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Huang H, Wu Y, Qian M, Yang X, Qi H. Iridium(III) solvent complex-based electrogenerated chemiluminescence and photoluminescence sensor array for the discrimination of bases in oligonucleotides. Bioelectrochemistry 2023; 150:108368. [PMID: 36634465 DOI: 10.1016/j.bioelechem.2023.108368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Development of rapid and sensitive method for the discrimination of bases in oligonucleotides is of great importance in clinical diagnosis. Here, we demonstrate the first case of single iridium(III) solvent complex-based electrogenerated chemiluminescence (ECL) and photoluminescence (PL) sensor array for the discrimination of bases in oligonucleotides. One iridium (III) solvent complex ([Ir(ppy)2(DMSO)Cl], ppy = 2-phenylpyridine, probe 1) was designed as both ECL and PL probe while five bases (guanine, adenine, cytosine, thymine and uracil) were chosen as analytes. Two-element sensor array was built for the discrimination of five bases based on the fingerprint response of probe 1 to bases via coordination interactions. The combination of unique ECL and PL variations with principal component analysis was applied for the quantitative analysis of five bases in a linear range of 1.0 μM-10 μM and for the effective discrimination of individual base, the mixture of bases and oligonucleotides. Moreover, the sensor array was successfully applied to discriminate different mismatched ss-DNAs from HIV gene (a fully-matched ss-DNA), even at single-base difference. This work demonstrates that the sensor array using single iridium (III) solvent complex is a promising approach for the discrimination of bases with good sensitivity and simpleness in clinical diagnosis.
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Affiliation(s)
- Hong Huang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Yang Wu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Manping Qian
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Xiaolin Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China.
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China.
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2
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Hussein EA, Rice B, White RJ. Recent advances in ion-channel probes for nanopore sensing: Insights into the probe architectures. Anal Chim Acta 2022; 1224:340162. [DOI: 10.1016/j.aca.2022.340162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/01/2022]
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3
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Denuga S, Whelan DE, O'Neill SP, Johnson RP. Capture and analysis of double‐stranded DNA with the α‐hemolysin nanopore: Fundamentals and applications. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202200001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
| | | | | | - Robert P. Johnson
- School of Chemistry University College Dublin Ireland
- UCD‐Centre for Food Safety University College Dublin Dublin Ireland
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4
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Zhong W, Yang Q, Fang K, Xiao D, Zhou C. Current Simultaneous Discrimination of Mismatched MicroRNAs Using Base-Flipping within the α-Hemolysin Latch. ACS Sens 2021; 6:4482-4488. [PMID: 34793139 DOI: 10.1021/acssensors.1c02005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The simultaneous discrimination of let-7 microRNAs (miRNAs) would greatly facilitate the early diagnosis and prognosis monitoring of diseases. In this work, a molecular beacon DNA probe was designed to be able to flip out its mismatched cytosine base within the α-hemolysin (α-HL) latch and generate completely separated blocking currents to identify the single-base difference. As a result, the characteristic blocking current of fully matched MB/let-7a and single-base mismatched MB/let-7f was 84.30 ± 0.92 and 87.05 ± 0.86% (confidence level P 95%), respectively. Let-7 miRNA family let-7a and let-7f were completely simultaneously discriminated, which could be attributed to the following strengths. (1) The statistic distribution of blocking current is extremely concentrated with a small relative standard deviation (RSD) of less than 1% and a narrow distribution range. (2) Complete separation is achieved with a high separation resolution of 1.54. (3) The cytosine base flipping out within the α-HL latch provides a universal labeling-free strategy to simultaneously discriminate the single-base mismatch. Overall, the target let-7f sequences were detected with a linear range from 0.001 to 10 pM in human serum samples containing 200 nM let-7a. Great potential has been demonstrated for precise detection, early diagnosis, and prognosis monitoring of diseases related to single-base difference.
