1
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Ahmed M, Wang C, Zhao Y, Sathish CI, Lei Z, Qiao L, Sun C, Wang S, Kennedy JV, Vinu A, Yi J. Bridging Together Theoretical and Experimental Perspectives in Single-Atom Alloys for Electrochemical Ammonia Production. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2308084. [PMID: 38243883 DOI: 10.1002/smll.202308084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/26/2023] [Indexed: 01/22/2024]
Abstract
Ammonia is an essential commodity in the food and chemical industry. Despite the energy-intensive nature, the Haber-Bosch process is the only player in ammonia production at large scales. Developing other strategies is highly desirable, as sustainable and decentralized ammonia production is crucial. Electrochemical ammonia production by directly reducing nitrogen and nitrogen-based moieties powered by renewable energy sources holds great potential. However, low ammonia production and selectivity rates hamper its utilization as a large-scale ammonia production process. Creating effective and selective catalysts for the electrochemical generation of ammonia is critical for long-term nitrogen fixation. Single-atom alloys (SAAs) have become a new class of materials with distinctive features that may be able to solve some of the problems with conventional heterogeneous catalysts. The design and optimization of SAAs for electrochemical ammonia generation have recently been significantly advanced. This comprehensive review discusses these advancements from theoretical and experimental research perspectives, offering a fundamental understanding of the development of SAAs for ammonia production.
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Affiliation(s)
- MuhammadIbrar Ahmed
- Global Innovative Center of Advanced Nanomaterials, School of Engineering, College of Engineering, Science, and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Cheng Wang
- CSIRO Energy Centre, 10 Murray Dwyer Circuit, Mayfield West, NSW, 2304, Australia
| | - Yong Zhao
- CSIRO Energy Centre, 10 Murray Dwyer Circuit, Mayfield West, NSW, 2304, Australia
| | - C I Sathish
- Global Innovative Center of Advanced Nanomaterials, School of Engineering, College of Engineering, Science, and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Zhihao Lei
- Global Innovative Center of Advanced Nanomaterials, School of Engineering, College of Engineering, Science, and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Liang Qiao
- University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chenghua Sun
- Centre for Translational Atomaterials, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, 3122, Australia
| | - Shaobin Wang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - John V Kennedy
- National Isotope Centre, GNS Science, P.O. Box 31312, Lower Hutt, 5010, New Zealand
| | - Ajayan Vinu
- Global Innovative Center of Advanced Nanomaterials, School of Engineering, College of Engineering, Science, and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Jiabao Yi
- Global Innovative Center of Advanced Nanomaterials, School of Engineering, College of Engineering, Science, and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
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2
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Single-Molecule Surface-Enhanced Raman Spectroscopy. SENSORS 2022; 22:s22134889. [PMID: 35808385 PMCID: PMC9269420 DOI: 10.3390/s22134889] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 12/04/2022]
Abstract
Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) has the potential to detect single molecules in a non-invasive, label-free manner with high-throughput. SM-SERS can detect chemical information of single molecules without statistical averaging and has wide application in chemical analysis, nanoelectronics, biochemical sensing, etc. Recently, a series of unprecedented advances have been realized in science and application by SM-SERS, which has attracted the interest of various fields. In this review, we first elucidate the key concepts of SM-SERS, including enhancement factor (EF), spectral fluctuation, and experimental evidence of single-molecule events. Next, we systematically discuss advanced implementations of SM-SERS, including substrates with ultra-high EF and reproducibility, strategies to improve the probability of molecules being localized in hotspots, and nonmetallic and hybrid substrates. Then, several examples for the application of SM-SERS are proposed, including catalysis, nanoelectronics, and sensing. Finally, we summarize the challenges and future of SM-SERS. We hope this literature review will inspire the interest of researchers in more fields.
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3
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Pandey P, Bhattarai N, Su L, Wang X, Leng F, Gerst-man B, Chapagain PP, He J. Detecting Individual Proteins and Their Surface Charge Variations in Solution by the Potentiometric Nanoimpact Method. ACS Sens 2022; 7:555-563. [PMID: 35060380 PMCID: PMC10631516 DOI: 10.1021/acssensors.1c02385] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Label-free detection and analysis of proteins in their natural form and their dynamic interactions with substrates at the single-molecule level are important for both fundamental studies and various applications. Herein, we demonstrate a simple potentiometric method to achieve this goal by detecting the native charge of protein in solution by utilizing the principle of single-entity electrochemistry techniques. When a charged protein moves near the vicinity of a floating carbon nanoelectrode connected to a high-impedance voltage meter, the distinct local electrostatic potential changes induced by the transient collision event of protein, also called the "nanoimpact" event, can be captured by the nanoelectrode as a potential probe. This potentiometric method is highly sensitive for charged proteins, and low-molecular-weight proteins less than 10 kDa can be detected in low-salt-concentration electrolytes. By analyzing the shape and magnitude of the recorded time-resolved potential change and its time derivative, we can reveal the charge and motion of the protein in the nonspecific protein-surface interaction event. The charge polarity variations of the proteins at different pH values were also successfully probed. Compared with synthetic spherical nanoparticles, the statistical analysis of many single-molecule nanoimpact events revealed a large variation in the recorded transient potential signals, which may be attributed to the intrinsic protein dynamics and surface charge heterogeneity, as suggested by the finite element method and molecular dynamic simulations.
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Affiliation(s)
- Popular Pandey
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Nisha Bhattarai
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Linjia Su
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, USA
| | - Xuewen Wang
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, USA
| | - Bernard Gerst-man
- Physics Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, USA
| | - Prem P. Chapagain
- Physics Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, USA
| | - Jin He
- Physics Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, USA
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4
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Tapio K, Mostafa A, Kanehira Y, Suma A, Dutta A, Bald I. A Versatile DNA Origami-Based Plasmonic Nanoantenna for Label-Free Single-Molecule Surface-Enhanced Raman Spectroscopy. ACS NANO 2021; 15:7065-7077. [PMID: 33872513 PMCID: PMC8155336 DOI: 10.1021/acsnano.1c00188] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA origami technology allows for the precise nanoscale assembly of chemical entities that give rise to sophisticated functional materials. We have created a versatile DNA origami nanofork antenna (DONA) by assembling Au or Ag nanoparticle dimers with different gap sizes down to 1.17 nm, enabling signal enhancements in surface-enhanced Raman scattering (SERS) of up to 1011. This allows for single-molecule SERS measurements, which can even be performed with larger gap sizes to accommodate differently sized molecules, at various excitation wavelengths. A general scheme is presented to place single analyte molecules into the SERS hot spots using the DNA origami structure exploiting covalent and noncovalent coupling schemes. By using Au and Ag dimers, single-molecule SERS measurements of three dyes and cytochrome c and horseradish peroxidase proteins are demonstrated even under nonresonant excitation conditions, thus providing long photostability during time-series measurement and enabling optical monitoring of single molecules.
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Affiliation(s)
- Kosti Tapio
- Institute
of Chemistry, University of Potsdam, Potsdam DE-14476, Germany
| | - Amr Mostafa
- Institute
of Chemistry, University of Potsdam, Potsdam DE-14476, Germany
| | - Yuya Kanehira
- Institute
of Chemistry, University of Potsdam, Potsdam DE-14476, Germany
| | - Antonio Suma
- Institute
for Computational Molecular Science, Temple
University, Philadelphia, Pennsylvania19122, United States
- Dipartimento
di Fisica, Università di Bari and
Sezione INFN di Bari, 70126 Bari, Italy
| | - Anushree Dutta
- Institute
of Chemistry, University of Potsdam, Potsdam DE-14476, Germany
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Potsdam DE-14476, Germany
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5
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Li L, Mahapatra S, Liu D, Lu Z, Jiang N. On-Surface Synthesis and Molecular Engineering of Carbon-Based Nanoarchitectures. ACS NANO 2021; 15:3578-3585. [PMID: 33606498 DOI: 10.1021/acsnano.0c08148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
On-surface synthesis via covalent coupling of adsorbed precursor molecules on metal surfaces has emerged as a promising strategy for the design and fabrication of novel organic nanoarchitectures with unique properties and potential applications in nanoelectronics, optoelectronics, spintronics, catalysis, etc. Surface-chemistry-driven molecular engineering (i.e., bond cleavage, linkage, and rearrangement) by means of thermal activation, light irradiation, and tip manipulation plays critical roles in various on-surface synthetic processes, as exemplified by the work from the Ernst group in a prior issue of ACS Nano. In this Perspective, we highlight recent advances in and discuss the outlook for on-surface syntheses and molecular engineering of carbon-based nanoarchitectures.
