1
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Fan P, Zhang S, Wang Y, Li T, Zhang H, Zhang P, Huang S. Nanopore analysis of salvianolic acids in herbal medicines. Nat Commun 2024; 15:1970. [PMID: 38443335 PMCID: PMC10915175 DOI: 10.1038/s41467-024-45543-1] [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: 05/10/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.
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Affiliation(s)
- Pingping Fan
- 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
| | - Shanyu Zhang
- 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
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Tian Li
- 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
| | - Hanhan Zhang
- 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
| | - 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.
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2
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Kim M, Foster JC, Moore MD, Chen M. Improving Single-Molecule Antibody Detection Selectivity through Optimization of Peptide Epitope Presentation in OmpG Nanopore. ACS Sens 2023. [PMID: 37379512 DOI: 10.1021/acssensors.3c00528] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Outer membrane protein G (OmpG) is a monomeric porin found in Escherichia coli, which possesses seven flexible loops. OmpG has been engineered as a nanopore sensor, where its loops can host affinity epitopes for selective detection of biological molecules. In this study, we investigated various loop positions to incorporate a FLAG peptide antigen epitope in the most flexible loop 6 and tested the efficacy and sensitivity of these nanopore constructs in antibody detection. We observed an OmpG construct containing inserted FLAG sequence, which exhibited strong interaction with anti-FLAG antibodies in flow cytometry; however, it could not translate molecule interactions into a readable signal in current recordings. Further optimization of the peptide presentation strategy by replacing specific sections of loop 6 sequences with the FLAG tag created a construct capable of generating unique and distinct signals when interacting with various monoclonal or polyclonal anti-FLAG clones IgG antibodies in the mixture. The peptide display scheme demonstrated in this study can be generalized for the engineering of OmpG sensors, which can be used for screening and validating positive clones during antibody development, as well as for real-time quality control of cell cultures in monoclonal antibody production.
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Affiliation(s)
- Minji Kim
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Matthew D Moore
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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3
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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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4
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Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.
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5
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Lucas FLR, Piso TRC, van der Heide NJ, Galenkamp NS, Hermans J, Wloka C, Maglia G. Automated Electrical Quantification of Vitamin B1 in a Bodily Fluid using an Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2021; 60:22849-22855. [PMID: 34390104 PMCID: PMC8518494 DOI: 10.1002/anie.202107807] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/20/2021] [Indexed: 12/27/2022]
Abstract
The ability to measure the concentration of metabolites in biological samples is important, both in the clinic and for home diagnostics. Here we present a nanopore-based biosensor and automated data analysis for quantification of thiamine in urine in less than a minute, without the need for recalibration. For this we use the Cytolysin A nanopore and equip it with an engineered periplasmic thiamine binding protein (TbpA). To allow fast measurements we tuned the affinity of TbpA for thiamine by redesigning the π-π stacking interactions between the thiazole group of thiamine and TbpA. This substitution resulted furthermore in a marked difference between unbound and bound state, allowing the reliable discrimination of thiamine from its two phosphorylated forms by residual current only. Using an array of nanopores, this will allow the quantification within seconds, paving the way for next-generation single-molecule metabolite detection systems.
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Affiliation(s)
- Florian Leonardus Rudolfus Lucas
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Tjemme Rinze Cornelis Piso
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
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6
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Lucas FLR, Piso TRC, Heide NJ, Galenkamp NS, Hermans J, Wloka C, Maglia G. Automated Electrical Quantification of Vitamin B1 in a Bodily Fluid using an Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Tjemme Rinze Cornelis Piso
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Nieck Jordy Heide
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Jos Hermans
- Analytical Biochemistry Department of Pharmacy University of Groningen Antonius Deusinglaan 1 Groningen 9713 AV The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
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7
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Chen X, Zhang Y, Arora P, Guan X. Nanopore Stochastic Sensing Based on Non-covalent Interactions. Anal Chem 2021; 93:10974-10981. [PMID: 34319076 DOI: 10.1021/acs.analchem.1c02102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A variety of species could be detected by using nanopores engineered with various recognition sites based upon non-covalent interactions, including electrostatic, aromatic, and hydrophobic interactions. The existence of these engineered non-covalent bonding sites was supported by the single-channel recording technique. The advantage of the non-covalent interaction-based sensing strategy was that the recognition site of the engineered nanopore was not specific for a particular molecule but instead selective for a class of species (e.g., cationic, anionic, aromatic, and hydrophobic). Since different species produce current modulations with quite different signatures represented by amplitude, residence time, and even characteristic voltage-dependence curve, the non-covalent interaction-based nanopore sensor could not only differentiate individual molecules in the same category but also enable differentiation between species with similar structures or molecular weights. Hence, our developed non-covalent interaction-based nanopore sensing strategy may find useful application in the detection of molecules of medical and/or environmental importance.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
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8
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Nanopore Enzymology to Study Protein Kinases and Their Inhibition by Small Molecules. Methods Mol Biol 2020. [PMID: 32918732 DOI: 10.1007/978-1-0716-0806-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Nanopore enzymology is a powerful single-molecule technique for the label-free study of enzymes using engineered protein nanopore sensors. The technique has been applied to protein kinases, where it has enabled the full repertoire of kinase function to be observed, including: kinetics of substrate binding and dissociation, product binding and dissociation, nucleotide binding, and reversible phosphorylation. Further, minor modifications enable the screening of type I kinase inhibitors and the determination of inhibition constants in a facile and label-free manner. Here, we describe the design and production of suitably engineered protein nanopores and their use for the determination of key mechanistic parameters of kinases. We also provide procedures for the determination of inhibition constants of protein kinase inhibitors.
