1
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Okyay C, Dessaux D, Ramirez R, Mathé J, Basdevant N. Exploring ssDNA translocation through α-hemolysin using coarse-grained steered molecular dynamics. NANOSCALE 2024; 16:15677-15689. [PMID: 39078242 DOI: 10.1039/d4nr01581a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside nanopores. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies ssDNA translocation through α-hemolysin nanopores exploiting steered MD using the MARTINI CG force field. The impacts of the sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing the experimental properties of ssDNA translocation, including a wide distribution in translocation times per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by the conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of obtaining sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.
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Affiliation(s)
- Cagla Okyay
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Évry-Courcouronnes, France.
| | - Delphine Dessaux
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Évry-Courcouronnes, France.
| | - Rosa Ramirez
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Évry-Courcouronnes, France.
| | - Jérôme Mathé
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Évry-Courcouronnes, France.
| | - Nathalie Basdevant
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Évry-Courcouronnes, France.
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2
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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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3
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Wang Z, Cui R, Liu L, Li L, Li Z, Liu X, Guo Y. Nanopore-Based Single-Molecule Investigation of Cation Effect on the i-Motif Structure. J Phys Chem B 2024; 128:6830-6837. [PMID: 38959208 DOI: 10.1021/acs.jpcb.4c02021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The i-motif, a secondary structure of a four-helix formed by cytosine-rich DNA (i-DNA) through C-C+ base pairing, is prevalent in human telomeres and promoters. This structure creates steric hindrance, thereby inhibiting both gene expression and protein coding. The conformation of i-DNA is intricately linked to the intracellular ionic environment. Hence, investigating its conformation under various ion conditions holds significant importance. In this study, we explored the impact of cations on the i-motif structure at the single-molecule level using the α-hemolysin (α-HL) nanochannel. Our findings reveal that the ability of i-DNA to fold into the i-motif structure follows the order Cs+ > Na+ > K+ > Li+ for monovalent cations. Furthermore, we observed the interconversion of single-stranded DNA (ss-DNA) and the i-motif structure at high and low concentrations of Mg2+ and Ba2+ electrolyte solutions. This study not only has the potential to extend the application of i-motif-based sensors in complex solution environments but also provides a new idea for the detection of metal ions.
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Affiliation(s)
- Zhenzhao Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Rikun Cui
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Lili Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Linna Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Zhen Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Xingtong Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
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4
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Liu W, Ma C, Wang H, Sha J. Conformation Influence of DNA on the Detection Signal through Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9622-9629. [PMID: 38652583 DOI: 10.1021/acs.langmuir.4c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The detection and identification of nanoscale molecules are crucial, but traditional technology comes with a high cost and requires skilled operators. Solid-state nanopores are new powerful tools for discerning the three-dimensional shape and size of molecules, enabling the translation of molecular structural information into electric signals. Here, DNA molecules with different shapes were designed to explore the effects of electroosmotic forces (EOF), electrophoretic forces (EPF), and volume exclusion on electric signals within solid-state nanopores. Our results revealed that the electroosmotic force was the main driving force for single-stranded DNA (ssDNA), whereas double-stranded DNA (dsDNA) was primarily dominated by electrophoretic forces in nanopores. Moreover, dsDNA caused greater amplitude signals and moved faster through the nanopore due to its larger diameter and carrying more charges. Furthermore, at the same charge level and amount of bases, circular dsDNA exhibited a tighter structure compared to brush DNA, resulting in a shorter length. Consequently, circular dsDNA caused higher current-blocking amplitudes and faster passage speeds. The characterization approach based on nanopores allows researchers to get molecular information about size and shape in real time. These findings suggest that nanopore detection has the potential to streamline nanoscale characterization and analysis, potentially reducing both the cost and complexity.
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Affiliation(s)
- Wei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Haiyan Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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5
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Arora P, Zheng H, Munusamy S, Jahani R, Wang L, Guan X. Probe-assisted detection of Fe 3+ ions in a multi-functionalized nanopore. Biosens Bioelectron 2024; 251:116125. [PMID: 38359668 PMCID: PMC10922892 DOI: 10.1016/j.bios.2024.116125] [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: 11/21/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/17/2024]
Abstract
Iron is an essential element that plays critical roles in many biological/metabolic processes, ranging from oxygen transport, mitochondrial respiration, to host defense and cell signaling. Maintaining an appropriate iron level in the body is vital to the human health. Iron deficiency or overload can cause life-threatening conditions. Thus, developing a new, rapid, cost-effective, and easy to use method for iron detection is significant not only for environmental monitoring but also for disease prevention. In this study, we report an innovative Fe3+ detection strategy by using both a ligand probe and an engineered nanopore with two binding sites. In our design, one binding site of the nanopore has a strong interaction with the ligand probe, while the other is more selective toward interfering species. Based on the difference in the number of ligand DTPMPA events in the absence and presence of ferric ions, micromolar concentrations of Fe3+ could be detected within minutes. Our method is selective: micromolar concentrations of Mg2+, Ca2+, Cd2+, Zn2+, Ni2+, Co2+, Mn2+, and Cu2+ would not interfere with the detection of ferric ions. Furthermore, Cu2+, Ni2+, Co2+, Zn2+, and Mn2+ produced current blockage events with quite different signatures from each other, enabling their simultaneous detection. In addition, simulated water and serum samples were successfully analyzed. The nanopore sensing strategy developed in this work should find useful application in the development of stochastic sensors for other substances, especially in situations where multi-analyte concurrent detection is desired.