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Affiliation(s)
- Linfei Li
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sayantan Mahapatra
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Dairong Liu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zhongyi Lu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Nan Jiang
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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6
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Palla M, Punthambaker S, Stranges B, Vigneault F, Nivala J, Wiegand D, Ayer A, Craig T, Gremyachinskiy D, Franklin H, Sun S, Pollard J, Trans A, Arnold C, Schwab C, Mcgaw C, Sarvabhowman P, Dalal D, Thai E, Amato E, Lederman I, Taing M, Kelley S, Qwan A, Fuller CW, Roever S, Church GM. Multiplex Single-Molecule Kinetics of Nanopore-Coupled Polymerases. ACS NANO 2021; 15:489-502. [PMID: 33370106 DOI: 10.1021/acsnano.0c05226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA polymerases have revolutionized the biotechnology field due to their ability to precisely replicate stored genetic information. Screening variants of these enzymes for specific properties gives the opportunity to identify polymerases with different features. We have previously developed a single-molecule DNA sequencing platform by coupling a DNA polymerase to an α-hemolysin pore on a nanopore array. Here, we use this approach to demonstrate a single-molecule method that enables rapid screening of polymerase variants in a multiplex manner. In this approach, barcoded DNA strands are complexed with polymerase variants and serve as templates for nanopore sequencing. Nanopore sequencing of the barcoded DNA reveals both the barcode identity and kinetic properties of the polymerase variant associated with the cognate barcode, allowing for multiplexed investigation of many polymerase variants in parallel on a single nanopore array. Further, we develop a robust classification algorithm that discriminates kinetic characteristics of the different polymerase mutants. As a proof of concept, we demonstrate the utility of our approach by screening a library of ∼100 polymerases to identify variants for potential applications of biotechnological interest. We anticipate our screening method to be broadly useful for applications that require polymerases with altered physical properties.
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Affiliation(s)
- Mirkó Palla
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Sukanya Punthambaker
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Benjamin Stranges
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
| | - Frederic Vigneault
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Jeff Nivala
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
| | - Daniel Wiegand
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Aruna Ayer
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Timothy Craig
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | | | - Helen Franklin
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Shaw Sun
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - James Pollard
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Andrew Trans
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Cleoma Arnold
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Charles Schwab
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Colin Mcgaw
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | | | - Dhruti Dalal
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Eileen Thai
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Evan Amato
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Ilya Lederman
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Meng Taing
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Sara Kelley
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Adam Qwan
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - Carl W Fuller
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
- Columbia University, Center for Genome Technology and Biomolecular Engineering, Department of Chemical Engineering, New York, New York 10027, United States
| | - Stefan Roever
- Roche Sequencing Solutions, Santa Clara, California 95050, United States
| | - George M Church
- Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
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7
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Casar JR, McLellan CA, Siefe C, Dionne JA. Lanthanide-Based Nanosensors: Refining Nanoparticle Responsiveness for Single Particle Imaging of Stimuli. ACS PHOTONICS 2021; 8:3-17. [PMID: 34307765 PMCID: PMC8297747 DOI: 10.1021/acsphotonics.0c00894] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lanthanide nanoparticles (LNPs) are promising sensors of chemical, mechanical, and temperature changes; they combine the narrow-spectral emission and long-lived excited states of individual lanthanide ions with the high spatial resolution and controlled energy transfer of nanocrystalline architectures. Despite considerable progress in optimizing LNP brightness and responsiveness for dynamic sensing, detection of stimuli with a spatial resolution approaching that of individual nanoparticles remains an outstanding challenge. Here, we highlight the existing capabilities and outstanding challenges of LNP sensors, en-route to nanometer-scale, single particle sensor resolution. First, we summarize LNP sensor read-outs, including changes in emission wavelength, lifetime, intensity, and spectral ratiometric values that arise from modified energy transfer networks within nanoparticles. Then, we describe the origins of LNP sensor imprecision, including sensitivity to competing conditions, interparticle heterogeneities, such as the concentration and distribution of dopant ions, and measurement noise. Motivated by these sources of signal variance, we describe synthesis characterization feedback loops to inform and improve sensor precision, and introduce noise-equivalent sensitivity as a figure of merit of LNP sensors. Finally, we project the magnitudes of chemical and pressure stimulus resolution achievable with single LNPs at nanoscale resolution. Our perspective provides a roadmap for translating ensemble LNP sensing capabilities to the single particle level, enabling nanometer-scale sensing in biology, medicine, and sustainability.
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Affiliation(s)
- Jason R Casar
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Claire A McLellan
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Chris Siefe
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Jennifer A Dionne
- Department of Materials Science and Engineering and Department of Radiology, Molecular Imaging Program, Stanford University, Stanford, California 94305, United States
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8
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Bi H, Lobet M, Saikin SK, Li Y, Huo C, Jian J, Wu X, Reichert J, Aspuru-Guzik A, Mazur E. Optically Induced Molecular Logic Operations. ACS NANO 2020; 14:15248-15255. [PMID: 33140948 DOI: 10.1021/acsnano.0c05513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular electronics is a promising route for down-sizing electronic devices. Tip-enhanced Raman spectroscopy provides us a setup to probe current-driven molecular junctions that are considered as prototypes of molecular electronic devices. In this setup, the plasmonic tip concentrates optical fields to a degree that allows observing optical response of single molecules. Simultaneously, the tip can also induce a localized optical angular momentum, which has been seldomly considered in previous studies. Here, we propose that the induced optical angular momentum can interact with the probed molecule and strongly modify the response signal. Specifically, we demonstrate the ability to control the vibrational resonance of current-driven molecular junctions with the optical angular momentum. This precise control of light-matter interactions at the nanoscale allows us to demonstrate multiple logic operations. These results provide a fundamental understanding of future molecular electronics applications.
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Affiliation(s)
- Hai Bi
- MIIT Key Laboratory of Critical Material Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
- School of Engineering and Applied Sciences, Harvard University, 9 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Michaël Lobet
- School of Engineering and Applied Sciences, Harvard University, 9 Oxford Street, Cambridge, Massachusetts 02138, United States
- Centre Spatial de Liège, Avenue du Pré-Aily, B-4031 Angleur, Belgium
| | - Semion K Saikin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Institute of Physics, Kazan Federal University, Kazan 420008, Russian Federation
- Kebotix, Inc., 501 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yang Li
- State Key Laboratory for Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Chanyuan Huo
- MIIT Key Laboratory of Critical Material Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jiahuang Jian
- MIIT Key Laboratory of Critical Material Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Xiaohong Wu
- MIIT Key Laboratory of Critical Material Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Joachim Reichert
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | - Alán Aspuru-Guzik
- Department of Chemistry and Department of Computer Sciences, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Eric Mazur
- School of Engineering and Applied Sciences, Harvard University, 9 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Physics, Harvard University, 9 Oxford Street, Cambridge, Massachusetts 02138, United States
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9
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Abstract
Cell surface proteins are known to assemble into nano- and microscale domains in order to govern biological processes, including cell adhesion, endocytosis, and immune responses. The small size and ephemerality of these structures have made their direct observation and functional analysis challenging. In this Perspective, I discuss recent progress made in applying nanotechniques to study protein clustering, emphasizing the use of state-of-the-art single-molecule atomic force microscopy, as reported by Strasser et al. in this issue of ACS Nano.
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Affiliation(s)
- Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Catholic University of Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
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10
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Single-molecule and -particle probing crystal edge/corner as highly efficient photocatalytic sites on a single TiO 2 particle. Proc Natl Acad Sci U S A 2019; 116:18827-18833. [PMID: 31484775 DOI: 10.1073/pnas.1907122116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The exposed active sites of semiconductor catalysts are essential to the photocatalytic energy conversion efficiency. However, it is difficult to directly observe such active sites and understand the photogenerated electron/hole pairs' dynamics on a single catalyst particle. Here, we applied a quasi-total internal reflection fluorescence microscopy and laser-scanning confocal microscopy to identify the photocatalytic active sites at a single-molecule level and visualized the photogenerated hole-electron pair dynamics on a single TiO2 particle, the most widely used photocatalyst. The experimental results and density functional theory calculations reveal that holes and electrons tend to reach and react at the same surface sites, i.e., crystal edge/corner, within a single anatase TiO2 particle owing to the highly exposed (001) and (101) facets. The observation provides solid proof for the existence of the surface junction "edge or corner" on single TiO2 particles. These findings also offer insights into the nature of the photocatalytic active sites and imply an activity-based strategy for rationally engineering catalysts for improved photocatalysis, which can be also applied for other catalytic materials.