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9
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Yadav V, Lekkala MMVSN, Surekha C, Neelapu NRR. Global Scenario of Advance Fungal Research in Crop Protection. Fungal Biol 2020. [DOI: 10.1007/978-3-030-48474-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Paoli R, Bulwan M, Castaño O, Engel E, Rodriguez-Cabello JC, Homs-Corbera A, Samitier J. Layer-by-layer modification effects on a nanopore's inner surface of polycarbonate track-etched membranes. RSC Adv 2020; 10:35930-35940. [PMID: 35517089 PMCID: PMC9056999 DOI: 10.1039/d0ra05322h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/17/2020] [Indexed: 11/21/2022] Open
Abstract
The control of the morphology, as well as the physical and chemical properties, of nanopores is a key issue for many applications. Reducing pore size is important in nanopore-based sensing applications as it helps to increase sensitivity. Changes of other physical properties such as surface net charge can also modify transport selectivity of the pores. We have studied how polyelectrolyte layer-by-layer (LBL) surface modification can be used to change the characteristics of nanoporous membranes. Studies were performed with a custom made three-dimensional multilayer microfluidic device able to fit membrane samples. The device allowed us to efficiently control LBL film deposition over blank low-cost commercially available polycarbonate track-etched (PCTE) membranes. We have demonstrated pore diameter reduction and deposition of the layers inside the pores through confocal and SEM images. Posterior impedance measurement studies served to evaluate experimentally the effect of the LBL deposition on the net inner nanopore surface charge and diameter. Measurements using direct current (DC) and alternative current (AC) voltages have demonstrated contrasted behaviors depending on the number and parity of deposited opposite charge layers. PCTE membranes are originally negatively charged and results evidenced higher impedance increases for paired charge LBL depositions. Impedance decreased when an unpaired positive layer was added. These results showed a different influence on the overall ion motility due to the effect of different surface charges. Results have been fit into a model that suggested a strong dependence of nanopores' impedance module to surface charge on conductive buffers, such as Phosphate Buffer Saline (PBS), even on relatively large nanopores. In AC significant differences between paired and unpaired charged LBL depositions tended to disappear as the total number of layers increased. The control of the morphology, as well as the physical and chemical properties, of nanopores is a key issue for many applications.![]()
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Affiliation(s)
- Roberto Paoli
- Nanobioengineering Group
- Institute for Bioengineering of Catalonia (IBEC)
- Barcelona Institute of Science and Technology (BIST)
- Barcelona 08028
- Spain
| | - Maria Bulwan
- Nanobioengineering Group
- Institute for Bioengineering of Catalonia (IBEC)
- Barcelona Institute of Science and Technology (BIST)
- Barcelona 08028
- Spain
| | - Oscar Castaño
- Department of Electronics and Biomedical Engineering
- University of Barcelona
- 08028 Barcelona
- Spain
- Biomaterials for Regenerative Therapies Group
| | - Elisabeth Engel
- Biomaterials for Regenerative Therapies Group
- Institute for Bioengineering of Catalonia (IBEC)
- Barcelona Institute of Science and Technology (BIST)
- Barcelona 08028
- Spain
| | - J. C. Rodriguez-Cabello
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN)
- 28029 Madrid
- Spain
- Bioforge Lab
- University of Valladolid
| | - Antoni Homs-Corbera
- Nanobioengineering Group
- Institute for Bioengineering of Catalonia (IBEC)
- Barcelona Institute of Science and Technology (BIST)
- Barcelona 08028
- Spain
| | - Josep Samitier
- Nanobioengineering Group
- Institute for Bioengineering of Catalonia (IBEC)
- Barcelona Institute of Science and Technology (BIST)
- Barcelona 08028
- Spain
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11
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Abstract
The molecular scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Recently, we have used the nanopore technique to dissect folding and unfolding mechanism of a single G-quadruplex DNA aptamer regulated by a variety of ions; we also created a portable and durable molecular device that integrated a protein pore sensor with a solidified lipid membrane for real-time detection.