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Affiliation(s)
- Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Haiyan Zheng
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | | | - Rana Jahani
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Xiyun Guan
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA.
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6
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Punia B, Chaudhury S. Macromolecular Crowding Facilitates ssDNA Capture within Biological Nanopores: Role of Size Variation and Solution Heterogeneity. J Phys Chem B 2024; 128:1876-1883. [PMID: 38355410 DOI: 10.1021/acs.jpcb.3c08350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Genetic sequencing is a vital process that requires the transport of charged nucleic acids through transmembrane nanopores. Single-molecule studies show that macromolecular bulk crowding facilitates the capture of these polymers, leading to a high throughput of nanopore sensors. Motivated by these observations, a minimal discrete-state stochastic framework was developed to describe the role of poly(ethylene glycol) (PEG) crowders in varying concentrations in the transport of ssDNA through α-hemolysin nanopores. This theory suggested that the cooperative partitioning of polycationic PEGs controls the capture of ssDNA due to underlying electrostatic interactions. Herein, we investigate the impact of the size variation of PEGs on the capture event. Even though larger crowders attract ssDNA strongly to enhance its capture, our results show that considerable cooperative partitioning of PEGs is also required to achieve high interevent frequency. The exact analytical results are supported by existing single-molecule studies. Since real cellular conditions are heterogeneous, its influence on the ssDNA capture rate is studied by introducing a binary mixture of crowders. Our results indicate that the "polymer-pushing-polymer" concept possibly affects the capture rate depending on the mixture composition. These new findings provide valuable insights into the microscopic mechanism of the capture process, which eventually allows for accurate genome sequencing in crowded solutions.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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7
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Mereuta L, Asandei A, Andricioaei I, Park J, Park Y, Luchian T. Considerable slowdown of short DNA fragment translocation across a protein nanopore using pH-induced generation of enthalpic traps inside the permeation pathway. NANOSCALE 2023; 15:14754-14763. [PMID: 37655668 DOI: 10.1039/d3nr03344a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
A pressing challenge in the realm of nanopore-based sensing technologies for nucleic acid characterization has been the cheap and efficient control of analyte translocation. To address this, a plethora of methods were tested, including mutagenesis, molecular motors, enzymes, or the optimization of experimental conditions. Herein, we present a paradigm exploiting the manipulation of electrostatic interactions between 22-mer single-stranded DNAs (22_ssDNA) and low pH-induced charges in the alpha-hemolysin (α-HL) nanopore, to efficiently control the passage of captured molecules. We discovered that in electrolytes buffered at pH = 5 and pH = 4.5 where the nanopore's vestibule and lumen become oppositely charged as compared to that at neutral pH, the electrostatic anchoring at these regions of a 22_ssDNA fragment leads to a dramatic increase of the translocation time, orders of magnitude larger compared to that at neutral pH. This pH-dependent tethering effect is reversible, side invariant, and sensitive to the ionic strength and ssDNA contour length. In the long run, our discovery has the potential to provide a simple read-out of the sequence of bases pertaining to short nucleotide sequences, thus extending the efficacy of current nanopore-based sequencers.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Ioan Andricioaei
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, CA 92617, USA
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, 61452, Republic of Korea.