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11
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Krmpot AJ, Nikolić SN, Oasa S, Papadopoulos DK, Vitali M, Oura M, Mikuni S, Thyberg P, Tisa S, Kinjo M, Nilsson L, Terenius L, Rigler R, Vukojević V. Functional Fluorescence Microscopy Imaging: Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells. Anal Chem 2019; 91:11129-11137. [PMID: 31364842 DOI: 10.1021/acs.analchem.9b01813] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Functional fluorescence microscopy imaging (fFMI), a time-resolved (21 μs/frame) confocal fluorescence microscopy imaging technique without scanning, is developed for quantitative characterization of fast reaction-transport processes in solution and in live cells. The method is based on massively parallel fluorescence correlation spectroscopy (FCS). Simultaneous excitation of fluorescent molecules in multiple spots in the focal plane is achieved using a diffractive optical element (DOE). Fluorescence from the DOE-generated 1024 illuminated spots is detected in a confocal arrangement by a matching matrix detector comprising 32 × 32 single-photon avalanche photodiodes (SPADs). Software for data acquisition and fast auto- and cross-correlation analysis by parallel signal processing using a graphic processing unit (GPU) allows temporal autocorrelation across all pixels in the image frame in 4 s and cross-correlation between first- and second-order neighbor pixels in 45 s. We present here this quantitative, time-resolved imaging method with single-molecule sensitivity and demonstrate its usefulness for mapping in live cell location-specific differences in the concentration and translational diffusion of molecules in different subcellular compartments. In particular, we show that molecules without a specific biological function, e.g., the enhanced green fluorescent protein (eGFP), exhibit uniform diffusion. In contrast, molecules that perform specialized biological functions and bind specifically to their molecular targets show location-specific differences in their concentration and diffusion, exemplified here for two transcription factor molecules, the glucocorticoid receptor (GR) before and after nuclear translocation and the Sex combs reduced (Scr) transcription factor in the salivary gland of Drosophila ex vivo.
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Affiliation(s)
- Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Institute of Physics Belgrade , University of Belgrade , Belgrade 11080 , Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Institute of Physics Belgrade , University of Belgrade , Belgrade 11080 , Serbia
| | - Sho Oasa
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
| | | | | | - Makoto Oura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Per Thyberg
- Department of Applied Physics , AlbaNova University Center, Royal Institute of Technology , Stockholm 10691 , Sweden
| | - Simone Tisa
- Micro Photon Devices (MPD) , Bolzano 39100 , Italy
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Lennart Nilsson
- Department of Biosciences and Nutrition , Karolinska Institutet , Huddinge 14183 , Sweden
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
| | - Rudolf Rigler
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Department of Medical Biochemistry and Biophysics (MBB) , Karolinska Institutet , Stockholm 17177 , Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
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12
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Goronzy DP, Ebrahimi M, Rosei F, Fang Y, De Feyter S, Tait SL, Wang C, Beton PH, Wee ATS, Weiss PS, Perepichka DF. Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity. ACS NANO 2018; 12:7445-7481. [PMID: 30010321 DOI: 10.1021/acsnano.8b03513] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.
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Affiliation(s)
- Dominic P Goronzy
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Maryam Ebrahimi
- INRS Centre for Energy, Materials and Telecommunications , 1650 Boul. Lionel Boulet , Varennes , Quebec J3X 1S2 , Canada
| | - Federico Rosei
- INRS Centre for Energy, Materials and Telecommunications , 1650 Boul. Lionel Boulet , Varennes , Quebec J3X 1S2 , Canada
- Institute for Fundamental and Frontier Science , University of Electronic Science and Technology of China , Chengdu 610054 , P.R. China
| | - Yuan Fang
- Department of Chemistry , McGill University , Montreal H3A 0B8 , Canada
| | - Steven De Feyter
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , Leuven 3001 , Belgium
| | - Steven L Tait
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Chen Wang
- National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Peter H Beton
- School of Physics & Astronomy , University of Nottingham , Nottingham NG7 2RD , United Kingdom
| | - Andrew T S Wee
- Department of Physics , National University of Singapore , 117542 Singapore
| | - Paul S Weiss
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Materials Science and Engineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Dmitrii F Perepichka
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry , McGill University , Montreal H3A 0B8 , Canada
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13
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Thomas JC, Goronzy DP, Serino AC, Auluck HS, Irving OR, Jimenez-Izal E, Deirmenjian JM, Macháček J, Sautet P, Alexandrova AN, Baše T, Weiss PS. Acid-Base Control of Valency within Carboranedithiol Self-Assembled Monolayers: Molecules Do the Can-Can. ACS NANO 2018; 12:2211-2221. [PMID: 29393628 PMCID: PMC6350814 DOI: 10.1021/acsnano.7b09011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We use simple acid-base chemistry to control the valency in self-assembled monolayers of two different carboranedithiol isomers on Au{111}. Monolayer formation proceeds via Au-S bonding, where manipulation of pH prior to or during deposition enables the assembly of dithiolate species, monothiol/monothiolate species, or combination. Scanning tunneling microscopy (STM) images identify two distinct binding modes in each unmodified monolayer, where simultaneous spectroscopic imaging confirms different dipole offsets for each binding mode. Density functional theory calculations and STM image simulations yield detailed understanding of molecular chemisorption modes and their relation with the STM images, including inverted contrast with respect to the geometric differences found for one isomer. Deposition conditions are modified with controlled equivalents of either acid or base, where the coordination of the molecules in the monolayers is controlled by protonating or deprotonating the second thiol/thiolate on each molecule. This control can be exercised during deposition to change the valency of the molecules in the monolayers, a process that we affectionately refer to as the "can-can." This control enables us to vary the density of molecule-substrate bonds by a factor of 2 without changing the molecular density of the monolayer.
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Affiliation(s)
- John C. Thomas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Dominic P. Goronzy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Andrew C. Serino
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Harsharn S. Auluck
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Olivia R. Irving
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Elisa Jimenez-Izal
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Kimika fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain
| | - Jacqueline M. Deirmenjian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Jan Macháček
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i. 250 68 Husinec-Řež, č.p. 1001, Czech Republic
| | - Philippe Sautet
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Tomáš Baše
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i. 250 68 Husinec-Řež, č.p. 1001, Czech Republic
| | - Paul S. Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
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14
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Keshavarz M, Tan B, Venkatakrishnan K. Multiplex Photoluminescent Silicon Nanoprobe for Diagnostic Bioimaging and Intracellular Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1700548. [PMID: 29593957 PMCID: PMC5867044 DOI: 10.1002/advs.201700548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/10/2017] [Indexed: 05/29/2023]
Abstract
Herein, a label-free multiplex photoluminescent silicon nanoprobe (PLSN-probe) is introduced as a potential substitute for quantum dots (QDs) in bioimaging. An inherently non-photoluminescent silicon substrate is altered to create the PLSN-probe, to overcome the major drawbacks of presently available QDs. Additionally, crystallinity alterations of the multiplane crystalline PLSN-probes lead to broad absorption and multiplex fluorescence emissions, which are attributed to the simultaneous existence of multiple crystal planes. The PLSN-probe not only demonstrates unique optical properties that can be exploited for bioimaging but also exhibits cell-selective uptake that allows the differentiation and diagnosis of HeLa and fibroblast cells. Moreover, multiplex emissions of the PLSN-probe illuminate different organelles such as the nucleus, nucleolemma, and cytoskeleton, depending on size-based preferential uptake by the cell organs. This in vitro study reveals that cancerous HeLa cells have a higher propensity for taking up the PLSN-probe compared to fibroblast cells, allowing the diagnosis of cancerous HeLa cells. Additionally, the fluorescence intensity per unit area of the cell is found to be a reliable means for distinguishing between dead and healthy cells. It is anticipated that the multifunctionality of the PLSN-probes will lead to better insight into the use of such probes for bioimaging and diagnosis applications.