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Affiliation(s)
- L Q Gu
- Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, USA
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12
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Tian L, Wang Y, Kang XF. Target-controlled liposome amplification for versatile nanopore analysis. Chem Commun (Camb) 2019; 55:5159-5162. [PMID: 30984931 DOI: 10.1039/c9cc00285e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have reported a versatile nanopore method based on the combination of analyte-controlled liposome signal amplification and the nanopore detection of a reporter molecule, which largely extends the nanopore application range, and easily elevates the nanopore sensitivity to the fM level from the μM level.
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Affiliation(s)
- Lei Tian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
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13
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Kang K, Jang Y, Jung J, Oh J. Controlled generation of nanopatterned electrical DNA interface. Sci Rep 2019; 9:2756. [PMID: 30808970 PMCID: PMC6391427 DOI: 10.1038/s41598-019-39444-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/25/2019] [Indexed: 11/09/2022] Open
Abstract
Techniques that manipulate DNA, a biomolecule with electrical properties, are in demand in various medical fields. This study fabricated a nanochannel with a conductive/semi-conductive interface using focused ion beams (FIBs) and introduced a nanochip technology to freely align, attach, and detach lambda DNAs in the interface via electrophoresis. Two-step fabrication process of nanochannels was quantitatively characterized according to the different conditions of the FIB dose (1~30 nC/μm2) and current (1~500 pA). For electrophoresis test, four different nanofluidic channels with depths of 200 nm and lengths of 0.5, 1.0, 1.5, and 2.0 μm were processed at the center of the rectangular channel (10 μm × 10 μm). Different voltages (1~30 V) were applied for 15 min to attach the DNAs. As the voltage increased, more lambda DNAs attached to the nanochannel interface. Furthermore, an inverse voltage (-30 V) was applied to the lambda DNAs attached to the interface for 15 min to confirm that DNAs could be successfully detached. The results showed that this method could produce a highly promising nanochip technology to align and manipulate DNAs in the desired direction according to a conductive/semi-conductive nano-sized interface, which is applicable in various biomedical fields.
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Affiliation(s)
- Kyoungin Kang
- Department of Mechanical Design Engineering, College of Engineering, Chonbuk National University, Jeonju, South Korea
| | - Yeongseok Jang
- Department of Mechanical Design Engineering, College of Engineering, Chonbuk National University, Jeonju, South Korea
| | - Jinmu Jung
- Department of Nano-bio Mechanical System Engineering, College of Engineering, Chonbuk National University, Jeonju, South Korea.
| | - Jonghyun Oh
- Department of Nano-bio Mechanical System Engineering, College of Engineering, Chonbuk National University, Jeonju, South Korea.
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14
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Guo Y, Niu A, Jian F, Wang Y, Yao F, Wei Y, Tian L, Kang X. Metal-organic complex-functionalized protein nanopore sensor for aromatic amino acids chiral recognition. Analyst 2018; 142:1048-1053. [PMID: 28280809 DOI: 10.1039/c7an00097a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chiral recognition at single-molecule level for small active molecules is important, as exhibited by many nanostructures and molecular assemblies in biological systems, but it presents a significant challenge. We report a simple and rapid sensing strategy to discriminate all enantiomers of natural aromatic amino acids (AAA) using a metal-organic complex-functionalized protein nanopore, in which a chiral recognition element and a chiral recognition valve were equipped. A trifunctional molecule, heptakis-(6-deoxy-6-amino)-β-cyclodextrin (am7βCD), was non-covalently lodged within the nanopore of an α-hemolysin (αHL) mutant, (M113R)7-αHL. Copper(ii) ion reversibly bonds to the amino group of am7βCD to form an am7βCD-CuII complex, which allowed chiral recognition for each enantiomer in the mixture of AAA by distinct current signals. The CuII plugging valve plays a crucial rule that holds chiral molecules in the nanocavity for a sufficient registering time. Importantly, six enantiomers of all nature AAA could be simultaneously recognized at one time. Enantiomeric excess (ee) could also be accurately detected by this approach. It should be possible to generalize this approach for sensing of other chiral molecules.
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Affiliation(s)
- Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Aihua Niu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Feifei Jian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Ying Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Yongfeng Wei
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Lei Tian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Xiaofeng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
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15
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Kim YH, Hang L, Cifelli JL, Sept D, Mayer M, Yang J. Frequency-Based Analysis of Gramicidin A Nanopores Enabling Detection of Small Molecules with Picomolar Sensitivity. Anal Chem 2018; 90:1635-1642. [DOI: 10.1021/acs.analchem.7b02961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | | | | | - David Sept
- Department
of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2110, United States
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
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16
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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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17
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Guo Y, Jian F, Kang X. Nanopore sensor for copper ion detection using a polyamine decorated β-cyclodextrin as the recognition element. RSC Adv 2017. [DOI: 10.1039/c7ra00454k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A novel and simple nanopore sensing method has been developed for the detection of CuII ions using polyamine decorated cyclodextrin as the recognition element.