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
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8
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Punia B, Chaudhury S. Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores. J Phys Chem B 2023. [PMID: 37294938 DOI: 10.1021/acs.jpcb.3c02792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing. A clear molecular-level understanding of how the presence of PEGs offers such desirable outcomes in nanopore sensing is still missing. In this work, we present a new theoretical approach to probe the effect of PEG crowders on DNA capture and translocation through the αHL nanopore. We develop an exactly solvable discrete-state stochastic model based on the cooperative partitioning of individual polycationic PEGs within the cavity of the αHL nanopore. It is argued that the apparent electrostatic interactions between the DNA and PEGs control all of the dynamic processes. Our analytical predictions find excellent agreements with existing experiments, thereby strongly supporting our theory.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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9
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Hu WH, Zhou K, Liu L, Wu HC. Construction of a pH-Mediated Single-Molecule Switch with a Nanopore-DNA Complex. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201650. [PMID: 35723176 DOI: 10.1002/smll.202201650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Indexed: 06/15/2023]
Abstract
A molecular switch is one of the simplest examples of artificial molecular machines. Even so, the development of molecular switches is still at its very early stage. Currently, building single-molecule switches mostly rely on the molecular junction technique, but many of their performance characteristics are device-dependent. Here, a pH-mediated single-molecule switch based on the combination of an α-hemolysin (αHL) nanopore and a hexacyclen-modified DNA strand is developed. The single-stranded DNA is suspended inside an αHL through biotin-streptavidin linkage and the hexacyclen-modified nucleobase interacts with amino acid residues at positions 111, 113, and 147 to cause current oscillations. Distinct current transitions are observed when pH is tuned back and forth in the range of 3.0-7.4, with a typical "up" level when pH > 6.5 and a "down" level when pH < 4.5. This nanopore-DNA complex possesses membrane-bound advantages and may find applications in single-cell studies where pH could be readily tuned to control ON-OFF functions.
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Affiliation(s)
- Wei-Hu Hu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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11
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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.
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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
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12
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Roozbahani GM, Chen X, Zhang Y, Wang L, Guan X. Nanopore detection of metal ions: Current status and future directions. SMALL METHODS 2020; 4:2000266. [PMID: 33365387 PMCID: PMC7751931 DOI: 10.1002/smtd.202000266] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Indexed: 05/27/2023]
Abstract
In this review, we highlight recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health. Protein pores use three stochastic sensing-based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nano-channel. Second, large molecules such as nucleic acids and especially peptides could be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion-ligand chelation / coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady-state analysis, synthetic nanopores mainly use two strategies (modification and modification-free) to detect metals. Given the advantages of high sensitivity & selectivity, and label-free detection, nanopore-based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.
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Affiliation(s)
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- The University of Chinese Academy of Science, Beijing, 100049, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
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13
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Zhao Y, Liu L, Tu Y, Wu H. Investigating the effect of mono‐ and multivalent counterions on the conformation of poly(styrenesulfonic acid) by nanopores. Electrophoresis 2019; 40:2180-2185. [DOI: 10.1002/elps.201800539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Yating Zhao
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou P. R. China
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Chinese Academy of Sciences Institute of Chemistry Beijing P. R. China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety Multidisciplinary Center Chinese Academy of Sciences Institute of High Energy Physics Beijing P. R. China
| | - Yingfeng Tu
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou P. R. China
| | - Hai‐Chen Wu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Chinese Academy of Sciences Institute of Chemistry Beijing P. R. China
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14
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Roozbahani GM, Chen X, Zhang Y, Juarez O, Li D, Guan X. Computation-Assisted Nanopore Detection of Thorium Ions. Anal Chem 2018; 90:5938-5944. [PMID: 29648804 DOI: 10.1021/acs.analchem.8b00848] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Thorium is a well-known radioactive and chemically toxic contaminant in the environment. The continuous exposure to thorium may cause an increased risk of developing lung and liver diseases as well as lung, pancreas, and bone cancer. Due to its use in nuclear industry and other industrial applications, thorium may be accidentally released to the environment from its mining and processing plants. In this work, we developed a rapid, real-time, and label-free nanopore sensor for Th4+ detection by using an aspartic acid containing peptide as a chelating agent and tuning the electrolyte solution pH to control the net charges of the peptide ligand and its metal ion complex. The method is highly sensitive with a detection limit of 0.45 nM. Furthermore, the sensor is selective: other metal ions (e.g., UO22+, Pb2+, Cu2+, Ni2+, Hg2+, Zn2+, As3+, Mg2+, and Ca2+) with concentrations of up to 3 orders of magnitude greater than that of Th4+ would not interfere with Th4+detection. In addition, simulated water samples were successfully analyzed. Our developed computation-assisted sensing strategy should find useful applications in the development of nanopore sensors for other metal ions.
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Affiliation(s)
- Golbarg M Roozbahani
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Xiaohan Chen
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Youwen Zhang
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Oscar Juarez
- Department of Biology , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Dien Li
- Environmental Sciences and Biotechnology , Savannah River National Laboratory , Aiken , South Carolina 29808 , United States
| | - Xiyun Guan
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
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15
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Zeng T, Fleming AM, Ding Y, Ren H, White HS, Burrows CJ. Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA. J Org Chem 2018; 83:3973-3978. [PMID: 29490132 DOI: 10.1021/acs.joc.8b00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.