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Affiliation(s)
- Meysam Keshavarz
- Nanocharacterization LaboratoryDepartment of Aerospace EngineeringRyerson University350 Victoria StreetTorontoONM5B 2K3Canada
- Institute for Biomedical EngineeringScience and Technology (iBEST)Partnership between Ryerson University and St. Michael's HospitalTorontoONM5B 1W8Canada
- Ultrashort Laser Nanomanufacturing Research FacilityDepartment of Mechanical and Industrial EngineeringRyerson University350 Victoria StreetTorontoONM5B 2K3Canada
- NanoBioInterface FacilityDepartment of Mechanical and Industrial EngineeringRyerson University350 Victoria StreetTorontoONM5B 2K3Canada
| | - Bo Tan
- Nanocharacterization LaboratoryDepartment of Aerospace EngineeringRyerson University350 Victoria StreetTorontoONM5B 2K3Canada
| | - Krishnan Venkatakrishnan
- Ultrashort Laser Nanomanufacturing Research FacilityDepartment of Mechanical and Industrial EngineeringRyerson University350 Victoria StreetTorontoONM5B 2K3Canada
- Keenan Research Centre for Biomedical ScienceSt. Michael's HospitalTorontoONM5B 1W8Canada
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15
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Harroun SG. The Controversial Orientation of Adenine on Gold and Silver. Chemphyschem 2018; 19:1003-1015. [DOI: 10.1002/cphc.201701223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Scott G. Harroun
- Department of Chemistry; Université de Montréal; Montréal Québec H3C 3J7 Canada
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16
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Peng S, Wang W, Chen C. Breaking the Concentration Barrier for Single-Molecule Fluorescence Measurements. Chemistry 2017; 24:1002-1009. [DOI: 10.1002/chem.201704065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sijia Peng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing, 100084 P.R. China
| | - Wenjuan Wang
- School of Life Sciences and Technology Center for Protein Sciences; Tsinghua University; Beijing, 100084 P.R. China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing, 100084 P.R. China
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17
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Freeley M, Worthy HL, Ahmed R, Bowen B, Watkins D, Macdonald JE, Zheng M, Jones DD, Palma M. Site-Specific One-to-One Click Coupling of Single Proteins to Individual Carbon Nanotubes: A Single-Molecule Approach. J Am Chem Soc 2017; 139:17834-17840. [PMID: 29148737 DOI: 10.1021/jacs.7b07362] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the site-specific coupling of single proteins to individual carbon nanotubes (CNTs) in solution and with single-molecule control. Using an orthogonal Click reaction, Green Fluorescent Protein (GFP) was engineered to contain a genetically encoded azide group and then bound to CNT ends in different configurations: in close proximity or at longer distances from the GFP's functional center. Atomic force microscopy and fluorescence analysis in solution and on surfaces at the single-protein level confirmed the importance of bioengineering optimal protein attachment sites to achieve direct protein-nanotube communication and bridging.
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Affiliation(s)
- Mark Freeley
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Harley L Worthy
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Rochelle Ahmed
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Ben Bowen
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Daniel Watkins
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - J Emyr Macdonald
- School of Physics and Astronomy, Cardiff University , Queens's Building, The Parade, Cardiff CF24 3AA, United Kingdom
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899-8542, United States
| | - D Dafydd Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Matteo Palma
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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18
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Yugay D, Goronzy DP, Kawakami LM, Claridge SA, Song TB, Yan Z, Xie YH, Gilles J, Yang Y, Weiss PS. Copper Ion Binding Site in β-Amyloid Peptide. NANO LETTERS 2016; 16:6282-6289. [PMID: 27616333 DOI: 10.1021/acs.nanolett.6b02590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
β-Amyloid aggregates in the brain play critical roles in Alzheimer's disease, a chronic neurodegenerative condition. Amyloid-associated metal ions, particularly zinc and copper ions, have been implicated in disease pathogenesis. Despite the importance of such ions, the binding sites on the β-amyloid peptide remain poorly understood. In this study, we use scanning tunneling microscopy, circular dichroism, and surface-enhanced Raman spectroscopy to probe the interactions between Cu2+ ions and a key β-amyloid peptide fragment, consisting of the first 16 amino acids, and define the copper-peptide binding site. We observe that in the presence of Cu2+, this peptide fragment forms β-sheets, not seen without the metal ion. By imaging with scanning tunneling microscopy, we are able to identify the binding site, which involves two histidine residues, His13 and His14. We conclude that the binding of copper to these residues creates an interstrand histidine brace, which enables the formation of β-sheets.
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Affiliation(s)
- Diana Yugay
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Dominic P Goronzy
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Lisa M Kawakami
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Shelley A Claridge
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Tze-Bin Song
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Zhongbo Yan
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Ya-Hong Xie
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Jérôme Gilles
- Department of Mathematics and Statistics, San Diego State University , San Diego, California 92182, United States
| | - Yang Yang
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Paul S Weiss
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
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19
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Andrews AM, Liao WS, Weiss PS. Double-Sided Opportunities Using Chemical Lift-Off Lithography. Acc Chem Res 2016; 49:1449-57. [PMID: 27064348 DOI: 10.1021/acs.accounts.6b00034] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We discuss the origins, motivation, invention, development, applications, and future of chemical lift-off lithography, in which a specified pattern of a self-assembled monolayer is removed, i.e., lifted off, using a reactive, patterned stamp that is brought into contact with the monolayer. For Au substrates, this process produces a supported, patterned monolayer of Au on the stamp in addition to the negative pattern in the original molecular monolayer. Both the patterned molecular monolayer on the original substrate and the patterned supported metal monolayer on the stamp are useful as materials and for further applications in sensing and other areas. Chemical lift-off lithography effectively lowers the barriers to and costs of high-resolution, large-area nanopatterning. On the patterned monolayer side, features in the single-nanometer range can be produced across large (square millimeter or larger) areas. Patterns smaller than the original stamp feature sizes can be produced by controlling the degree of contact between the stamp and the lifted-off monolayer. We note that this process is different than conventional lift-off processes in lithography in that chemical lift-off lithography removes material, whereas conventional lift-off is a positive-tone patterning method. Chemical lift-off lithography is in some ways similar to microtransfer printing. Chemical lift-off lithography has critical advantages in the preparation of biocapture surfaces because the molecules left behind are exploited to space and to orient functional(ized) molecules. On the supported metal monolayer side, a new two-dimensional material has been produced. The useful important chemical properties of Au (vis-à-vis functionalization with thiols) are retained, but the electronic and optical properties of bulk Au or even Au nanoparticles are not. These metal monolayers do not quench excitation and may be useful in optical measurements, particularly in combination with selective binding due to attached molecular recognition elements. In contrast to materials such as graphene that have bonding confined to two dimensions, these metal monolayers can be straightforwardly patterned-by patterning the stamp, the initial monolayer, or the initial substrate. Well-developed thiol-Au and related chemistries can be used on the supported monolayers. As there is little quenching and photoabsorption, spectroscopic imaging methods can be used on these functionalized materials. We anticipate that the properties of the metal monolayers can be tuned by varying the chemical, physical, and electronic connections made by and to the supporting molecular layers. That is, the amount of charge in the layer can be determined by controlling the density of S-Au (or other) connections and the molecular backbone and functionality, which determine the strength with which the chemical contact withdraws charge from the metal. This process should work for other coinage-metal substrates and additional systems where the binding of the outermost layers to the substrate is weaker than the molecule-substrate attachment.
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Affiliation(s)
- Anne M. Andrews
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Psychiatry, Hatos Center for Neuropharmacology, and Semel Institute
for Neuroscience and Human Behavior, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Wei-Ssu Liao
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Paul S. Weiss
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University of California, Los Angeles, Los
Angeles, California 90095, United States
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20
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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21
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Theoretical simulation of chromatographic separation based on random diffusion in the restricted space. Sci China Chem 2016. [DOI: 10.1007/s11426-016-5565-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Thomas JC, Goronzy DP, Dragomiretskiy K, Zosso D, Gilles J, Osher SJ, Bertozzi AL, Weiss PS. Mapping Buried Hydrogen-Bonding Networks. ACS NANO 2016; 10:5446-51. [PMID: 27096290 DOI: 10.1021/acsnano.6b01717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We map buried hydrogen-bonding networks within self-assembled monolayers of 3-mercapto-N-nonylpropionamide on Au{111}. The contributing interactions include the buried S-Au bonds at the substrate surface and the buried plane of linear networks of hydrogen bonds. Both are simultaneously mapped with submolecular resolution, in addition to the exposed interface, to determine the orientations of molecular segments and directional bonding. Two-dimensional mode-decomposition techniques are used to elucidate the directionality of these networks. We find that amide-based hydrogen bonds cross molecular domain boundaries and areas of local disorder.
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Affiliation(s)
- John C Thomas
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Dominic P Goronzy
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Konstantin Dragomiretskiy
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Mathematics, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Dominique Zosso
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Mathematics, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Jérôme Gilles
- Department of Mathematics and Statistics, San Diego State University , San Diego, California 92182, United States
| | - Stanley J Osher
- Department of Mathematics, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Andrea L Bertozzi
- Department of Mathematics, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Paul S Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
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23
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Nano-Modeling and Computation in Bio and Brain Dynamics. Bioengineering (Basel) 2016; 3:bioengineering3020011. [PMID: 28952573 PMCID: PMC5597135 DOI: 10.3390/bioengineering3020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 03/17/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022] Open
Abstract
The study of brain dynamics currently utilizes the new features of nanobiotechnology and bioengineering. New geometric and analytical approaches appear very promising in all scientific areas, particularly in the study of brain processes. Efforts to engage in deep comprehension lead to a change in the inner brain parameters, in order to mimic the external transformation by the proper use of sensors and effectors. This paper highlights some crossing research areas of natural computing, nanotechnology, and brain modeling and considers two interesting theoretical approaches related to brain dynamics: (a) the memory in neural network, not as a passive element for storing information, but integrated in the neural parameters as synaptic conductances; and (b) a new transport model based on analytical expressions of the most important transport parameters, which works from sub-pico-level to macro-level, able both to understand existing data and to give new predictions. Complex biological systems are highly dependent on the context, which suggests a “more nature-oriented” computational philosophy.