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Affiliation(s)
- Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
| | - Feifei Jian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
| | - Xiaofeng Kang
- 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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18
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Tan S, Wang L, Liu H, Wu H, Liu Q. Single Nanoparticle Translocation Through Chemically Modified Solid Nanopore. NANOSCALE RESEARCH LETTERS 2016; 11:50. [PMID: 26831688 PMCID: PMC4735043 DOI: 10.1186/s11671-016-1255-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/15/2016] [Indexed: 05/29/2023]
Abstract
The nanopore sensor as a high-throughput and low-cost technology can detect single nanoparticle in solution. In the present study, the silicon nitride nanopores were fabricated by focused Ga ion beam (FIB), and the surface was functionalized with 3-aminopropyltriethoxysilane to change its surface charge density. The positively charged nanopore surface attracted negatively charged nanoparticles when they were in the vicinity of the nanopore. And, nanoparticle translocation speed was slowed down to obtain a clear and deterministic signal. Compared with previous studied small nanoparticles, the electrophoretic translocation of negatively charged polystyrene (PS) nanoparticles (diameter ~100 nm) was investigated in solution using the Coulter counter principle in which the time-dependent nanopore current was recorded as the nanoparticles were driven across the nanopore. A linear dependence was found between current drop and biased voltage. An exponentially decaying function (t d ~ e (-v/v0) ) was found between the duration time and biased voltage. The interaction between the amine-functionalized nanopore wall and PS microspheres was discussed while translating PS microspheres. We explored also translocations of PS microspheres through amine-functionalized solid-state nanopores by varying the solution pH (5.4, 7.0, and 10.0) with 0.02 M potassium chloride (KCl). Surface functionalization showed to provide a useful step to fine-tune the surface property, which can selectively transport molecules or particles. This approach is likely to be applied to gene sequencing.
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Affiliation(s)
- Shengwei Tan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Sipailou Campus, No. 2, Sipailou, Nanjing, 210096, People's Republic of China.
| | - Lei Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Sipailou Campus, No. 2, Sipailou, Nanjing, 210096, People's Republic of China.
| | - Hang Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Sipailou Campus, No. 2, Sipailou, Nanjing, 210096, People's Republic of China.
| | - Hongwen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Sipailou Campus, No. 2, Sipailou, Nanjing, 210096, People's Republic of China.
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Sipailou Campus, No. 2, Sipailou, Nanjing, 210096, People's Republic of China.
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19
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Dwyer JR, Bandara YMNDY, Whelan JC, Karawdeniya BI, Nichols JW. Silicon Nitride Thin Films for Nanofluidic Device Fabrication. NANOFLUIDICS 2016. [DOI: 10.1039/9781849735230-00190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.
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Affiliation(s)
- J. R. Dwyer
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | | | - J. C. Whelan
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - B. I. Karawdeniya
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - J. W. Nichols
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
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20
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Liu L, Wu HC. DNA-Based Nanopore Sensing. Angew Chem Int Ed Engl 2016; 55:15216-15222. [DOI: 10.1002/anie.201604405] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/13/2016] [Indexed: 01/09/2023]
Affiliation(s)
- 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
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
- 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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21
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Affiliation(s)
- Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Peking 100190 China
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22
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Jacques DA, McEwan WA, Hilditch L, Price AJ, Towers GJ, James LC. HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis. Nature 2016; 536:349-53. [PMID: 27509857 PMCID: PMC4998957 DOI: 10.1038/nature19098] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/12/2016] [Indexed: 12/21/2022]
Abstract
During the early stages of infection, the HIV-1 capsid protects viral components from cytosolic sensors and nucleases such as cGAS and TREX, respectively, while allowing access to nucleotides for efficient reverse transcription. Here we show that each capsid hexamer has a size-selective pore bound by a ring of six arginine residues and a 'molecular iris' formed by the amino-terminal β-hairpin. The arginine ring creates a strongly positively charged channel that recruits the four nucleotides with on-rates that approach diffusion limits. Progressive removal of pore arginines results in a dose-dependent and concomitant decrease in nucleotide affinity, reverse transcription and infectivity. This positively charged channel is universally conserved in lentiviral capsids despite the fact that it is strongly destabilizing without nucleotides to counteract charge repulsion. We also describe a channel inhibitor, hexacarboxybenzene, which competes for nucleotide binding and efficiently blocks encapsidated reverse transcription, demonstrating the tractability of the pore as a novel drug target.
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23
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Schmidt J. Membrane platforms for biological nanopore sensing and sequencing. Curr Opin Biotechnol 2016; 39:17-27. [PMID: 26773300 DOI: 10.1016/j.copbio.2015.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
In the past two decades, biological nanopores have been developed and explored for use in sensing applications as a result of their exquisite sensitivity and easily engineered, reproducible, and economically manufactured structures. Nanopore sensing has been shown to differentiate between highly similar analytes, measure polymer size, detect the presence of specific genes, and rapidly sequence nucleic acids translocating through the pore. Devices featuring protein nanopores have been limited in part by the membrane support containing the nanopore, the shortcomings of which have been addressed in recent work developing new materials, approaches, and apparatus resulting in membrane platforms featuring automatability and increased robustness, lifetime, and measurement throughput.