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Affiliation(s)
- Tao Zeng
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Yun Ding
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
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16
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Wang Y, Tian K, Du X, Shi RC, Gu LQ. Remote Activation of a Nanopore for High-Performance Genetic Detection Using a pH Taxis-Mimicking Mechanism. Anal Chem 2017; 89:13039-13043. [PMID: 29183111 PMCID: PMC6174115 DOI: 10.1021/acs.analchem.7b03979] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aerolysin protein pore has been widely used for sensing peptides and proteins. However, only a few groups explored this nanopore for nucleic acids detection. The challenge is the extremely low capture efficiency for nucleic acids (>10 bases), which severely lowers the sensitivity of an aerolysin-based genetic biosensor. Here we reported a simple and easy-to-operate approach to noncovalently transform aerolysin into a highly nucleic acids-sensitive nanopore. Through a remote pH-modulation mechanism, we simply lower the pH on one side of the pore, then aerolysin is immediately "activated" and enabled to capture target DNA/RNA efficiently from the opposite side of the pore. This mechanism also decelerates DNA translocation, a desired property for sequencing and gene detection, allowing temporal separation of DNAs in different lengths. This method provides insight into the nanopore engineering for biosensing, making aerolysin applicable in genetic and epigenetic detections of long nucleic acids.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiao Du
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Rui-Cheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
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17
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Roozbahani GM, Chen X, Zhang Y, Xie R, Ma R, Li D, Li H, Guan X. Peptide-Mediated Nanopore Detection of Uranyl Ions in Aqueous Media. ACS Sens 2017; 2:703-709. [PMID: 28580428 PMCID: PMC5450019 DOI: 10.1021/acssensors.7b00210] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/04/2017] [Indexed: 01/31/2023]
Abstract
![]()
Uranium
is one of the most common radioactive contaminants in the
environment. As a major nuclear material in production, environmental
samples (like soil and groundwater) can provide signatures on uranium
production activity inside the facility. Thus, developing a new and
portable analytical technology for uranium in aqueous media is significant
not only for environmental monitoring, but also for nonproliferation.
In this work, a label-free method for the detection of uranyl (UO22+) ions is developed by monitoring the translocation
of a peptide probe in a nanopore. Based on the difference in the number
of peptide events in the absence and presence of uranyl ions, nanomolar
concentration of UO22+ ions could be detected
in minutes. The method is highly selective; micromolar concentrations
of Cd2+, Cu2+, Zn2+, Ni2+, Pb2+, Hg2+, Th4+, Mg2+, and Ca2+ would not interfere with the detection of UO22+ ions. In addition, simulated water samples were
successfully analyzed.
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Affiliation(s)
- Golbarg M. Roozbahani
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiaohan Chen
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Youwen Zhang
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Ruiqi Xie
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Rui Ma
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Dien Li
- Environmental
Sciences and Biotechnology, Savannah River National Laboratory, Aiken, South Carolina 29808, United States
| | - Huazhong Li
- Henan Jintai Biological Technology Co., Ltd., ZhengZhou, Henan, 450016, PR China
| | - Xiyun Guan
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
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18
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Guo B, Yao Z, Liu L, Wu HC. Revealing different aggregational states of a conjugated polymer in solution by a nanopore sensor. Chem Sci 2016; 7:5287-5293. [PMID: 30155179 PMCID: PMC6020615 DOI: 10.1039/c6sc00296j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/04/2016] [Indexed: 11/30/2022] Open
Abstract
Nanopores are effective and powerful tools for the analysis of conformational and aggregational states of conjugated polymers in solution.
The functionalities of conjugated polymers are determined not only by local molecular structure, but also by the mesoscale conformational and morphological states of the polymer chains. Simulation studies have successfully established the connections between molecular structure and conformational states of certain conjugated polymers. However, experimental tools that can accurately discriminate between different conformational and morphological states of conjugated polymers are still scarce. Here, we use a nanopore sensor to analyze different aggregational states of a polythiophene derivative by threading the polymer through the pore under applied potentials. When the fluorescence of the polythiophene is quenched by pH tuning or the presence of Dy3+, the UV-vis and fluorescence spectra of the two solutions appear indistinguishable. However, threading the polymer molecules of these two solutions through an α-hemolysin nanopore affords entirely different translocation profiles owing to their different aggregational states. We further substantiate the results by conducting aggregational interconversion experiments and TEM measurements. This work has clearly indicated that nanopores are promising tools for the analysis of aggregational changes of conjugated polymers and may open new avenues for the investigation of aggregational states of biomacromolecules in the context of early disease diagnosis and prognosis.