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24
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Aragonès AC, Haworth NL, Darwish N, Ciampi S, Bloomfield NJ, Wallace GG, Diez-Perez I, Coote ML. Electrostatic catalysis of a Diels–Alder reaction. Nature 2016; 531:88-91. [DOI: 10.1038/nature16989] [Citation(s) in RCA: 439] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 01/07/2016] [Indexed: 01/20/2023]
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25
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Sigle DO, Kasera S, Herrmann LO, Palma A, de Nijs B, Benz F, Mahajan S, Baumberg JJ, Scherman OA. Observing Single Molecules Complexing with Cucurbit[7]uril through Nanogap Surface-Enhanced Raman Spectroscopy. J Phys Chem Lett 2016; 7:704-10. [PMID: 26766205 DOI: 10.1021/acs.jpclett.5b02535] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In recent years, single-molecule sensitivity achievable by surface-enhanced Raman spectroscopy (SERS) has been widely reported. We use this to investigate supramolecular host-guest chemistry with the macrocyclic host cucurbit[7]uril, on a few-to-single-molecule level. A nanogap geometry, comprising individual gold nanoparticles on a planar gold surface spaced by a single layer of molecules, gives intense SERS signals. Plasmonic coupling between the particle and the surface leads to strongly enhanced optical fields in the gap between them, with single-molecule sensitivity established using a modification of the well-known bianalyte method. Changes in the Raman modes of the host molecule are observed when single guests included inside its cavity internally stretch it. Anisotropic intermolecular interactions with the guest are found which show additional distinct features in the Raman modes of the host molecule.
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Affiliation(s)
- Daniel O Sigle
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Setu Kasera
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Lars O Herrmann
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Aniello Palma
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Bart de Nijs
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Felix Benz
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Sumeet Mahajan
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Jeremy J Baumberg
- Nanophotonics Centre, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS NANO 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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27
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Russell SR, Claridge SA. Peptide interfaces with graphene: an emerging intersection of analytical chemistry, theory, and materials. Anal Bioanal Chem 2016; 408:2649-58. [DOI: 10.1007/s00216-015-9262-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/27/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
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Sokolov I, Zorn G, Nichols JM. A study of molecular adsorption of a cationic surfactant on complex surfaces with atomic force microscopy. Analyst 2016; 141:1017-26. [PMID: 26730682 DOI: 10.1039/c5an01941a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The study of molecular adsorption on solid surfaces is of broad interest. However, so far the study has been restricted to idealized flat smooth rigid surfaces which are rarely the case in real world applications. Here we describe a study of molecular adsorption on a complex surface of the submicron fibers of a fibrous membrane of regenerated cellulose in aqueous media. We use a cationic surfactant, cetyltrimethylammonium chloride (CTAC), as the adsorbing molecule. We study the equilibrium adsorption of CTAC molecules on the same area of the fibers by sequentially immersing the membrane in pure water, 1 mM and then a 20 mM solution of CTAC. Atomic force microscopy (AFM) is applied to study the adsorption. The force-volume mode is used to record the force-deformation curves of the adsorbed molecules on the fiber surface. We suggest a model to separate the forces due to the adsorbed molecules from the elastic deformation of the fiber. Interestingly, knowledge of the surface geometry is not required in this model provided the surface is made of elastically homogeneous material. Different models are investigated to estimate the amount of the adsorbed molecules based on the obtained force curves. The exponential steric repulsion model fits the force data the best. The amount of the adsorbed surfactant molecules and its dependence on the concentration are found to be reasonable compared to the data previously measured by means of Raman scattering done on a flat surface of silica.
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Affiliation(s)
- I Sokolov
- Departments of ME, BME, Physics, Tufts University, Medford, MA 02155, USA.
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29
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Ju L, Qian J, Zhu C. Transport regulation of two-dimensional receptor-ligand association. Biophys J 2016; 108:1773-1784. [PMID: 25863068 DOI: 10.1016/j.bpj.2015.02.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/15/2015] [Accepted: 02/24/2015] [Indexed: 01/12/2023] Open
Abstract
The impact of flow disturbances on platelet adhesion is complex and incompletely understood. At the molecular scale, platelet glycoprotein Ibα (GPIbα) must associate with the von Willebrand factor A1 domain (VWF-A1) with a rapid on-rate under high hemodynamic forces, as occurs in arterial thrombosis, where various transport mechanisms are at work. Here, we theoretically modeled the coupled transport-reaction process of the two-dimensional (2D) receptor-ligand association kinetics in a biomembrane force probe to explicitly account for the effects of molecular length, confinement stiffness, medium viscosity, surface curvature, and separation distance. We experimentally verified the theoretical approach by visualizing association and dissociation of individual VWF-A1-GPIbα bonds in a real-time thermal fluctuation assay. The apparent on-rate, reciprocal of the average time intervals between sequential bonds, decreased with the increasing gap distance between A1- and GPIbα-bearing surfaces with an 80-nm threshold (beyond which bond formation became prohibitive) identified as the combined contour length of the receptor and ligand molecules. The biomembrane force probe spring constant and diffusivity of the protein-bearing beads also significantly influenced the apparent on-rate, in accordance with the proposed transport mechanisms. The global agreement between the experimental data and the model predictions supports the hypothesis that receptor-ligand association behaves distinctly in the transport- and reaction-limited scenarios. To our knowledge, our results represent the first detailed quantification of physical regulation of the 2D on-rate that allows platelets to sense and respond to local changes in their hemodynamic environment. In addition, they provide an approach for determining the intrinsic kinetic parameters that employs simultaneous experimental measurements and theoretical modeling of bond association in a single assay. The 2D intrinsic forward rate for VWF-A1-GPIbα association was determined from the measurements to be (3.5 ± 0.67) × 10(-4)μm(2) s(-1).
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Affiliation(s)
- Lining Ju
- Coulter School of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia; Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Jin Qian
- Department of Engineering Mechanics, Zhejiang University, Hangzhou, China
| | - Cheng Zhu
- Coulter School of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia; Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia; Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia.
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30
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Larsen MB, Boydston AJ. Investigations in Fundamental and Applied Polymer Mechanochemistry. MACROMOL CHEM PHYS 2015. [DOI: 10.1002/macp.201500292] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael B. Larsen
- Department of Chemistry; University of Washington; Seattle WA 98195 USA
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31
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Gethers ML, Thomas JC, Jiang S, Weiss NO, Duan X, Goddard WA, Weiss PS. Holey Graphene as a Weed Barrier for Molecules. ACS NANO 2015; 9:10909-10915. [PMID: 26426746 DOI: 10.1021/acsnano.5b03936] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We demonstrate the use of "holey" graphene as a mask against molecular adsorption. Prepared porous graphene is transferred onto a Au{111} substrate, annealed, and then exposed to dilute solutions of 1-adamantanethiol. In the pores of the graphene lattice, we find islands of organized, self-assembled molecules. The bare Au in the pores can be regenerated by postdeposition annealing, and new molecules can be self-assembled in the exposed Au region. Graphene can serve as a robust, patternable mask against the deposition of self-assembled monolayers.