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Affiliation(s)
- Jacob Schmidt
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA.
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24
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Stefan-van Staden RI, Comnea-Stancu IR, Surdu-Bob CC, Badulescu M. Nanostructured materials detect epidermal growth factor receptor, neuron specific enolase and carcinoembryonic antigen. NANOSCALE 2015; 7:15689-94. [PMID: 26350155 DOI: 10.1039/c5nr04476f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
New nanostructured materials based on thin films of Cu and Ni deposited on textile material (veil), as well as gold nanostructured microspheres were used for the design of new stochastic sensors. The stochastic sensors were able to detect simultaneously a panel of biomarkers comprising epidermal growth factor receptor, neuron specific enolase, and carcinoembryonic antigen from whole blood samples with high reliabilities - recovery tests higher than 97.00%, with a RSD (%) lower than 0.1%. The stochastic sensors had shown high sensitivities and low determination levels for the detection of the proposed panel of biomarkers making early detection of lung cancer possible by fast screening of whole blood.
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Affiliation(s)
- Raluca-Ioana Stefan-van Staden
- Laboratory of Electrochemistry and PATLAB Bucharest, National Institute of Research for Electrochemistry and Condensed Matter, 202 Splaiul Independentei St., Bucharest, 060021, Romania.
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25
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Tan S, Wang L, Yu J, Hou C, Jiang R, Li Y, Liu Q. DNA-functionalized silicon nitride nanopores for sequence-specific recognition of DNA biosensor. NANOSCALE RESEARCH LETTERS 2015; 10:205. [PMID: 25977675 PMCID: PMC4420758 DOI: 10.1186/s11671-015-0909-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/22/2015] [Indexed: 05/29/2023]
Abstract
Nanopores have been proven to be novel and versatile single-molecule sensors for individual unlabeled biopolymer detection and characterization. In the present study, a relatively large silicon nitride (Si3N4) nanopore with a diameter of approximately 60 nm was fabricated successfully using a focused Ga ion beam (FIB). We demonstrated a simple ex situ silanization procedure to control the size and functionality of solid-state nanopores. The presented results show that by varying the silanization time, it is possible to adjust the efficiency of probe molecule attachment, thus shrinking the pore to the chosen size, while introducing selective sensing probes. The functionalization of nanopores was verified by analysis of field-emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDS), and electrical measurements. Based on this study, we envision that the functionalized silicon nitride nanopores with the DNA probe might provide a biosensing platform for the detection and discrimination of a short single-stranded DNA oligomer of unknown sequences in the future.
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Affiliation(s)
- Shengwei Tan
- />State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing, 210096 People’s Republic of China
| | - Lei Wang
- />State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing, 210096 People’s Republic of China
| | - Jingjing Yu
- />State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing, 210096 People’s Republic of China
| | - Chuanrong Hou
- />State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing, 210096 People’s Republic of China
| | - Rui Jiang
- />Department of Automation, Tsinghua University, No. 1 Tsinghua Yuan, Beijing, 1000084 People’s Republic of China
| | - Yanping Li
- />Jiangxi-OAI Joint Research Institute, Nanchang University, No. 235 Nanjing Dong Lu, Nanchang, 330047 People’s Republic of China
| | - Quanjun Liu
- />State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing, 210096 People’s Republic of China
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26
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Lin Q, Wang T, Li H, London E. Decreasing Transmembrane Segment Length Greatly Decreases Perfringolysin O Pore Size. J Membr Biol 2015; 248:517-27. [PMID: 25850715 DOI: 10.1007/s00232-015-9798-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/25/2015] [Indexed: 01/06/2023]
Abstract
Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30-50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakage assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.
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Affiliation(s)
- Qingqing Lin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794-5215, USA
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27
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Feng Y, Zhang Y, Ying C, Wang D, Du C. Nanopore-based fourth-generation DNA sequencing technology. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:4-16. [PMID: 25743089 PMCID: PMC4411503 DOI: 10.1016/j.gpb.2015.01.009] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/14/2015] [Accepted: 01/23/2015] [Indexed: 12/24/2022]
Abstract
Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein. Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale. In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.