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Affiliation(s)
- Bingyuan Guo
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Zhiyi Yao
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745.,Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
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19
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Angevine CE, Seashols-Williams SJ, Reiner JE. Infrared Laser Heating Applied to Nanopore Sensing for DNA Duplex Analysis. Anal Chem 2016; 88:2645-51. [DOI: 10.1021/acs.analchem.5b03631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Christopher E. Angevine
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Sarah J. Seashols-Williams
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E. Reiner
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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20
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Arjmandi-Tash H, Belyaeva LA, Schneider GF. Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond. Chem Soc Rev 2015; 45:476-93. [PMID: 26612268 PMCID: PMC4766581 DOI: 10.1039/c5cs00512d] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Graphene and other two dimensional (2D) materials are currently integrated into nanoscaled devices that may – one day – sequence genomes.
Graphene and other two dimensional (2D) materials are currently integrated into nanoscaled devices that may – one day – sequence genomes. The challenge to solve is conceptually straightforward: cut a sheet out of a 2D material and use the edge of the sheet to scan an unfolded biomolecule from head to tail. As the scan proceeds – and because 2D materials are atomically thin – the information provided by the edge might be used to identify different segments – ideally single nucleotides – in the biomolecular strand. So far, the most efficient approach was to drill a nano-sized pore in the sheet and use this pore as a channel to guide and detect individual molecules by measuring the electrochemical ionic current. Nanoscaled gaps between two electrodes in 2D materials recently emerged as powerful alternatives to nanopores. This article reviews the current status and prospects of integrating 2D materials in nanopores, nanogaps and similar devices for single molecule biosensing applications. We discuss the pros and cons, the challenges, and the latest achievements in the field. To achieve high-throughput sequencing with 2D materials, interdisciplinary research is essential.
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Affiliation(s)
- Hadi Arjmandi-Tash
- Faculty of Science, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands.
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21
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Bearden S, Simpanen E, Zhang G. Active current gating in electrically biased conical nanopores. NANOTECHNOLOGY 2015; 26:185502. [PMID: 25865738 DOI: 10.1088/0957-4484/26/18/185502] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We observed that the ionic current through a gold/silicon nitride (Si3N4) nanopore could be modulated and gated by electrically biasing the gold layer. Rather than employing chemical modification to alter device behavior, we achieved control of conductance directly by electrically biasing the gold portion of the nanopore. By stepping through a range of bias potentials under a constant trans-pore electric field, we observed a gating phenomenon in the trans-pore current response in a variety of solutions including potassium chloride (KCl), sodium chloride (NaCl), and potassium iodide (KI). A computational model with a conical nanopore was developed to examine the effect of the Gouy-Chapman-Stern electrical double layer along with nanopore geometry, work function potentials, and applied electrical bias on the ionic current. The numerical results indicated that the observed modulation and gating behavior was due to dynamic reorganization of the electrical double layer in response to changes in the electrical bias. Specifically, in the conducting state, the nanopore conductance (both numerical and experimental) is linearly proportional to the applied bias due to accumulation of charge in the diffuse layer. The gating effect occurs due to the asymmetric charge distribution in the fluid induced by the distribution of potentials at the nanopore surface. Time dependent changes in current due to restructuring of the electrical double layer occur when the electrostatic bias is instantaneously changed. The nanopore device demonstrates direct external control over nanopore behavior via modulation of the electrical double layer by electrostatic biasing.
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Affiliation(s)
- Samuel Bearden
- Department of Bioengineering, Clemson University, 301 Rhodes Research Center, Clemson, SC 29634-0905, USA
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22
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Liu L, Li C, Ma J, Wu Y, Ni Z, Chen Y. Theoretical and experimental studies on ionic currents in nanopore-based biosensors. IET Nanobiotechnol 2014; 8:247-56. [PMID: 25429504 DOI: 10.1049/iet-nbt.2013.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Novel generation of analytical technology based on nanopores has provided possibilities to fabricate nanofluidic devices for low-cost DNA sequencing or rapid biosensing. In this paper, a simplified model was suggested to describe DNA molecule's translocation through a nanopore, and the internal potential, ion concentration, ionic flowing speed and ionic current in nanopores with different sizes were theoretically calculated and discussed on the basis of Poisson-Boltzmann equation, Navier-Stokes equation and Nernst-Planck equation by considering several important parameters, such as the applied voltage, the thickness and the electric potential distributions in nanopores. In this way, the basic ionic currents, the modulated ionic currents and the current drops induced by translocation were obtained, and the size effects of the nanopores were carefully compared and discussed based on the calculated results and experimental data, which indicated that nanopores with a size of 10 nm or so are more advantageous to achieve high quality ionic current signals in DNA sensing.
