisticated channels called porins. One of them, maltoporin, is a passive specific channel for the maltodextrin uptake. This channel was also named LamB as the bacterial virus phage Lambda mis-uses this channel to recognise the bacteria. The first step is a reversible binding followed after a lag phase by DNA injection. To date little is known about the binding capacity and less on the DNA injection mechanism. To elucidate the mechanism and to show the sensitivity of our method we reconstituted maltoporin in planar lipid membranes. Application of an external transmembrane electric field causes an ion current across the channel. Maltoporin channel diameter is around a few Angstroem. At this size the ion current is extremely sensitive to any modification of the channels surface. Protein conformational changes, substrate binding etc will cause fluctuations reflecting the molecular interactions with the channel wall. The recent improvement in ion current fluctuation analysis allows now studying the interaction of solutes with the channel on a single molecular level. Results We could demonstrate the asymmetry of the bacterial phage Lambda binding to its natural receptor maltoporin. Conclusion We suggest that this type of measurement can be used as a new type of biosensors.
Collapse
Affiliation(s)
- E Berkane
- Institut Pharmacologie & Biologie Structurale-CNRS UMR5089, 205, rte de Narbonne, F-31077 Toulouse, France
- Lehrstuhl für Biotechnologie, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
| | - F Orlik
- Lehrstuhl für Biotechnologie, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
| | - A Charbit
- Inserm U-570, CHU Necker-Enfants Malades, 156, rue de Vaugirard, F- 75730 Paris Cedex 15, France
| | - C Danelon
- Institut Pharmacologie & Biologie Structurale-CNRS UMR5089, 205, rte de Narbonne, F-31077 Toulouse, France
| | - D Fournier
- Institut Pharmacologie & Biologie Structurale-CNRS UMR5089, 205, rte de Narbonne, F-31077 Toulouse, France
| | - R Benz
- Lehrstuhl für Biotechnologie, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
| | - M Winterhalter
- Institut Pharmacologie & Biologie Structurale-CNRS UMR5089, 205, rte de Narbonne, F-31077 Toulouse, France
- International University Bremen, School of Engineering and Science, D-28727 Bremen, Germany
| |
Collapse
|
49
|
Ashkenasy N, Sánchez-Quesada J, Bayley H, Ghadiri MR. Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. Angew Chem Int Ed Engl 2005; 44:1401-4. [PMID: 15666419 PMCID: PMC1828035 DOI: 10.1002/anie.200462114] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nurit Ashkenasy
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | | |
Collapse
|
50
|
Ashkenasy N, Sánchez-Quesada J, Bayley H, Ghadiri MR. Recognizing a Single Base in an Individual DNA Strand: A Step Toward DNA Sequencing in Nanopores. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462114] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|