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Taylor JN, Pirchi M, Haran G, Komatsuzaki T. Deciphering hierarchical features in the energy landscape of adenylate kinase folding/unfolding. J Chem Phys 2018; 148:123325. [DOI: 10.1063/1.5016487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. Nicholas Taylor
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020, Japan
| | | | - Gilad Haran
- Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 001-0020, Japan
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2
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Tavakoli M, Taylor JN, Li CB, Komatsuzaki T, Pressé S. Single Molecule Data Analysis: An Introduction. ADVANCES IN CHEMICAL PHYSICS 2017. [DOI: 10.1002/9781119324560.ch4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meysam Tavakoli
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - J. Nicholas Taylor
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Chun-Biu Li
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
- Department of Mathematics; Stockholm University; 106 91 Stockholm Sweden
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Steve Pressé
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Cell and Integrative Physiology; Indiana University School of Medicine; Indianapolis IN 46202 USA
- Department of Physics and School of Molecular Sciences; Arizona State University; Tempe AZ 85287 USA
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3
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Kobayashi S, Fujii S, Koga A, Wakai S, Matubayasi N, Sambongi Y. Pseudomonas aeruginosa cytochrome c551 denaturation by five systematic urea derivatives that differ in the alkyl chain length. Biosci Biotechnol Biochem 2017; 81:1274-1278. [DOI: 10.1080/09168451.2017.1303361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Abstract
Reversible denaturation of Pseudomonas aeruginosa cytochrome c551 (PAc551) could be followed using five systematic urea derivatives that differ in the alkyl chain length, i.e. urea, N-methylurea (MU), N-ethylurea (EU), N-propylurea (PU), and N-butylurea (BU). The BU concentration was the lowest required for the PAc551 denaturation, those of PU, EU, MU, and urea being gradually higher. Furthermore, the accessible surface area difference upon PAc551 denaturation caused by BU was found to be the highest, those by PU, EU, MU, and urea being gradually lower. These findings indicate that urea derivatives with longer alkyl chains are stronger denaturants. In this study, as many as five systematic urea derivatives could be applied for the reversible denaturation of a single protein, PAc551, for the first time, and the effects of the alkyl chain length on protein denaturation were systematically verified by means of thermodynamic parameters.
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Affiliation(s)
- Shinya Kobayashi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Aya Koga
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Satoshi Wakai
- Graduate School of Science Technology and Innovation, Kobe University, Kobe, Japan
| | - Nobuyuki Matubayasi
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto, Japan
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
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Galievsky VA, Stasheuski AS, Krylov SN. "Getting the best sensitivity from on-capillary fluorescence detection in capillary electrophoresis" - A tutorial. Anal Chim Acta 2016; 935:58-81. [PMID: 27543015 DOI: 10.1016/j.aca.2016.06.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/09/2016] [Accepted: 06/11/2016] [Indexed: 01/09/2023]
Abstract
Capillary electrophoresis with Laser-Induced Fluorescence (CE-LIF) detection is being applied to new analytical problems which challenge both the power of CE separation and the sensitivity of LIF detection. On-capillary LIF detection is much more practical than post-capillary detection in a sheath-flow cell. Therefore, commercial CE instruments utilize solely on-capillary CE-LIF detection with a Limit of Detection (LOD) in the nM range, while there are multiple applications of CE-LIF that require pM or lower LODs. This tutorial analyzes all aspects of on-capillary LIF detection in CE in an attempt to identify means for improving LOD of CE-LIF with on-capillary detection. We consider principles of signal enhancement and noise reduction, as well as relevant areas of fluorophore photochemistry and fluorescent microscopy.
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Affiliation(s)
- Victor A Galievsky
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Alexander S Stasheuski
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
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Banterle N, Lemke EA. Nanoscale devices for linkerless long-term single-molecule observation. Curr Opin Biotechnol 2016; 39:105-112. [PMID: 26990172 PMCID: PMC7611743 DOI: 10.1016/j.copbio.2016.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 01/07/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) can offer favorably high signal-to-noise observation of biological mechanisms. TIRFM can be used routinely to observe even single fluorescent molecules for a long duration (several seconds) at millisecond time resolution. However, to keep the investigated sample in the evanescent field, chemical surface immobilization techniques typically need to be implemented. In this review, we describe some of the recently developed novel nanodevices that overcome this limitation enabling long-term observation of free single molecules and outline their biological applications. The working concept of many devices is compatible with high-throughput strategies, which will further help to establish unbiased single molecule observation as a routine tool in biology to study the molecular underpinnings of even the most complex biological mechanisms.
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Affiliation(s)
- Niccolò Banterle
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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6
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Oikawa H, Kamagata K, Arai M, Takahashi S. Complexity of the folding transition of the B domain of protein A revealed by the high-speed tracking of single-molecule fluorescence time series. J Phys Chem B 2015; 119:6081-91. [PMID: 25938341 DOI: 10.1021/acs.jpcb.5b00414] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The equilibrium unfolding transition of the B domain of protein A (BdpA) was investigated by using single-molecule fluorescence spectroscopy based on line-confocal detection of fast-flowing samples. The method achieved the time resolution of 120 μs and the observation time of a few milliseconds in the single-molecule time-series measurements of fluorescence resonance energy transfer (FRET). Two samples of BdpA doubly labeled with donor and acceptor fluorophores, the first possessing fluorophores at residues 22 and 55 (sample 1) and the second at residues 5 and 55 (sample 2), were prepared. The equilibrium unfolding transition induced by guanidium chloride (GdmCl) was monitored by bulk measurements and demonstrated that the both samples obey the apparent two-state unfolding. In the absence of GdmCl, the single-molecule FRET measurements for the both samples showed a single peak assignable to the native state (N). The FRET efficiency for N shifts to lower values as the increase of GdmCl concentration, suggesting the swelling of the native state structure. At the higher concentration of GdmCl, the both samples convert to the unfolded state (U). Near the unfolding midpoint for sample 1, the kinetic exchange between N and U causes the averaging of the two states and the higher values of the relative fluctuation. The time series for different molecules in U showed slightly different FRET efficiencies, suggesting the apparent heterogeneity. Thus, the high-speed tracking of fluorescence signals from single molecules revealed a complexity and heterogeneity hidden in the apparent two-state behavior of protein folding.