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Affiliation(s)
- Lei Liu
- Suzhou Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Suzhou Research Institute of Southeast University, Suzhou 215123, People's Republic of China.
| | - Chu Li
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Jian Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Yingdong Wu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
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23
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Han Y, Zhou S, Wang L, Guan X. Nanopore back titration analysis of dipicolinic acid. Electrophoresis 2014; 36:467-70. [PMID: 25074707 DOI: 10.1002/elps.201400255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 11/07/2022]
Abstract
Here, we report a novel label-free nanopore back titration method for the detection of dipicolinic acid, a marker molecule for bacterial spores. By competitive binding of the target analyte and a large ligand probe to metal ions, dipicolinic acid could be sensitively and selectively detected. This nanopore back titration approach should find useful applications in the detection of other species of medical, biological, or environmental importance if their direct detection is difficult to achieve.
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Affiliation(s)
- Yujing Han
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
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24
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Zhang Y, Wu G, Si W, Sha J, Liu L, Chen Y. Retarding and manipulating of DNA molecules translocation through nanopores. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0655-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Wang G, Wang L, Han Y, Zhou S, Guan X. Nanopore stochastic detection: diversity, sensitivity, and beyond. Acc Chem Res 2013; 46:2867-77. [PMID: 23614724 DOI: 10.1021/ar400031x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanopore sensors have emerged as a label-free and amplification-free technique for measuring single molecules. First proposed in the mid-1990s, nanopore detection takes advantage of the ionic current modulations produced by the passage of target analytes through a single nanopore at a fixed applied potential. Over the last 15 years, these nanoscale pores have been used to sequence DNA, to study covalent and non-covalent bonding interactions, to investigate biomolecular folding and unfolding, and for other applications. A major issue in the application of nanopore sensors is the rapid transport of target analyte molecules through the nanopore. Current recording techniques do not always accurately detect these rapid events. Therefore, researchers have looked for methods that slow molecular and ionic transport. Thus far, several strategies can improve the resolution and sensitivity of nanopore sensors including variation of the experimental conditions, use of a host compound, and modification of the analyte molecule and the nanopore sensor. In this Account, we highlight our recent research efforts that have focused on applications of nanopore sensors including the differentiation of chiral molecules, the study of enzyme kinetics, and the determination of sample purity and composition. Then we summarize our efforts to regulate molecular transport. We show that the introduction of various surface functional groups such as hydrophobic, aromatic, positively charged, and negatively charged residues in the nanopore interior, an increase in the ionic strength of the electrolyte solution, and the use of ionic liquid solutions as the electrolyte instead of inorganic salts may improve the resolution and sensitivity of nanopore stochastic sensors. Our experiments also demonstrate that the introduction of multiple functional groups into a single nanopore and the development of a pattern-recognition nanopore sensor array could further enhance sensor resolution. Although we have demonstrated the feasibility of nanopore sensors for various applications, challenges remain before nanopore sensing is deployed for routine use in applications such as medical diagnosis, homeland security, pharmaceutical screening, and environmental monitoring.
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Affiliation(s)
- Guihua Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Liang Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Yujing Han
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Shuo Zhou
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Xiyun Guan
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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26
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Liu L, Zhu L, Ni Z, Chen Y. Detecting a single molecule using a micropore-nanopore hybrid chip. NANOSCALE RESEARCH LETTERS 2013; 8:498. [PMID: 24261484 PMCID: PMC4221642 DOI: 10.1186/1556-276x-8-498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/05/2013] [Indexed: 06/02/2023]
Abstract
Nanopore-based DNA sequencing and biomolecule sensing have attracted more and more attention. In this work, novel sensing devices were built on the basis of the chips containing nanopore arrays in polycarbonate (PC) membranes and micropores in Si3N4 films. Using the integrated chips, the transmembrane ionic current induced by biomolecule's translocation was recorded and analyzed, which suggested that the detected current did not change linearly as commonly expected with increasing biomolecule concentration. On the other hand, detailed translocation information (such as translocation gesture) was also extracted from the discrete current blockages in basic current curves. These results indicated that the nanofluidic device based on the chips integrated by micropores and nanopores possessed comparative potentials in biomolecule sensing.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
- Suzhou Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Suzhou Research Institute of Southeast University, Suzhou 215123, People's Republic of China
| | - Lizhong Zhu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
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27
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Wang G, Wang L, Han Y, Zhou S, Guan X. Nanopore detection of copper ions using a polyhistidine probe. Biosens Bioelectron 2013; 53:453-8. [PMID: 24211457 DOI: 10.1016/j.bios.2013.10.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 01/14/2023]
Abstract
We report a stochastic nanopore sensing method for the detection of Cu(2+) ions. By employing a polyhistidine molecule as a chelating agent, and based on the different signatures of the events produced by the translocation of the chelating agent through an α-hemolysin pore in the absence and presence of target analytes, trace amounts of copper ions could be detected with a detection limit of 40 nM. Importantly, although Co(2+), Ni(2+), and Zn(2+) also interacts with the polyhistidine molecule, since the event residence times and/or blockage amplitudes for these metal chelates are significantly different from those of copper chelates, these metal ions do not interfere with Cu(2+) detection. This chelating reaction approach should find useful application in the development of nanopore sensors for other metal ions.