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Affiliation(s)
- Wenjun Zhong
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Qiufang Yang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Kerui Fang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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5
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Lv P, Yang Y, Li S, Tan CS, Ming D. Biological nanopore approach for single‐molecule analysis of nucleobase modifications. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100119] [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] Open
Affiliation(s)
- Pengrui Lv
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Yongyi Yang
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Cherie S. Tan
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Dong Ming
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
- Department of Biomedical Engineering College of Precision Instruments and Optoelectronics Engineering Tianjin University Tianjin China
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6
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Khamari L, Pramanik S, Shekhar S, Mahato P, Mukherjee S. Preferential Binding of Epirubicin Hydrochloride with Single Nucleotide Mismatched DNA and Subsequent Sequestration by a Mixed Micelle. J Phys Chem B 2021; 125:11660-11672. [PMID: 34652157 DOI: 10.1021/acs.jpcb.1c06944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Targeting mismatched base pairs containing DNA using small molecules and exploring the underlying mechanism involved during the binding interactions is one of the fundamental aspects of drug design. These molecules in turn are used in nucleic acid targeted therapeutics and cancer diagnosis. In this work, we systematically delineate the binding of the anticancer drug, epirubicin hydrochloride (EPR) with 20-mer duplex DNA, having both natural nucleobase pairing and thermodynamically least stable non-Watson-Crick base pairing. From the thermal denaturation studies, we observed that EPR can remarkably enhance the thermal stability of cytosine-cytosine (CC) and cytosine-thymine (CT) mismatched (MM) DNA over other 20-mer duplex DNA. From steady-state fluorescence spectroscopy and isothermal titration calorimetry studies, we concluded that EPR binds strongly with the mismatched duplex DNA through the intercalation binding mode. The interaction of EPR and duplex DNA has also been monitored at a single molecular resolution using fluorescence correlation spectroscopy (FCS). Dynamic quantitates such as diffusion coefficients and hydrodynamic radii obtained from an FCS study along with association and dissociation rate constants estimated from intensity time trace analyses further substantiate the stronger binding affinity of EPR to the thermally less stable mismatched DNA, formed by the most discriminating nucleobase (viz. cytosine). Additionally, we have shown that EPR can be sequestered from nucleic acids using a mixed micellar system of an anionic surfactant and a triblock copolymer. From thermal denaturation studies and circular dichroism spectroscopy, we found that the extent of drug sequestration depends on the binding affinity of EPR to the duplex DNA, and this mixed micellar system can be employed for the removal of excess drug in the case of a drug overdose.
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Affiliation(s)
- Laxmikanta Khamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Shashi Shekhar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Paritosh Mahato
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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7
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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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8
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Affiliation(s)
- Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Xiao Zhuge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
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9
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Ren H, Edwards MA. Stochasticity in Single-Entity Electrochemistry. CURRENT OPINION IN ELECTROCHEMISTRY 2021; 25:100632. [PMID: 33102927 PMCID: PMC7584144 DOI: 10.1016/j.coelec.2020.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Most electrochemical processes are stochastic and discrete in nature. Yet experimental observables, e.g., i vs E, are typically smooth and deterministic, due to many events/processes, e.g., electron transfers, being averaged together. However, when the number of entities measured approaches a few or even one, stochasticity frequently emerges. Yet all is not lost! Probabilistic and statistical interpretation can generate insights matching or superseding those from macroscale/ensemble measurements, revealing phenomena that were hitherto averaged over. Herein, we review recent literature examples of stochastic processes in single-entity electrochemistry, highlighting strategies for interpreting stochasticity, contrasting them with macroscale measurements, and describing the insights generated.
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Affiliation(s)
- Hang Ren
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH 45056
| | - Martin A Edwards
- Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville, AR 72701
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10
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Liu SC, Ying YL, Li WH, Wan YJ, Long YT. Snapshotting the transient conformations and tracing the multiple pathways of single peptide folding using a solid-state nanopore. Chem Sci 2021; 12:3282-3289. [PMID: 34164097 PMCID: PMC8179386 DOI: 10.1039/d0sc06106a] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A fundamental question relating to protein folding/unfolding is the time evolution of the folding of a protein into its precisely defined native structure. The proper identification of transition conformations is essential for accurately describing the dynamic protein folding/unfolding pathways. Owing to the rapid transitions and sub-nm conformation differences involved, the acquisition of the transient conformations and dynamics of proteins is difficult due to limited instrumental resolution. Using the electrochemical confinement effect of a solid-state nanopore, we were able to snapshot the transient conformations and trace the multiple transition pathways of a single peptide inside a nanopore. By combining the results with a Markov chain model, this new single-molecule technique is applied to clarify the transition pathways of the β-hairpin peptide, which shows nonequilibrium fluctuations among several blockage current stages. This method enables the high-throughput investigation of transition pathways experimentally to access previously obscure peptide dynamics, which is significant for understanding the folding/unfolding mechanisms and misfolding of peptides or proteins. A solid-state nanopore based method is described for resolving protein-folding-related problems via snapshotting the folding intermediates and characterizing the kinetics of a single peptide.![]()