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Affiliation(s)
- Matthew L Gethers
- Materials and Process Simulation Center and ‡Department of Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
- Department of Chemistry and Biochemistry and California NanoSystems Institute and ⊥Department of Materials Science and Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, and #Department of Materials Science, Chemistry, California Institute of Technology , Pasadena, California 91125, United States
| | - John C Thomas
- Materials and Process Simulation Center and ‡Department of Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
- Department of Chemistry and Biochemistry and California NanoSystems Institute and ⊥Department of Materials Science and Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, and #Department of Materials Science, Chemistry, California Institute of Technology , Pasadena, California 91125, United States
| | - Shan Jiang
- Materials and Process Simulation Center and ‡Department of Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
- Department of Chemistry and Biochemistry and California NanoSystems Institute and ⊥Department of Materials Science and Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, and #Department of Materials Science, Chemistry, California Institute of Technology , Pasadena, California 91125, United States
| | - Nathan O Weiss
- Materials and Process Simulation Center and ‡Department of Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
- Department of Chemistry and Biochemistry and California NanoSystems Institute and ⊥Department of Materials Science and Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, and #Department of Materials Science, Chemistry, California Institute of Technology , Pasadena, California 91125, United States
| | - Xiangfang Duan
- Materials and Process Simulation Center and ‡Department of Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
- Department of Chemistry and Biochemistry and California NanoSystems Institute and ⊥Department of Materials Science and Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, and #Department of Materials Science, Chemistry, California Institute of Technology , Pasadena, California 91125, United States
| | - William A Goddard
- Materials and Process Simulation Center and ‡Department of Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
- Department of Chemistry and Biochemistry and California NanoSystems Institute and ⊥Department of Materials Science and Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, and #Department of Materials Science, Chemistry, California Institute of Technology , Pasadena, California 91125, United States
| | - Paul S Weiss
- Materials and Process Simulation Center and ‡Department of Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
- Department of Chemistry and Biochemistry and California NanoSystems Institute and ⊥Department of Materials Science and Engineering, University of California , Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry, and #Department of Materials Science, Chemistry, California Institute of Technology , Pasadena, California 91125, United States
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32
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Nanayakkara SU, van de Lagemaat J, Luther JM. Scanning Probe Characterization of Heterostructured Colloidal Nanomaterials. Chem Rev 2015. [PMID: 26196958 DOI: 10.1021/cr500280t] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Sanjini U. Nanayakkara
- National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Jao van de Lagemaat
- National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Joseph M. Luther
- National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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33
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Park J, Park H, Ercius P, Pegoraro AF, Xu C, Kim JW, Han SH, Weitz DA. Direct Observation of Wet Biological Samples by Graphene Liquid Cell Transmission Electron Microscopy. NANO LETTERS 2015; 15:4737-4744. [PMID: 26065925 DOI: 10.1021/acs.nanolett.5b01636] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent development of liquid phase transmission electron microscopy (TEM) enables the study of specimens in wet ambient conditions within a liquid cell; however, direct structural observation of biological samples in their native solution using TEM is challenging since low-mass biomaterials embedded in a thick liquid layer of the host cell demonstrate low contrast. Furthermore, the integrity of delicate wet samples is easily compromised during typical sample preparation and TEM imaging. To overcome these limitations, we introduce a graphene liquid cell (GLC) using multilayer graphene sheets to reliably encapsulate and preserve biological samples in a liquid for TEM observation. We achieve nanometer scale spatial resolution with high contrast using low-dose TEM at room temperature, and we use the GLC to directly observe the structure of influenza viruses in their native buffer solution at room temperature. The GLC is further extended to investigate whole cells in wet conditions using TEM. We also demonstrate the potential of the GLC for correlative studies by TEM and fluorescence light microscopy imaging.
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Affiliation(s)
- Jungwon Park
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Hyesung Park
- §School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, South Korea
| | - Peter Ercius
- ∥The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Adrian F Pegoraro
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Chen Xu
- ⊥Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Jin Woong Kim
- #Department of Applied Chemistry, Hanyang University, Ansan 426-791, South Korea
- ∇Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | | | - David A Weitz
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
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34
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Thomas JC, Schwartz JJ, Hohman JN, Claridge SA, Auluck HS, Serino AC, Spokoyny AM, Tran G, Kelly KF, Mirkin CA, Gilles J, Osher SJ, Weiss PS. Defect-Tolerant Aligned Dipoles within Two-Dimensional Plastic Lattices. ACS NANO 2015; 9:4734-4742. [PMID: 25867638 DOI: 10.1021/acsnano.5b01329] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Carboranethiol molecules self-assemble into upright molecular monolayers on Au{111} with aligned dipoles in two dimensions. The positions and offsets of each molecule's geometric apex and local dipole moment are measured and correlated with sub-Ångström precision. Juxtaposing simultaneously acquired images, we observe monodirectional offsets between the molecular apexes and dipole extrema. We determine dipole orientations using efficient new image analysis techniques and find aligned dipoles to be highly defect tolerant, crossing molecular domain boundaries and substrate step edges. The alignment observed, consistent with Monte Carlo simulations, forms through favorable intermolecular dipole-dipole interactions.
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Affiliation(s)
- John C Thomas
- †Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jeffrey J Schwartz
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- §Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - J Nathan Hohman
- †Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Shelley A Claridge
- †Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- ⊥Department of Chemistry and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47904, United States
| | - Harsharn S Auluck
- †Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Andrew C Serino
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- ∥Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Alexander M Spokoyny
- †Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- ¶Department of Chemistry and the International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Giang Tran
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- #Department of Mathematics, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kevin F Kelly
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- ▽Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Chad A Mirkin
- ¶Department of Chemistry and the International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Jerome Gilles
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- #Department of Mathematics, University of California, Los Angeles, Los Angeles, California 90095, United States
- ○Department of Mathematics and Statistics, San Diego State University, San Diego, California 92182, United States
| | - Stanley J Osher
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- #Department of Mathematics, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S Weiss
- †Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- ∥Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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35
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Mohamad NR, Marzuki NHC, Buang NA, Huyop F, Wahab RA. An overview of technologies for immobilization of enzymes and surface analysis techniques for immobilized enzymes. BIOTECHNOL BIOTEC EQ 2015; 29:205-220. [PMID: 26019635 PMCID: PMC4434042 DOI: 10.1080/13102818.2015.1008192] [Citation(s) in RCA: 700] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/07/2014] [Indexed: 01/28/2023] Open
Abstract
The current demands of sustainable green methodologies have increased the use of enzymatic technology in industrial processes. Employment of enzyme as biocatalysts offers the benefits of mild reaction conditions, biodegradability and catalytic efficiency. The harsh conditions of industrial processes, however, increase propensity of enzyme destabilization, shortening their industrial lifespan. Consequently, the technology of enzyme immobilization provides an effective means to circumvent these concerns by enhancing enzyme catalytic properties and also simplify downstream processing and improve operational stability. There are several techniques used to immobilize the enzymes onto supports which range from reversible physical adsorption and ionic linkages, to the irreversible stable covalent bonds. Such techniques produce immobilized enzymes of varying stability due to changes in the surface microenvironment and degree of multipoint attachment. Hence, it is mandatory to obtain information about the structure of the enzyme protein following interaction with the support surface as well as interactions of the enzymes with other proteins. Characterization technologies at the nanoscale level to study enzymes immobilized on surfaces are crucial to obtain valuable qualitative and quantitative information, including morphological visualization of the immobilized enzymes. These technologies are pertinent to assess efficacy of an immobilization technique and development of future enzyme immobilization strategies.
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Affiliation(s)
- Nur Royhaila Mohamad
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Nur Haziqah Che Marzuki
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Nor Aziah Buang
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai81310, Johor, Malaysia
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36
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Walia S, Shah AK, Stoddart PR, Bhaskaran M, Sriram S. Electric field induced surface-enhanced Raman spectroscopy for multianalyte detection. Phys Chem Chem Phys 2015; 17:7095-9. [DOI: 10.1039/c4cp04912h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This work demonstrates the ability to detect and isolate an analyte from a multianalyte mixture by SERS sensing.
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Affiliation(s)
- Sumeet Walia
- Functional Materials and Microsystems Research Group
- RMIT University
- Melbourne
- Australia
- Micro Nano Research Facility
| | - Aditya K. Shah
- Functional Materials and Microsystems Research Group
- RMIT University
- Melbourne
- Australia
- Micro Nano Research Facility
| | - Paul R. Stoddart
- Faculty of Engineering and Industrial Science
- Swinburne University of Technology
- Hawthorn
- Australia
| | - Madhu Bhaskaran
- Functional Materials and Microsystems Research Group
- RMIT University
- Melbourne
- Australia
- Micro Nano Research Facility
| | - Sharath Sriram
- Functional Materials and Microsystems Research Group
- RMIT University
- Melbourne
- Australia
- Micro Nano Research Facility
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37
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Drexler CI, Causey CP, Mullen TJ. 1-Adamantanethiol as a versatile nanografting tool. SCANNING 2015; 37:6-16. [PMID: 25377299 DOI: 10.1002/sca.21173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/11/2014] [Accepted: 10/06/2014] [Indexed: 06/04/2023]
Abstract
Strategies to regulate the self-assembly of adsorbates to create surface structures with molecular-scale features and organization are of broad interest to nanoscience, biochemistry, and engineering. One approach utilizes molecules with tailored intermolecular interaction strengths and topologies to direct molecular self-assembly as exemplified by the adsorption of 1-adamantanethiol molecules on Au{111} substrates. 1-Adamantanethiolate self-assembled monolayers exhibit decreased packing densities and weaker intermolecular interaction strengths than n-alkanethiolate self-assembled monolayers, which result in their complete displacement upon exposure to n-alkanethiol molecules. Herein, we explore the capabilities of the atomic force microscopy-based lithographic technique, nanografting, to fabricate chemical patterns comprised of 1-adamantanethiolate monolayers. Positive 1-adamantanethiolate patterns are generated by nanografting 1-adamantanethiol molecules into preexisting n-alkanethiolate self-assembled monolayers, and negative 1-adamantanethiolate patterns are created by nanografting n-alkanethiol molecules into preexisting 1-adamantanethiolate self-assembled monolayers. The patterned 1-adamantanethiolate regions are displaced upon exposure to solutions of n-alkanethiol molecules. This two-step nanografting-displacement strategy minimizes pattern dissolution as 1-adamantanethiol molecules do not intercalate into the preexisting self-assembled monolayer during nanografting. 1-Adamantanethiol can be utilized create high-resolution sacrificial chemical patterns with feature sizes beyond those afforded other 1-adamantanethiol patterning strategies for applications such as resists for metallic and organic structures.