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Affiliation(s)
- Guihua Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
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28
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Soskine M, Biesemans A, De Maeyer M, Maglia G. Tuning the size and properties of ClyA nanopores assisted by directed evolution. J Am Chem Soc 2013; 135:13456-63. [PMID: 23919630 PMCID: PMC4410319 DOI: 10.1021/ja4053398] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores have recently emerged as powerful tools in single-molecule investigations. Biological nanopores, however, have drawbacks, including a fixed size and limited stability in lipid bilayers. Inspired by the great success of directed evolution approaches in tailoring enzyme properties, in this work we evolved Cytolysin A from Salmonella typhi (ClyA) to a high level of soluble expression and desired electrical properties in lipid bilayers. Evolved ClyA nanopores remained open up to -150 mV applied potential, which allowed the detailed characterization of folded proteins by ionic current recordings. Remarkably, we also found that ClyA forms several nanopore species; among which we could isolate and characterize three nanopore types most likely corresponding to the 12mer, 13mer, and 14mer oligomeric forms of ClyA. Protein current blockades to the three ClyA nanopores showed that subnanometer variations in the diameter of nanopores greatly affect the recognition of analyte proteins.
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Affiliation(s)
- Misha Soskine
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Annemie Biesemans
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Marc De Maeyer
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Giovanni Maglia
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
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29
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Cracknell JA, Japrung D, Bayley H. Translocating kilobase RNA through the Staphylococcal α-hemolysin nanopore. NANO LETTERS 2013; 13:2500-5. [PMID: 23678965 PMCID: PMC3712197 DOI: 10.1021/nl400560r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The electrophoretic translocation of polynucleotides through nanopores may permit direct single-molecule nucleic acid sequencing. Here we describe the translocation of ssRNA heteropolymers (91-6083 bases) through the α-hemolysin nanopore. Translocation of these long ssRNAs is characterized by surprisingly long, almost complete ionic current blockades with durations averaging milliseconds per base (at +180 mV). The event durations decrease exponentially with increased transmembrane potential but are largely unaffected by the presence of urea. When the ssRNA is coupled at the 3' end to streptavidin, which cannot translocate through the pore, permanent blockades are observed, supporting our conclusion that the transient blockades arise from ssRNA translocation.
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Wolna AH, Fleming AM, An N, He L, White HS, Burrows CJ. Electrical Current Signatures of DNA Base Modifications in Single Molecules Immobilized in the α-Hemolysin Ion Channel. Isr J Chem 2013; 53:417-430. [PMID: 24052667 PMCID: PMC3773884 DOI: 10.1002/ijch.201300022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nanopore technology holds high potential for next-generation DNA sequencing. This method operates by drawing an individual single-stranded DNA molecule through a nanoscale pore while monitoring the current deflections that occur as the DNA passes through. Individual current levels for the four DNA nucleotides have been established by immobilization of an end biotinylated strand in the pore in which the nucleotide of interest is suspended at the most sensitive region of the ion channel. Due to the inherent reactivity of the DNA bases, many modified nucleotides in the genome exist resulting from oxidative and UV insults, among others. Herein, the current levels for the common DNA damages 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), uridine (U), abasic sites (AP), thymine dimers (T=T), thymine glycol (Tg) and 5-iodocytosine (5-I-C) were assessed via immobilization experiments. In some cases, the current difference between the damaged and canonical nucleotides was not well resolved; therefore, we took advantage of the chemical reactivity of the new functional groups present to make amine adducts that shifted the current levels outside the range of the native nucleotides. Among adducts studied, only the 2-aminomethyl-18-crown-6 adduct was able to give a large current shift in the immobilization experiment, as well as to be observed in a translocation experiment. The results show potential in providing current level modulators for identification of some types of DNA damage. In principle, any DNA base modification that can be converted chemically or enzymatically to an abasic site could be identified in this way.