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Affiliation(s)
- Hiroyuki Oikawa
- †Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan
| | - Kiyoto Kamagata
- †Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan
| | - Munehito Arai
- ‡Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.,§PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Satoshi Takahashi
- †Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan
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Kim JY, Kim C, Lee NK. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering. Nat Commun 2015; 6:6992. [PMID: 25908552 PMCID: PMC4421855 DOI: 10.1038/ncomms7992] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 03/23/2015] [Indexed: 01/15/2023] Open
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s–1 between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution. Single-molecule fluorescence resonance energy transfer is widely used to probe biomolecular dynamics, but is limited by its temporal resolution. Here, Kim et al. push the limit to submillisecond for the duration of tens of milliseconds by tethering target molecules to liposomes in buffer solutions.
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Affiliation(s)
- Jae-Yeol Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Nam Ki Lee
- 1] Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea [2] School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, Korea
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Taylor JN, Li CB, Cooper DR, Landes CF, Komatsuzaki T. Error-based extraction of states and energy landscapes from experimental single-molecule time-series. Sci Rep 2015; 5:9174. [PMID: 25779909 PMCID: PMC4361849 DOI: 10.1038/srep09174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/20/2015] [Indexed: 12/21/2022] Open
Abstract
Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.
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Affiliation(s)
- J Nicholas Taylor
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020 Japan
| | - Chun-Biu Li
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020 Japan
| | - David R Cooper
- Department of Chemistry, Rice University, P.O. Box 1892, Houston. TX 77005
| | - Christy F Landes
- Department of Chemistry, Rice University, P.O. Box 1892, Houston. TX 77005
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020 Japan
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Yamanaka M, Nagao S, Komori H, Higuchi Y, Hirota S. Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping. Protein Sci 2015; 24:366-75. [PMID: 25586341 DOI: 10.1002/pro.2627] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 01/20/2023]
Abstract
Cytochrome c555 from hyperthermophilic bacteria Aquifex aeolicus (AA cyt c555 ) is a hyperstable protein belonging to the cyt c protein family, which possesses a unique long 310 -α-310 helix containing the heme-ligating Met61. Herein, we show that AA cyt c555 forms dimers by swapping the region containing the extra 310 -α-310 helix and C-terminal α-helix. The asymmetric unit of the crystal of dimeric AA cyt c555 contained two dimer structures, where the structure of the hinge region (Val53-Lys57) was different among all four protomers. Dimeric AA cyt c555 dissociated to monomers at 92 ± 1°C according to DSC measurements, showing that the dimer was thermostable. According to CD measurements, the secondary structures of dimeric AA cyt c555 were maintained at pH 2.2-11.0. CN(-) and CO bound to dimeric AA cyt c555 in the ferric and ferrous states, respectively, owing to the flexibility of the hinge region close to Met61 in the dimer, whereas these ligands did not bind to the monomer under the same conditions. In addition, CN(-) and CO bound to the oxidized and reduced dimer at neutral pH and a wide range of pH (pH 2.2-11.0), respectively, in a wide range of temperature (25-85°C), owing to the thermostability and pH tolerance of the dimer. These results show that the ligand binding character of hyperstable AA cyt c555 changes upon dimerization by domain swapping.
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Affiliation(s)
- Masaru Yamanaka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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Sultana T, Takagi H, Morimatsu M, Teramoto H, Li CB, Sako Y, Komatsuzaki T. Non-Markovian properties and multiscale hidden Markovian network buried in single molecule time series. J Chem Phys 2013; 139:245101. [DOI: 10.1063/1.4848719] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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12
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Oikawa H, Suzuki Y, Saito M, Kamagata K, Arai M, Takahashi S. Microsecond dynamics of an unfolded protein by a line confocal tracking of single molecule fluorescence. Sci Rep 2013; 3:2151. [PMID: 23827883 PMCID: PMC3701896 DOI: 10.1038/srep02151] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 06/20/2013] [Indexed: 02/03/2023] Open
Abstract
We present a new method for high speed tracking of fluorescence time series from single proteins. The method uses a fast sample flow and a modified confocal microscopy, line confocal microscopy, and achieves the time resolution of less than 20 μs. The obtained time series from the B domain of protein A labeled with donor and acceptor fluorophores suggest conformational heterogeneity and dynamic fluctuations in the unfolded state.
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Affiliation(s)
- Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan
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Pompidor G, Dworkowski FSN, Thominet V, Schulze-Briese C, Fuchs MR. A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:765-76. [PMID: 23955041 PMCID: PMC3747950 DOI: 10.1107/s0909049513016063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/10/2013] [Indexed: 05/08/2023]
Abstract
The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years.
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Affiliation(s)
| | | | | | | | - Martin R. Fuchs
- Paul Scherrer Institut, CH-5232 Villigen, Switzerland
- Correspondence e-mail:
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Schuler B, Hofmann H. Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales. Curr Opin Struct Biol 2013; 23:36-47. [DOI: 10.1016/j.sbi.2012.10.008] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
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Affiliation(s)
- Min Ju Shon
- Department of Chemistry
and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138,
United States
| | - Adam E. Cohen
- Department of Chemistry
and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138,
United States
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