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Affiliation(s)
- Shao-Chuang Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Department of Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Department of Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Wei-Hua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Yong-Jing Wan
- School of Information Science and Engineering, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Department of Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
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11
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Ge L, Wu J, Wang C, Zhang F, Liu Z. Engineering artificial switchable nanochannels for selective monitoring of nitric oxide release from living cells. Biosens Bioelectron 2020; 169:112606. [DOI: 10.1016/j.bios.2020.112606] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/22/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022]
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12
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Peng Y, Wang Y, Wang X. Exploring the Thermodynamics of 7-Amino Actinomycin D-Induced Single-Stranded DNA Hairpin by Spectroscopic Techniques and Computational Simulations. J Phys Chem B 2020; 124:10007-10013. [PMID: 33136398 DOI: 10.1021/acs.jpcb.0c05593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
NMR studies have indicated that the anti-tumor therapeutic agent actinomycin D (ACTD) can induce seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT3GTGG-3' to form a hairpin structure with tandem GT mismatches at the stem region next to a loop of three stacked thymine bases. In an effort to uncover the preference of binding sequence and to elucidate the thermodynamics properties of the binding, a combination of spectroscopic techniques and computational simulation studies was performed with d(CCGTTnGTGG) and d(CCGAAnGAGG) (denoted as GTTn and GAAn, respectively; n = 3, 5, and 7) sequences. In the presence of 7-amino actinomycin D (7AACTD), all the six oligomers formed stable hairpin structures. The GTT5-7AACTD/GAA5-7AACTD hairpin structure was more stable than the corresponding GTTn-7AACTD and GAAn-7AACTD (n = 3, 7). No significant ΔG difference was observed between GTTn-7AACTD and GAAn-7AACTD complexes with the same loop length. In agreement with the 7AACTD-induced hairpin stability results, the binding affinity of GTTn and GAAn with 7AACTD increased from n = 3 to n = 5 and then decreased when n is 7. Moreover, GTTn and GAAn with the same loop length showed comparable binding affinities to 7AACTD. Furthermore, molecular dynamics simulations found that van der Waals interactions between GTTn/GAAn and 7AACTD were the primary attractive forces for 7AACTD binding, and the electrostatic interactions between the carbonyl groups of 7AACTD and bases in the hairpin were the major unfavorable forces. These findings furthered our understanding that 7AACTD is sensitive to the loop size and sequence as well as tandem GT/GA mismatches of their deoxyribonucleic acid (DNA) targets. A deep understanding of the thermodynamics and the molecular recognition mechanism of 7AACTD with ssDNAs would further the development of ACTD-like antitumor agents.
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Affiliation(s)
- Yinghua Peng
- Key Laboratory of Special Animal Molecular Biology of Jilin Province, Specialty Research Institute of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130022, China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
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13
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Chen R, Alanis K, Welle TM, Shen M. Nanoelectrochemistry in the study of single-cell signaling. Anal Bioanal Chem 2020; 412:6121-6132. [PMID: 32424795 DOI: 10.1007/s00216-020-02655-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 12/28/2022]
Abstract
Label-free biosensing has been the dream of scientists and biotechnologists as reported by Vollmer and Arnold (Nat Methods 5:591-596, 2008). The ability of examining living cells is crucial to cell biology as noted by Fang (Int J Electrochem 2011:460850, 2011). Chemical measurement with electrodes is label-free and has demonstrated capability of studying living cells. In recent years, nanoelectrodes of different functionality have been developed. These nanometer-sized electrodes, coupled with scanning electrochemical microscopy (SECM), have further enabled nanometer spatial resolution study in aqueous environments. Developments in the field of nanoelectrochemistry have allowed measurement of signaling species at single cells, contributing to better understanding of cell biology. Leading studies using nanoelectrochemistry of a variety of cellular signaling molecules, including redox-active neurotransmitter (e.g., dopamine), non-redox-active neurotransmitter (e.g., acetylcholine), reactive oxygen species (ROS), and reactive nitrogen species (RNS), are reviewed here.
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Affiliation(s)
- Ran Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Kristen Alanis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Theresa M Welle
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Mei Shen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
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14
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Misawa N, Osaki T, Takeuchi S. Membrane protein-based biosensors. J R Soc Interface 2019; 15:rsif.2017.0952. [PMID: 29669891 DOI: 10.1098/rsif.2017.0952] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/19/2018] [Indexed: 01/09/2023] Open
Abstract
This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.