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Affiliation(s)
- Yanxiao Feng
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuechuan Zhang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Cuifeng Ying
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; MOE Key Laboratory of Weak-light Nonlinear Photonics, School of Physics, Nankai University, Tianjin 300071, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chunlei Du
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
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28
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Fahie M, Chisholm C, Chen M. Resolved single-molecule detection of individual species within a mixture of anti-biotin antibodies using an engineered monomeric nanopore. ACS NANO 2015; 9:1089-98. [PMID: 25575121 PMCID: PMC4958048 DOI: 10.1021/nn506606e] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Oligomeric protein nanopores with rigid structures have been engineered for the purpose of sensing a wide range of analytes including small molecules and biological species such as proteins and DNA. We chose a monomeric β-barrel porin, OmpG, as the platform from which to derive the nanopore sensor. OmpG is decorated with seven flexible loops that move dynamically to create a distinct gating pattern when ionic current passes through the pore. Biotin was chemically tethered to the most flexible one of these loops. The gating characteristic of the loop's movement in and out of the porin was substantially altered by analyte protein binding. The gating characteristics of the pore with bound targets were remarkably sensitive to molecular identity, even providing the ability to distinguish between homologues within an antibody mixture. A total of five gating parameters were analyzed for each analyte to create a unique fingerprint for each biotin-binding protein. Our exploitation of gating noise as a molecular identifier may allow more sophisticated sensor design, while OmpG's monomeric structure greatly simplifies nanopore production.
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Affiliation(s)
- Monifa Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Christina Chisholm
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
- Address correspondence to:
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29
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Czekalska MA, Kaminski TS, Jakiela S, Tanuj Sapra K, Bayley H, Garstecki P. A droplet microfluidic system for sequential generation of lipid bilayers and transmembrane electrical recordings. LAB ON A CHIP 2015; 15:541-8. [PMID: 25412368 DOI: 10.1039/c4lc00985a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper demonstrates a microfluidic system that automates i) formation of a lipid bilayer at the interface between a pair of nanoliter-sized aqueous droplets in oil, ii) exchange of one droplet of the pair to form a new bilayer, and iii) current measurements on single proteins. A new microfluidic architecture is introduced - a set of traps designed to localize the droplets with respect to each other and with respect to the recording electrodes. The system allows for automated execution of experimental protocols by active control of the flow on chip with the use of simple external valves. Formation of stable artificial lipid bilayers, incorporation of α-hemolysin into the bilayers and electrical measurements of ionic transport through the protein pore are demonstrated.
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Affiliation(s)
- Magdalena A Czekalska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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30
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Gurnev PA, Nestorovich EM. Channel-forming bacterial toxins in biosensing and macromolecule delivery. Toxins (Basel) 2014; 6:2483-540. [PMID: 25153255 PMCID: PMC4147595 DOI: 10.3390/toxins6082483] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022] Open
Abstract
To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.
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Affiliation(s)
- Philip A Gurnev
- Physics Department, University of Massachusetts, Amherst, MA 01003, USA.
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31
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Zeng T, Li T, Li Y, Liu L, Wang X, Liu Q, Zhao Y, Wu HC. DNA-based detection of mercury(II) ions through characteristic current signals in nanopores with high sensitivity and selectivity. NANOSCALE 2014; 6:8579-8584. [PMID: 24975417 DOI: 10.1039/c4nr02062f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report single-molecule detection of Hg(2+) by threading an Hg(2+)-mediated DNA duplex through α-hemolysin nanopores, which generates characteristic three-level current patterns and enables the unambiguous detection of Hg(2+). This strategy precludes any background interference and features high sensitivity and selectivity. Moreover, the platform could be readily integrated with aptamers and molecular beacons, offering extended possibilities for the construction of a new DNA-based nanopore sensing system.
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Affiliation(s)
- Tao Zeng
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety
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33
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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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34
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Matsumoto A, Miyahara Y. Current and emerging challenges of field effect transistor based bio-sensing. NANOSCALE 2013; 5:10702-10718. [PMID: 24064964 DOI: 10.1039/c3nr02703a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Field-effect-transistor (FET) based electrical signal transduction is an increasingly prevalent strategy for bio-sensing. This technique, often termed "Bio-FETs", provides an essentially label-free and real-time based bio-sensing platform effective for a variety of targets. This review highlights recent progress and challenges in the field. A special focus is on the comprehension of emerging nanotechnology-based approaches to facilitate signal-transduction and amplification. Some new targets of Bio-FETs and the future perspectives are also discussed.
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Affiliation(s)
- Akira Matsumoto
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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35
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Ayub M, Hardwick SW, Luisi BF, Bayley H. Nanopore-based identification of individual nucleotides for direct RNA sequencing. NANO LETTERS 2013; 13:6144-50. [PMID: 24171554 PMCID: PMC3899427 DOI: 10.1021/nl403469r] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe a label-free ribobase identification method, which uses ionic current measurement to resolve ribonucleoside monophosphates or diphosphates in α-hemolysin protein nanopores containing amino-cyclodextrin adapters. The accuracy of base identification is further investigated through the use of a guanidino-modified adapter. On the basis of these findings, an exosequencing approach is envisioned in which a processive exoribonuclease (polynucleotide phosphorylase) presents sequentially cleaved ribonucleoside diphosphates to a nanopore.