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Affiliation(s)
- Chad I Drexler
- Department of Chemistry, University of North Florida, Jacksonville, Florida
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38
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Liu N, Chen Y, Peng B, Lin Y, Wang Q, Su Z, Zhang W, Li H, Shen J. Single-molecule force spectroscopy study on the mechanism of RNA disassembly in tobacco mosaic virus. Biophys J 2014; 105:2790-800. [PMID: 24359751 DOI: 10.1016/j.bpj.2013.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/22/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022] Open
Abstract
To explore the disassembly mechanism of tobacco mosaic virus (TMV), a model system for virus study, during infection, we have used single-molecule force spectroscopy to mimic and follow the process of RNA disassembly from the protein coat of TMV by the replisome (molecular motor) in vivo, under different pH and Ca(2+) concentrations. Dynamic force spectroscopy revealed the unbinding free-energy landscapes as that at pH 4.7 the disassembly process is dominated by one free-energy barrier, whereas at pH 7.0 the process is dominated by one barrier and that there exists a second barrier. The additional free-energy barrier at longer distance has been attributed to the hindrance of disordered loops within the inner channel of TMV, and the biological function of those protein loops was discussed. The combination of pH increase and Ca(2+) concentration drop could weaken RNA-protein interactions so much that the molecular motor replisome would be able to pull and disassemble the rest of the genetic RNA from the protein coat in vivo. All these facts provide supporting evidence at the single-molecule level, to our knowledge for the first time, for the cotranslational disassembly mechanism during TMV infection under physiological conditions.
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Affiliation(s)
- Ningning Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China; School of Chemistry and Material Science, Liaoning Shihua University, Fushun, P. R. China
| | - Ying Chen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China
| | - Bo Peng
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Yuan Lin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Qian Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China; Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina.
| | - Zhaohui Su
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China.
| | - Hongbin Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiacong Shen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China
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Hohman JN, Thomas JC, Zhao Y, Auluck H, Kim M, Vijselaar W, Kommeren S, Terfort A, Weiss PS. Exchange Reactions between Alkanethiolates and Alkaneselenols on Au{111}. J Am Chem Soc 2014; 136:8110-21. [DOI: 10.1021/ja503432f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- J. Nathan Hohman
- California
NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - John C. Thomas
- California
NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yuxi Zhao
- California
NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Harsharn Auluck
- California
NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Moonhee Kim
- California
NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Wouter Vijselaar
- Department
of Science and Technology, University of Twente, P.O. Box 217, 7500
AE Enschede, The Netherlands
| | - Sander Kommeren
- Department
of Science and Technology, University of Twente, P.O. Box 217, 7500
AE Enschede, The Netherlands
| | - Andreas Terfort
- Institut
für Anorganische und Analytische Chemie, Universität Frankfurt, Frankfurt 60438, Germany
| | - Paul S. Weiss
- California
NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University of California, Los Angeles, California 90095, United States
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40
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Sengupta E, Yan Y, Wang X, Munechika K, Ginger DS. Dynamic force spectroscopy of photoswitch-modified DNA. ACS NANO 2014; 8:2625-2631. [PMID: 24502655 DOI: 10.1021/nn406334b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We apply a combination of photoswitch-modified DNA and AFM-based pulling measurements to study the force-induced melting of double-stranded DNA in the unzipping geometry. We measure the differences in peak rupture force for azobenzene-modified DNA, as the incorporated azobenzenes are photoswitched reversibly between the trans and the cis form. Fitting our rupture force versus loading rate data, we obtain off rate (koff) at zero force values in the range of ∼10 s(-1). We show that the change in peak rupture force and koff induced by destabilizing the DNA duplex depends on the position of the destabilizing azobenzene photoswitch relative to the force-loading site. When the azobenzenes are proximal to the unzipping end, the decrease in peak force and koff upon azobenzene photoisomerization is significantly larger than when the azobenzene is distal to the site of force loading. We interpret these results as experimental evidence supporting the picture that the destabilization of a double-stranded DNA by a photoswitch isomerization is localized to a small bubble around the photoswitch.
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Affiliation(s)
- Esha Sengupta
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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41
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Genovese D, Rampazzo E, Bonacchi S, Montalti M, Zaccheroni N, Prodi L. Energy transfer processes in dye-doped nanostructures yield cooperative and versatile fluorescent probes. NANOSCALE 2014; 6:3022-3036. [PMID: 24531884 DOI: 10.1039/c3nr05599j] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fast and efficient energy transfer among dyes confined in nanocontainers provides the basis of outstanding functionalities in new-generation luminescent probes. This feature article provides an overview of recent research achievements on luminescent Pluronic-Silica NanoParticles (PluS NPs), a class of extremely monodisperse core-shell nanoparticles whose design can be easily tuned to match specific needs for diverse applications based on luminescence, and that have already been successfully tested in in vivo imaging. An outline of their outstanding properties, such as tuneability, bright and photoswitchable fluorescence and electrochemiluminescence, will be supported by a critical discussion of our recent works in this field. Furthermore, novel data and simulations will be presented to (i) thoroughly examine common issues arising from the inclusion of multiple dyes in a small silica core, and (ii) show the emergence of a cooperative behaviour among embedded dyes. Such cooperative behaviour provides a handle for fine control of brightness, emission colour and self-quenching phenomena in PluS NPs, leading to significantly enhanced signal to noise ratios.
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Affiliation(s)
- Damiano Genovese
- Dipartimento di Chimica "Giacomo Ciamician", via Selmi 2, Bologna 40126, Bologna, Italy.
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42
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Guo J, Sachs F, Meng F. Fluorescence-based force/tension sensors: a novel tool to visualize mechanical forces in structural proteins in live cells. Antioxid Redox Signal 2014; 20:986-99. [PMID: 24205787 PMCID: PMC3924807 DOI: 10.1089/ars.2013.5708] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
SIGNIFICANCE Three signaling systems, chemical, electrical, and mechanical, ubiquitously contribute to cellular activities. There is limited information on the mechanical signaling system because of a lack of tools to measure stress in specific proteins. Although significant advances in methodologies such as atomic force microscopy and laser tweezers have achieved great success in single molecules and measuring the mean properties of cells and tissues, they cannot deal with specific proteins in live cells. RECENT ADVANCES To remedy the situation, we developed a family of genetically encoded optical force sensors to measure the stress in structural proteins in living cells. The sensors can be incorporated into specific proteins and are not harmful in transgenic animals. The chimeric proteins distribute and function as their wild-type counterparts, and local stress can be read out from changes in Förster resonance energy transfer (FRET). CRITICAL ISSUES Our original sensor used two mutant green fluorescence proteins linked by an alpha helix that served as a linking spring. Ever since, we have improved the probe design in a number of ways. For example, we replaced the helical linker with more common elastic protein domains to better match the compliance of the wild-type hosts. We greatly improved sensitivity by using the angular dependence of FRET rather than the distance dependence as the transduction mechanism, because that has nearly 100% efficiency at rest and nearly zero when stretched. FUTURE DIRECTIONS These probes enable researchers to investigate the roles of mechanical force in cellular activities at the level of single molecules, cells, tissues, and whole animals.