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Affiliation(s)
- Nobuo Misawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan .,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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15
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Ying YL, Long YT. Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge. J Am Chem Soc 2019; 141:15720-15729. [DOI: 10.1021/jacs.8b11970] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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16
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Edwards MA, Robinson DA, Ren H, Cheyne CG, Tan CS, White HS. Nanoscale electrochemical kinetics & dynamics: the challenges and opportunities of single-entity measurements. Faraday Discuss 2019; 210:9-28. [PMID: 30264833 DOI: 10.1039/c8fd00134k] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The development of nanoscale electrochemistry since the mid-1980s has been predominately coupled with steady-state voltammetric (i-E) methods. This research has been driven by the desire to understand the mechanisms of very fast electrochemical reactions, by electroanalytical measurements in small volumes and unusual media, including in vivo measurements, and by research on correlating electrocatalytic activity, e.g., O2 reduction reaction, with nanoparticle size and structure. Exploration of the behavior of nanoelectrochemical structures (nanoelectrodes, nanoparticles, nanogap cells, etc.) of a characteristic dimension λ using steady-state i-E methods generally relies on the well-known relationship, λ2 ∼ Dt, which relates diffusional lengths to time, t, through the coefficient, D. Decreasing λ, by performing measurements at a nanometric length scales, results in a decrease in the effective timescale of the measurement, and provides a direct means to probe the kinetics of steps associated with very rapid electrochemical reactions. For instance, steady-state voltammetry using a nanogap twin-electrode cell of characteristic width, λ ∼ 10 nm, allows investigations of events occurring at timescales on the order of ∼100 ns. Among many other advantages, decreasing λ also increases spatial resolution in electrochemical imaging, e.g., in scanning electrochemical microscopy, and allows probing of the electric double layer. This Introductory Lecture traces the evolution and driving forces behind the "λ2 ∼ Dt" steady-state approach to nanoscale electrochemistry, beginning in the late 1950s with the introduction of the rotating ring-disk electrode and twin-electrode thin-layer cells, and evolving to current-day investigations using nanoelectrodes, scanning nanocells for imaging, nanopores, and nanoparticles. The recent focus on so-called "single-entity" electrochemistry, in which individual and very short redox events are probed, is a significant departure from the steady-state approach, but provides new opportunities to probe reaction dynamics. The stochastic nature of very fast single-entity events challenges current electrochemical methods and modern electronics, as illustrated using recent experiments from the authors' laboratory.
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Affiliation(s)
- M A Edwards
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA.
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17
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Haugland MM, Borsley S, Cairns-Gibson DF, Elmi A, Cockroft SL. Synthetically Diversified Protein Nanopores: Resolving Click Reaction Mechanisms. ACS NANO 2019; 13:4101-4110. [PMID: 30864781 DOI: 10.1021/acsnano.8b08691] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopores are emerging as a powerful tool for the investigation of nanoscale processes at the single-molecule level. Here, we demonstrate the methionine-selective synthetic diversification of α-hemolysin (α-HL) protein nanopores and their exploitation as a platform for investigating reaction mechanisms. A wide range of functionalities, including azides, alkynes, nucleotides, and single-stranded DNA, were incorporated into individual pores in a divergent fashion. The ion currents flowing through the modified pores were used to observe the trajectory of a range of azide-alkyne click reactions and revealed several short-lived intermediates in Cu(I)-catalyzed azide-alkyne [3 + 2] cycloadditions (CuAAC) at the single-molecule level. Analysis of ion-current fluctuations enabled the populations of species involved in rapidly exchanging equilibria to be determined, facilitating the resolution of several transient intermediates in the CuAAC reaction mechanism. The versatile pore-modification chemistry offers a useful approach for enabling future physical organic investigations of reaction mechanisms at the single-molecule level.