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Affiliation(s)
- Mariam Ayub
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Steven W. Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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36
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Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate. Proc Natl Acad Sci U S A 2013; 110:E4417-26. [PMID: 24194548 DOI: 10.1073/pnas.1312739110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In stochastic sensing, the association and dissociation of analyte molecules is observed as the modulation of an ionic current flowing through a single engineered protein pore, enabling the label-free determination of rate and equilibrium constants with respect to a specific binding site. We engineered sensors based on the staphylococcal α-hemolysin pore to allow the single-molecule detection and characterization of protein kinase-peptide interactions. We enhanced this approach by using site-specific proteolysis to generate pores bearing a single peptide sensor element attached by an N-terminal peptide bond to the trans mouth of the pore. Kinetics and affinities for the Pim protein kinases (Pim-1, Pim-2, and Pim-3) and cAMP-dependent protein kinase were measured and found to be independent of membrane potential and in good agreement with previously reported data. Kinase binding exhibited a distinct current noise behavior that forms a basis for analyte discrimination. Finally, we observed unusually high association rate constants for the interaction of Pim kinases with their consensus substrate Pimtide (~10(7) to 10(8) M(-1) · s(-1)), the result of electrostatic enhancement, and propose a cellular role for this phenomenon.
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37
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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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38
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An engineered dimeric protein pore that spans adjacent lipid bilayers. Nat Commun 2013; 4:1725. [PMID: 23591892 PMCID: PMC3644966 DOI: 10.1038/ncomms2726] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/08/2013] [Indexed: 01/15/2023] Open
Abstract
The bottom-up construction of artificial tissues is an underexplored area of synthetic biology. An important challenge is communication between constituent compartments of the engineered tissue, and between the engineered tissue and additional compartments, including extracellular fluids, further engineered tissue and living cells. Here we present a dimeric transmembrane pore that can span two adjacent lipid bilayers, and thereby allow aqueous compartments to communicate. Two heptameric staphylococcal α-hemolysin pores were covalently linked in an aligned cap-to-cap orientation. The structure of the dimer, (α7)2, was confirmed by biochemical analysis, transmission electron microscopy and single-channel electrical recording. We show that one of two β-barrels of (α7)2 can insert into the lipid bilayer of a small unilamellar vesicle, while the other spans a planar lipid bilayer. The (α7)2 pores spanning two bilayers were also observed by transmission electron microscopy.
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39
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Boersma A, Sidaway P, Bayley H, Brain K. Detecting purines, catecholamines and other transmitters with a mutant α-haemolysin pore one molecule at a time. Auton Neurosci 2013. [DOI: 10.1016/j.autneu.2013.08.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Haque F, Li J, Wu HC, Liang XJ, Guo P. Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA. NANO TODAY 2013; 8:56-74. [PMID: 23504223 PMCID: PMC3596169 DOI: 10.1016/j.nantod.2012.12.008] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghong Li
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Beijing 100084, China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Jie Liang
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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41
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Affiliation(s)
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, U.S.A
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42
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Abstract
A stable tetraporphyrin metallacycle with Re(I) corners (1) is capable of forming nanopores in a liposomial membrane, provided that the porphyrin units are properly functionalized with peripheral carboxylic acid residues that, by establishing an hydrogen bond network, allow the formation of dimers that span the depth of the membrane.
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Affiliation(s)
- Mariangela Boccalon
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via Giorgieri 1, I-34127, Trieste, Italy
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43
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Boersma AJ, Brain KL, Bayley H. Real-time stochastic detection of multiple neurotransmitters with a protein nanopore. ACS NANO 2012; 6:5304-8. [PMID: 22616662 DOI: 10.1021/nn301125y] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The detection of several different neurotransmitters with the same sensor in real-time would be a powerful asset to the field of neurochemistry. We have developed a detector for a broad range of neurotransmitters including amino acids, catecholamines, and nucleotides, which relies on the reversible binding of the analytes to a copper(II) complex within an engineered protein nanopore.
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Affiliation(s)
- Arnold J Boersma
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
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44
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Shim J, Gu LQ. Single-molecule investigation of G-quadruplex using a nanopore sensor. Methods 2012; 57:40-6. [PMID: 22487183 DOI: 10.1016/j.ymeth.2012.03.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 01/01/2023] Open
Abstract
This review article introduces the nanopore single-molecule method for the study of G-quadruplex nucleic acid structures. Single G-quadruplexes can be trapped into a 2 nm protein pore embedded in the lipid bilayer membrane. The trapped G-quadruplex specifically blocks the current through the nanopore, creating a signature event for quantitative analysis of G-quadruplex properties, from cation-determined folding and unfolding kinetics to the interactions with the protein ligand. The nanopore single-molecule method is simple, accurate, and requires no labels. It can be used to evaluate G-quadruplex mechanisms and it may have applications in G-quadruplex-based biosensors, nanomachines, and nanostructure assembly.