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Affiliation(s)
- Anna H. Wolna
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Aaron M. Fleming
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Na An
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Lidong He
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Henry S. White
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Cynthia J. Burrows
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
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Liu L, Wang B, Sha J, Yang Y, Hou Y, Ni Z, Chen Y. Voltage-driven translocation behaviors of IgG molecule through nanopore arrays. NANOSCALE RESEARCH LETTERS 2013; 8:229. [PMID: 23676116 PMCID: PMC3664219 DOI: 10.1186/1556-276x-8-229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 01/12/2013] [Indexed: 06/01/2023]
Abstract
Nanopore-based biosensing has attracted more and more interests in the past years, which is also regarded as an emerging field with major impact on bio-analysis and fundamental understanding of nanoscale interactions down to single-molecule level. In this work, the voltage-driven translocation properties of goat antibody to human immunoglobulin G (IgG) are investigated using nanopore arrays in polycarbonate membranes. Obviously, the background ionic currents are modulated by IgG molecules for their physical place-holding effect. However, the detected ionic currents do 'not' continuously decrease as conceived; the currents first decrease, then increase, and finally stabilize with increasing IgG concentration. To understand this phenomenon, a simplified model is suggested, and the calculated results contribute to the understanding of the abnormal phenomenon in the actual ionic current changing tendency.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Bing Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yue Yang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yaozong Hou
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
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Wang G, Zhao Q, Kang X, Guan X. Probing mercury(II)-DNA interactions by nanopore stochastic sensing. J Phys Chem B 2013; 117:4763-9. [PMID: 23565989 DOI: 10.1021/jp309541h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, DNA-Hg(II) interactions were investigated by monitoring the translocation of DNA hairpins in a protein ion channel in the absence and presence of metal ions. Our experiments demonstrate that target-specific hairpin structures could be stabilized much more significantly by mercuric ions than by the stem length and the loop size of the hairpin due to the formation of Thymine-Hg(II)-Thymine complexes. In addition, the designed DNA probe allows the development of a highly sensitive nanopore sensor for Hg(2+) with a detection limit of 25 nM. Further, the sensor is specific, and other tested metal ions including Pb(2+), Cu(2+), Cd(2+), and so on with concentrations of up to 2 orders of magnitude greater than that of Hg(2+) would not interfere with the mercury detection.
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Affiliation(s)
- Guihua Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
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Göpfrich K, Kulkarni CV, Pambos OJ, Keyser UF. Lipid nanobilayers to host biological nanopores for DNA translocations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:355-364. [PMID: 23214950 DOI: 10.1021/la3041506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We characterize a recently introduced novel nanobilayer technique [Gornall, J. L., Mahendran, K. R., Pambos, O. J., Steinbock, L. J., Otto, O., Chimerel, C., Winterhalter, M., and Keyser, U. F. Simple reconstitution of protein pores in nano lipid bilayers. Nano Lett. 2011, 11 (8), 3334-3340] and its practical aspects for incorporating the biological nanopore α-hemolysin from Staphylococcus aureus and subsequent studies on the translocation of biomolecules under various conditions. This technique provides advantages over classical bilayer methods, especially the quick formation and extended stability of a bilayer. We have also developed a methodology to prepare a uniform quality of giant unilamellar vesicles (GUVs) in a reproducible way for producing nanobilayers. The process and the characteristics of the reconstitution of α-hemolysin in nanobilayers were examined by exploiting various important parameters, including pH, applied voltage, salt concentration, and number of nanopores. Protonation of α-hemolysin residues in the low pH region affects the translocation durations, which, in turn, changes the statistics of event types as a result of electrostatics and potentially the structural changes in DNA. When the pH and applied voltage were varied, it was possible to investigate and partly control the capture rates and type of translocation events through α-hemolysin nanopores. This study could be helpful to use the nanobilayer technique for further explorations, particularly owing to its advantages and technical ease compared to existing bilayer methods.
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Affiliation(s)
- Kerstin Göpfrich
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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Jayawardhana DA, Sengupta MK, Krishantha DM, Gupta J, Armstrong DW, Guan X. Chemical-induced pH-mediated molecular switch. Anal Chem 2011; 83:7692-7. [PMID: 21919492 PMCID: PMC3214665 DOI: 10.1021/ac2019393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transmembrane protein α-hemolysin pore has been used to develop ultrasensitive biosensors, study biomolecular folding and unfolding, investigate covalent and noncovalent bonding interactions, and probe enzyme kinetics. Here, we report that, by addition of ionic liquid tetrakis(hydroxymethyl)phosphonium chloride solution to the α-hemolysin pore, the α-hemolysin channel can be controlled open or closed by adjusting the pH of the solution. This approach can be employed to develop a novel molecular switch to regulate molecular transport and should find potential applications as a "smart" drug delivery method.
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Affiliation(s)
- Dilani A. Jayawardhana
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Mrinal K. Sengupta
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - D.M. Milan Krishantha
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Jyoti Gupta
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Daniel W. Armstrong
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Xiyun Guan
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
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