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Affiliation(s)
- Marius M Haugland
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Stefan Borsley
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Dominic F Cairns-Gibson
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Alex Elmi
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Scott L Cockroft
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
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18
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Cox BD, Woodworth PH, Wilkerson PD, Bertino MF, Reiner JE. Ligand-Induced Structural Changes of Thiolate-Capped Gold Nanoclusters Observed with Resistive-Pulse Nanopore Sensing. J Am Chem Soc 2019; 141:3792-3796. [DOI: 10.1021/jacs.8b12535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Bobby D. Cox
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Patrick H. Woodworth
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Peter D. Wilkerson
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Massimo F. Bertino
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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19
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Shi R, Nejad MI, Zhang X, Gu LQ, Gates KS. Generation and Single-Molecule Characterization of a Sequence-Selective Covalent Cross-Link Mediated by Mechlorethamine at a C–C Mismatch in Duplex DNA for Discrimination of a Disease-Relevant Single Nucleotide Polymorphism. Bioconjug Chem 2018; 29:3810-3816. [DOI: 10.1021/acs.bioconjchem.8b00663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ruicheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | | | - Xinyue Zhang
- 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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20
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Tan CS, Fleming AM, Ren H, Burrows CJ, White HS. γ-Hemolysin Nanopore Is Sensitive to Guanine-to-Inosine Substitutions in Double-Stranded DNA at the Single-Molecule Level. J Am Chem Soc 2018; 140:14224-14234. [PMID: 30269492 DOI: 10.1021/jacs.8b08153] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biological nanopores provide a unique single-molecule sensing platform to detect target molecules based on their specific electrical signatures. The γ-hemolysin (γ-HL) protein produced by Staphylococcus aureus is able to assemble into an octamer nanopore with a ∼2.3 nm diameter β-barrel. Herein, we demonstrate the first application of γ-HL nanopore for DNA structural analysis. To optimize conditions for ion-channel recording, the properties of the γ-HL pore (e.g., conductance, voltage-dependent gating, and ion-selectivity) were characterized at different pH, temperature, and electrolyte concentrations. The optimal condition for DNA analysis using γ-HL corresponds to 3 M KCl, pH 5, and T = 20 °C. The γ-HL protein nanopore is able to translocate dsDNA at about ∼20 bp/ms, and the unique current-signature of captured dsDNA can directly distinguish guanine-to-inosine substitutions at the single-molecule level with ∼99% accuracy. The slow dsDNA threading and translocation processes indicate this wild-type γ-HL channel has potential to detect other base modifications in dsDNA.
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Affiliation(s)
- Cherie S Tan
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
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21
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Johnson RP, Perera RT, Fleming AM, Burrows CJ, White HS. Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin. Faraday Discuss 2018; 193:471-485. [PMID: 27711888 DOI: 10.1039/c6fd00058d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the α-hemolysin (αHL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180°. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix. Here, temperature dependent ion channel recordings of individual double-stranded DNA duplexes inside αHL are used to derive thermodynamic (ΔH, ΔS) and kinetic (EA) parameters for base flipping of a cytosine at an unstable cytosine-cytosine mismatch site. The measured activation energy for flipping a cytosine located at the latch of αHL out of the helix (18 ± 1 kcal mol-1) is comparable to that previously reported for base flipping at mismatch sites from NMR measurements and potential mean force calculations. We propose that the αHL nanopore is a useful tool for measuring conformational changes in dsDNA at the single molecule level.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Rukshan T Perera
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Henry S White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
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22
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Robinson DA, Edwards MA, Ren H, White HS. Effects of Instrumental Filters on Electrochemical Measurement of Single‐Nanoparticle Collision Dynamics. ChemElectroChem 2018. [DOI: 10.1002/celc.201800696] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Donald A. Robinson
- Department of Chemistry University of Utah, Salt Lake City Utah 84112 United States
| | - Martin A. Edwards
- Department of Chemistry University of Utah, Salt Lake City Utah 84112 United States
| | - Hang Ren
- Department of Chemistry University of Utah, Salt Lake City Utah 84112 United States
| | - Henry S. White
- Department of Chemistry University of Utah, Salt Lake City Utah 84112 United States
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23
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Zhang F, Ma J, Sun Y, Mei Y, Chen X, Wang W, Li H. Construction of a Switchable Nanochannel for Protein Transport via a Pillar[5]arene-Based Host–Guest System. Anal Chem 2018; 90:8270-8275. [DOI: 10.1021/acs.analchem.8b01948] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fan Zhang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Junkai Ma
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Yue Sun
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Yuxiao Mei
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Xue Chen
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Wenqian Wang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
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24
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Ren H, Cheyne CG, Fleming AM, Burrows CJ, White HS. Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA. J Am Chem Soc 2018; 140:5153-5160. [PMID: 29562130 DOI: 10.1021/jacs.8b00593] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( kintra-extra) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( kextra-intra) remains unchanged. Both kintra-extra and kextra-intra are on the order of 1 × 10-2 s-1 to 1 × 10-1 s-1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H+ into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for kintra-extra ( kH/ kD ≈ 5) but a limited KIE for kextra-intra ( kH/ kD ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.