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Affiliation(s)
- Jiwook Shim
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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45
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Rotem D, Jayasinghe L, Salichou M, Bayley H. Protein detection by nanopores equipped with aptamers. J Am Chem Soc 2012; 134:2781-7. [PMID: 22229655 PMCID: PMC3278221 DOI: 10.1021/ja2105653] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Protein nanopores have been used as stochastic sensors
for the
detection of analytes that range from small molecules to proteins.
In this approach, individual analyte molecules modulate the ionic
current flowing through a single nanopore. Here, a new type of stochastic
sensor based on an αHL pore modified with an aptamer is described.
The aptamer is bound to the pore by hybridization to an oligonucleotide
that is attached covalently through a disulfide bond to a single cysteine
residue near a mouth of the pore. We show that the binding of thrombin
to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex,
alters the ionic current through the pore. The approach allows the
quantification of nanomolar concentrations of thrombin, and provides
association and dissociation rate constants and equilibrium dissociation
constants for thrombin·aptamer interactions. Aptamer-based nanopores
have the potential to be integrated into arrays for the parallel detection
of multiple analytes.
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Affiliation(s)
- Dvir Rotem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
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46
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Nannenga BL, Baneyx F. Folding engineering strategies for efficient membrane protein production in E. coli. Methods Mol Biol 2012; 899:187-202. [PMID: 22735954 DOI: 10.1007/978-1-61779-921-1_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Membrane proteins are notoriously difficult to produce at the high levels required for structural and biochemical characterization. Among the various expression systems used to date, the enteric bacterium Escherichia coli remains one of the best characterized and most versatile. However, membrane protein overexpression in E. coli is often accompanied by toxicity and low yields of functional product. Here, we briefly review the involvement of signal recognition particle, trigger factor, and YidC in α-helical membrane protein biogenesis and describe a set of strains, vectors, and chaperone co-expression plasmids that can lead to significant gains in the production of recombinant membrane proteins in E. coli. Methods to quantify membrane proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis are also provided.
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Affiliation(s)
- Brent L Nannenga
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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47
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Jung JY, Jun EJ, Kwon YU, Yoon J. Recognition of myo-inositol 1,4,5-trisphosphate using a fluorescent imidazolium receptor. Chem Commun (Camb) 2012; 48:7928-30. [DOI: 10.1039/c2cc33717g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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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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49
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de Zoysa RSS, Krishantha DMM, Zhao Q, Gupta J, Guan X. Translocation of single-stranded DNA through the α-hemolysin protein nanopore in acidic solutions. Electrophoresis 2011; 32:3034-41. [PMID: 21997574 DOI: 10.1002/elps.201100216] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 06/02/2011] [Accepted: 06/09/2011] [Indexed: 11/12/2022]
Abstract
The effect of acidic pH on the translocation of single-stranded DNA through the α-hemolysin pore is investigated. Two significantly different types of events, i.e. deep blockades and shallow blockades, are observed at low pH. The residence times of the shallow blockades are not significantly different from those of the DNA translocation events obtained at or near physiological pH, whereas the deep blockades have much larger residence times and blockage amplitudes. With a decrease in the pH of the electrolyte solution, the percentage of the deep blockades in the total events increases. Furthermore, the mean residence time of these long-lived events is dependent on the length of DNA, and also varies with the nucleotide base, suggesting that they are appropriate for use in DNA analysis. In addition to being used as an effective approach to affect DNA translocation in the nanopore, manipulation of the pH of the electrolyte solution provides a potential means to greatly enhance the sensitivity of nanopore stochastic sensing.
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Affiliation(s)
- Ranulu S S de Zoysa
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019-0065, USA
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50
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Liu A, Zhao Q, Krishantha DM, Guan X. Unzipping of Double-stranded DNA in Engineered α-Hemolysin Pores. J Phys Chem Lett 2011; 2:1372-1376. [PMID: 21709813 PMCID: PMC3119559 DOI: 10.1021/jz200525v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Biological protein α-hemolysin nanopore is under intense investigation as a potential platform for rapid and low-cost DNA sequencing. However, due to its narrow constriction, analysis of DNA in the α-hemolysin pore has long time been restricted to single strands. In this paper, we report that by introducing new surface functional groups into the α-hemolysin pore, facilitated unzipping of double-stranded DNA through the channel could be achieved. Since the mean residence time of the DNA events is dependent on the length of the duplex, and also varies with the nucleotide base composition, the modified protein pore approach offers the potential for rapid double-stranded DNA analysis, including sequencing.
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Affiliation(s)
- Aihua Liu
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
- Laboratory for Nanobioelectronics & Biosensors, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, P. R. China
| | - Qitao Zhao
- 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
| | - Xiyun Guan
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
- Corresponding author: Tel: 817-272-6086; Fax: 817-272-3808;
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