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Affiliation(s)
- Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cameron G Cheyne
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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25
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Huang G, Willems K, Soskine M, Wloka C, Maglia G. Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores. Nat Commun 2017; 8:935. [PMID: 29038539 PMCID: PMC5715100 DOI: 10.1038/s41467-017-01006-4] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
Biological nanopores are nanoscale sensors employed for high-throughput, low-cost, and long read-length DNA sequencing applications. The analysis and sequencing of proteins, however, is complicated by their folded structure and non-uniform charge. Here we show that an electro-osmotic flow through Fragaceatoxin C (FraC) nanopores can be engineered to allow the entry of polypeptides at a fixed potential regardless of the charge composition of the polypeptide. We further use the nanopore currents to discriminate peptide and protein biomarkers from 25 kDa down to 1.2 kDa including polypeptides differing by one amino acid. On the road to nanopore proteomics, our findings represent a rationale for amino-acid analysis of folded and unfolded polypeptides with nanopores. Biological nanopore–based protein sequencing and recognition is challenging due to the folded structure or non-uniform charge of peptides. Here the authors show that engineered FraC nanopores can overcome these problems and recognize biomarkers in the form of oligopeptides, polypeptides and folded proteins.
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Affiliation(s)
- Gang Huang
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Kherim Willems
- KU Leuven Department of Chemistry, Celestijnenlaan 200G, 3001, Leuven, Belgium.,Imec, Kapeldreef 75, 3001, Leuven, Belgium
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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26
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Wloka C, Van Meervelt V, van Gelder D, Danda N, Jager N, Williams CP, Maglia G. Label-Free and Real-Time Detection of Protein Ubiquitination with a Biological Nanopore. ACS NANO 2017; 11:4387-4394. [PMID: 28353339 PMCID: PMC5444049 DOI: 10.1021/acsnano.6b07760] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/17/2017] [Indexed: 05/18/2023]
Abstract
The covalent addition of ubiquitin to target proteins is a key post-translational modification that is linked to a myriad of biological processes. Here, we report a fast, single-molecule, and label-free method to probe the ubiquitination of proteins employing an engineered Cytolysin A (ClyA) nanopore. We show that ionic currents can be used to recognize mono- and polyubiquitinated forms of native proteins under physiological conditions. Using defined conjugates, we also show that isomeric monoubiquitinated proteins can be discriminated. The nanopore approach allows following the ubiquitination reaction in real time, which will accelerate the understanding of fundamental mechanisms linked to protein ubiquitination.
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Affiliation(s)
- Carsten Wloka
- Chemical
Biology I, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Dewi van Gelder
- Molecular
Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Natasha Danda
- Molecular
Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Nienke Jager
- Chemical
Biology I, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Chris P. Williams
- Molecular
Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
- E-mail:
| | - Giovanni Maglia
- Chemical
Biology I, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
- E-mail:
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27
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Peng R, Li D. Detection and sizing of nanoparticles and DNA on PDMS nanofluidic chips based on differential resistive pulse sensing. NANOSCALE 2017; 9:5964-5974. [PMID: 28440838 DOI: 10.1039/c7nr00488e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The RPS (Resistive Pulse Sensing) technique is a popular tool for the label-free detection of particles. This paper describes a simple, cost-effective PDMS nanofluidic chip for the detection and characterization of nanoparticles based on the differential RPS technique with high resolution and sensitivity. The chip is composed of two layers of PDMS slabs. Microchannel systems fabricated by the photolithography method on the top layer are used for sample loading and differential signal acquisition, and a straight nanochannel on the bottom layer fabricated by an unconventional approach bridging the gap between the microchannels works as an RPS sensing gate. A single-stage differential amplifier is used to amplify the RPS signals when particles or DNA pass through the sensing gate. It was demonstrated that this nanofluidic RPS chip can detect nanoparticles as small as 23 nm with a high SNR (Signal-to-Noise Ratio). The experimental results also show that the device is able to distinguish nanoparticles of smaller size differences such as 60 nm and 83 nm with high resolution, showing superior performance in comparison with the results obtained from DLS (Dynamic Light Scattering). This differential nano-RPS chip was also applied to detect the translocation of dsDNA molecules.
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Affiliation(s)
- Ran Peng
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, Ontario, CanadaN2L 3G1.
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28
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Lin X, Ivanov AP, Edel JB. Selective single molecule nanopore sensing of proteins using DNA aptamer-functionalised gold nanoparticles. Chem Sci 2017; 8:3905-3912. [PMID: 28626560 PMCID: PMC5465561 DOI: 10.1039/c7sc00415j] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/14/2017] [Indexed: 01/26/2023] Open
Abstract
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor. We show that this approach offers numerous advantages including: high levels of selectivity, efficient capture from a complex mixture, enhanced signal, minimized analyte-sensor surface interactions, and finally can be used to enhance the event detection rate. This is demonstrated by incorporating a lysozyme binding aptamer to a 5 nm AuNP carrier to selectively probe lysozyme within a cocktail of proteins. We show that nanopores can reveal sub-complex molecular information, by discriminating the AuNP from the protein analyte, indicating the potential use of this technology for single molecule analysis of different molecular analytes specifically bound to AuNP.
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Affiliation(s)
- Xiaoyan Lin
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Aleksandar P Ivanov
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
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29
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Abstract
Ubiquitous conserved processes that repair DNA damage are essential for the maintenance and propagation of genomes over generations. Then again, inaccuracies in DNA transactions and failures to remove mutagenic lesions cause heritable genome changes. Building on decades of research using genetics and biochemistry, unprecedented quantitative insight into DNA repair mechanisms has come from the new-found ability to measure single proteins in vitro and inside individual living cells. This has brought together biologists, chemists, engineers, physicists, and mathematicians to solve long-standing questions about the way in which repair enzymes search for DNA lesions and form protein complexes that act in DNA repair pathways. Furthermore, unexpected discoveries have resulted from capabilities to resolve molecular heterogeneity and cell subpopulations, provoking new questions about the role of stochastic processes in DNA repair and mutagenesis. These studies are leading to new technologies that will find widespread use in basic research, biotechnology, and medicine.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; ,
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30
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Zeng T, Fleming AM, Ding Y, White HS, Burrows CJ. Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the α-Hemolysin Latch. Biochemistry 2017; 56:1596-1603. [PMID: 28230976 DOI: 10.1021/acs.biochem.6b01175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spiroiminodihydantoin (Sp) is a hyperoxidized form of guanine (G) resulting from oxidation by reactive oxygen species. The lesion is highly mutagenic, and the stereocenter renders the two isomers with distinct behaviors in chemical, spectroscopic, enzymatic, and computational studies. In this work, the α-hemolysin (αHL) latch sensing zone was employed to investigate the base pairing properties of the Sp diastereomers embedded in a double-stranded DNA. Duplexes containing (S)-Sp consistently gave deeper current blockage, and a baseline resolution of ∼0.8 pA was achieved between (S)-Sp:G and (R)-Sp:G base pairs. Ion fluxes were generally more hindered when Sp was placed opposite pyrimidines. Analysis of the current noise of blockade events further provided dynamics information about the Sp-containing base pairs. In general, base pairs comprised of (S)-Sp generated current fluctuations larger than those of their (R)-Sp counterparts, suggesting enhanced base pairing dynamics. The current noise was also substantially affected by the identity of the base opposite Sp, increasing in the following order: A < G < T < C. This report provides information about the dynamic structure of Sp in the DNA duplex and therefore has implications for the enzymatic repair of the Sp diastereomers.
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Affiliation(s)
- Tao Zeng
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Yun Ding
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Henry S White
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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31
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Johnson RP, Fleming AM, Perera RT, Burrows CJ, White HS. Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine. J Am Chem Soc 2017; 139:2750-2756. [PMID: 28125225 DOI: 10.1021/jacs.6b12284] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The identification and discrimination of four epigenetic modifications to cytosine in the proposed active demethylation cycle is demonstrated at the single-molecule level, without the need for chemical pretreatment or labeling. The wild-type protein nanopore α-hemolysin is used to capture individual DNA duplexes containing a single cytosine-cytosine mismatch. The mismatch is held at the latch constriction of α-hemolysin, which is used to monitor the kinetics of base-flipping at the mismatch site. Base-flipping and the subsequent interactions between the DNA and the protein are dramatically altered when one of the cytosine bases is replaced with methyl-, hydroxymethyl-, formyl-, or carboxylcytosine. As well as providing a route to single-molecule analysis of important epigenetic markers in DNA, our results provide important insights into how the introduction of biologically relevant, but poorly understood, modifications to cytosine affect the local conformational dynamics of a DNA duplex in a confined environment.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Rukshan T Perera
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Henry S White
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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32
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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33
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Zhang JH, Liu XL, Hu ZL, Ying YL, Long YT. Intelligent identification of multi-level nanopore signatures for accurate detection of cancer biomarkers. Chem Commun (Camb) 2017; 53:10176-10179. [DOI: 10.1039/c7cc04745b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We combined a modified DBSCAN algorithm with the Hidden Markov Model (HMM) for the intelligent recognition of multi-level current blockage events from the measured nanopore data of serum samples.
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Affiliation(s)
- Jian-Hua Zhang
- School of Information Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Xiu-Ling Liu
- School of Information Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Zheng-Li Hu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
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34
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Tan CS, Riedl J, Fleming AM, Burrows CJ, White HS. Kinetics of T3-DNA Ligase-Catalyzed Phosphodiester Bond Formation Measured Using the α-Hemolysin Nanopore. ACS NANO 2016; 10:11127-11135. [PMID: 28024377 PMCID: PMC5302010 DOI: 10.1021/acsnano.6b05995] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The latch region of the wild-type α-hemolysin (α-HL) protein channel can be used to distinguish single base modifications in double-stranded DNA (dsDNA) via ion channel measurements upon electrophoretic capture of dsDNA in the vestibule of α-HL. Herein, we investigated the use of the latch region to detect a nick in the phosphodiester DNA backbone. The presence of a nick in the phosphodiester backbone of one strand of the duplex results in a significant increase in both the blockade current and noise level relative to the intact duplex. Differentiation between the nicked and intact duplexes based on blockade current or noise, with near baseline resolution, allows real-time monitoring of the rate of T3-DNA ligase-catalyzed phosphodiester bond formation. Under low ionic strength conditions containing divalent cations and a molecular crowding agent (75 mg mL-1 PEG), the rate of enzyme-catalyzed reaction in the bulk solution was continuously monitored by electrophoretically capturing reaction substrate or product dsDNA in the α-HL protein channel vestibule. Enzyme kinetic results obtained from the nanopore experiments match those from gel electrophoresis under the same reaction conditions, indicating the α-HL nanopore measurement provides a viable approach for monitoring enzymatic DNA repair activity.
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Affiliation(s)
- Toshihisa Osaki
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
| | - Shoji Takeuchi
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
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Koo H, Park I, Lee Y, Kim HJ, Jung JH, Lee JH, Kim Y, Kim JH, Park JW. Visualization and Quantification of MicroRNA in a Single Cell Using Atomic Force Microscopy. J Am Chem Soc 2016; 138:11664-71. [PMID: 27529574 DOI: 10.1021/jacs.6b05048] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) play critical roles in controlling various cellular processes, and the expression levels of individual miRNAs can be considerably altered in pathological conditions such as cancer. Accurate quantification of miRNA at the single-cell level will lead to a better understanding of miRNA function. Here, we present a direct and sensitive method for miRNA detection using atomic force microscopy (AFM). A hybrid binding domain (HBD)-tethered tip enabled mature miRNAs, but not premature miRNAs, to be located individually on an adhesion force map. By scanning several sections of a micrometer-sized DNA spot, we were able to quantify the copy number of miR-134 in a single neuron and demonstrate that the expression was increased upon cell activation. Moreover, we visualized individual miR-134s on fixed neurons after membrane removal and observed 2-4 miR-134s in the area of 1.0 × 1.0 μm(2) of soma. The number increased to 8-14 in stimulated neurons, and this change matches the ensemble-averaged increase in copy number. These findings indicate that miRNAs can be reliably quantified at the single cell level with AFM and that their distribution can be mapped at nanometric lateral resolution without modification or amplification. Furthermore, the analysis of miRNAs, mRNAs, and proteins in the same sample or region by scanning sequentially with different AFM tips would let us accurately understand the post-transcriptional regulation of biological processes.
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Affiliation(s)
- Hyunseo Koo
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ikbum Park
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Yoonhee Lee
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Hyun Jin Kim
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Jung Hoon Jung
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joo Han Lee
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Youngkyu Kim
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joung-Hun Kim
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joon Won Park
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
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Petrosko SH, Johnson R, White H, Mirkin CA. Nanoreactors: Small Spaces, Big Implications in Chemistry. J Am Chem Soc 2016; 138:7443-5. [DOI: 10.1021/jacs.6b05393] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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