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Affiliation(s)
- Jun Guo
- 1 Department of Biochemistry, Nanjing Medical University , Nanjing, People's Republic of China
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43
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Joshi GK, Blodgett KN, Muhoberac BB, Johnson MA, Smith KA, Sardar R. Ultrasensitive photoreversible molecular sensors of azobenzene-functionalized plasmonic nanoantennas. NANO LETTERS 2014; 14:532-40. [PMID: 24393014 DOI: 10.1021/nl403576c] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This Letter describes an unprecedentedly large and photoreversible localized surface plasmon resonance (LSPR) wavelength shift caused by photoisomerization of azobenzenes attached to gold nanoprisms that act as nanoantennas. The blue light-induced cis to trans azobenzene conformational change occurs in the solid state and controls the optical properties of the nanoprisms shifting their LSPR peak up to 21 nm toward longer wavelengths. This shift is consistent with the increase in thickness of the local dielectric environment (0.6 nm) surrounding the nanoprism and perhaps a contribution from plasmonic energy transfer between the nanoprism and azobenzenes. The effects of the azobenzene conformational change and its photoreversibility were also probed through surface-enhanced Raman spectroscopy (SERS) showing that the electronic interaction between the nanoprisms and bound azobenzenes in their cis conformation significantly enhances the intensity of the Raman bands of the azobenzenes. The SERS data suggests that the isomerization is controlled by first-order kinetics with a rate constant of 1.0 × 10(-4) s(-1). Our demonstration of light-induced photoreversibility of this type of molecular machine is the first-step toward removing present limitations on detection of molecular motion in solid-state devices using LSPR spectroscopy with nanoprisms. Modulating the LSPR peak position and controlling energy transfer across the nanostructure-organic molecule interface are very important for the fabrication of plasmonic-based nanoscale devices.
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Affiliation(s)
- Gayatri K Joshi
- Department of Chemistry and Chemical Biology and ‡Integrated Nanosystems Development Institute, Indiana University-Purdue University Indianapolis , 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
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44
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Claridge SA, Thomas JC, Silverman MA, Schwartz JJ, Yang Y, Wang C, Weiss PS. Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy. J Am Chem Soc 2013; 135:18528-35. [PMID: 24219245 PMCID: PMC4117194 DOI: 10.1021/ja408550a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer's and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.
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Affiliation(s)
- Shelley A. Claridge
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - John C. Thomas
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - Miles A. Silverman
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - Jeffrey J. Schwartz
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - Yanlian Yang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
| | - Chen Wang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
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45
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Linkov P, Artemyev M, Efimov AE, Nabiev I. Comparative advantages and limitations of the basic metrology methods applied to the characterization of nanomaterials. NANOSCALE 2013; 5:8781-8798. [PMID: 23934544 DOI: 10.1039/c3nr02372a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fabrication of modern nanomaterials and nanostructures with specific functional properties is both scientifically promising and commercially profitable. The preparation and use of nanomaterials require adequate methods for the control and characterization of their size, shape, chemical composition, crystalline structure, energy levels, pathways and dynamics of physical and chemical processes during their fabrication and further use. In this review, we discuss different instrumental methods for the analysis and metrology of materials and evaluate their advantages and limitations at the nanolevel.
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Affiliation(s)
- Pavel Linkov
- Laboratory of Nano-Bioengineering, National Research Nuclear University, Moscow Engineering Physics Institute, 31 Kashirskoe sh., 115409 Moscow, Russian Federation.
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46
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Direct measurement and modulation of single-molecule coordinative bonding forces in a transition metal complex. Nat Commun 2013; 4:2121. [DOI: 10.1038/ncomms3121] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 06/06/2013] [Indexed: 01/11/2023] Open
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47
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Claridge SA, Liao WS, Thomas JC, Zhao Y, Cao H, Cheunkar S, Serino AC, Andrews AM, Weiss PS. From the bottom up: dimensional control and characterization in molecular monolayers. Chem Soc Rev 2013; 42:2725-45. [PMID: 23258565 PMCID: PMC3596502 DOI: 10.1039/c2cs35365b] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Self-assembled monolayers are a unique class of nanostructured materials, with properties determined by their molecular lattice structures, as well as the interfaces with their substrates and environments. As with other nanostructured materials, defects and dimensionality play important roles in the physical, chemical, and biological properties of the monolayers. In this review, we discuss monolayer structures ranging from surfaces (two-dimensional) down to single molecules (zero-dimensional), with a focus on applications of each type of structure, and on techniques that enable characterization of monolayer physical properties down to the single-molecule scale.
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Affiliation(s)
- Shelley A. Claridge
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Wei-Ssu Liao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - John C. Thomas
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yuxi Zhao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Huan Cao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Sarawut Cheunkar
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Andrew C. Serino
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Anne M. Andrews
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Psychiatry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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48
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Affiliation(s)
- Bala Krishna Pathem
- California NanoSystems Institute,
- Department of Chemistry and Biochemistry, and
| | - Shelley A. Claridge
- California NanoSystems Institute,
- Department of Chemistry and Biochemistry, and
| | - Yue Bing Zheng
- California NanoSystems Institute,
- Department of Chemistry and Biochemistry, and
| | - Paul S. Weiss
- California NanoSystems Institute,
- Department of Chemistry and Biochemistry, and
- Department of Materials Science and Engineering, University of California, Los Angeles, California 90095;
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49
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Alivisatos AP, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X. Nanotools for neuroscience and brain activity mapping. ACS NANO 2013; 7:1850-66. [PMID: 23514423 PMCID: PMC3665747 DOI: 10.1021/nn4012847] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.
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Affiliation(s)
- A. Paul Alivisatos
- Department of Chemistry, University of California, Berkeley, California 94720, and Lawrence Berkeley Laboratory, Berkeley, California 94720-1460
| | - Anne M. Andrews
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Psychiatry, and Semel Institute for Neuroscience & Human Behavior, Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095
| | - Edward S. Boyden
- Media Laboratory, Department of Biological Engineering, Brain and Cognitive Sciences, and McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | | | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University, Boston, Massachusetts 02115
| | - Karl Deisseroth
- Howard Hughes Medical Institute, Stanford University, Stanford California 94305
- Departments of Bioengineering and Psychiatry, Stanford University, Stanford California 94305
| | - John P. Donoghue
- Department of Neuroscience, Division of Engineering, Department of Computer Science, Brown University, Providence, Rhode Island 02912
| | - Scott E. Fraser
- Departments of Biological Sciences, Biomedical Engineering, Physiology and Biophysics, Stem Cell Biology and Regenerative Medicine, and Pediatrics, Radiology and Ophthalmology, University of Southern California, Los Angeles, California 90089
| | - Jennifer Lippincott-Schwartz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Sotiris Masmanidis
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Neurobiology, University of California, Los Angeles, California 90095
- Address correspondence to , , ,
| | - Paul L. McEuen
- Department of Physics, Laboratory of Atomic and Solid State Physics, and Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853
| | - Arto V. Nurmikko
- Department of Physics and Division of Engineering, Brown University, Providence, Rhode Island 02912
| | - Hongkun Park
- Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138
| | - Darcy S. Peterka
- Howard Hughes Medical Institute and Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Clay Reid
- Allen Institute for Brain Science, Seattle, Washington 98103
| | - Michael L. Roukes
- Kavli Nanoscience Institute, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Departments of Physics, Applied Physics, and Bioengineering, California Institute of Technology, MC 149-33, Pasadena, California 91125
| | - Axel Scherer
- Kavli Nanoscience Institute, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Departments of Electrical Engineering, Applied Physics, and Physics, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Address correspondence to , , ,
| | - Mark Schnitzer
- Howard Hughes Medical Institute, Stanford University, Stanford California 94305
- Departments of Applied Physics and Biology, James H. Clark Center, Stanford University, Stanford, California 94305
| | - Terrence J. Sejnowski
- Howard Hughes Medical Institute, Computational Neurobiology Laboratory, Salk Institute, La Jolla, California 92037, and Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, New York 10027
| | - Doris Tsao
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Gina Turrigiano
- Department of Biology and Center for Complex Systems, Brandeis University, Waltham, Massachusetts 02254
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Chemistry & Biochemistry, Department of Materials Science & Engineering, University of California, Los Angeles, California 90095
- Address correspondence to , , ,
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853
| | - Rafael Yuste
- Howard Hughes Medical Institute and Department of Biological Sciences, Columbia University, New York, New York 10027
- Kavli Institute for Brain Science, Columbia University, New York, New York 10027
- Address correspondence to , , ,
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Departments of Chemistry and Chemical Biology and Physics, Harvard University, Cambridge, Massachusetts 02138
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50
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Choi Y, Olsen TJ, Sims PC, Moody IS, Corso BL, Dang MN, Weiss GA, Collins PG. Dissecting single-molecule signal transduction in carbon nanotube circuits with protein engineering. NANO LETTERS 2013; 13:625-31. [PMID: 23323846 PMCID: PMC3575522 DOI: 10.1021/nl304209p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, nonfluorescent single-molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems.
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Affiliation(s)
- Yongki Choi
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
| | - Tivoli J. Olsen
- Department of Chemistry, University of California, Irvine, CA 92697, United States
| | - Patrick C. Sims
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
| | - Issa S. Moody
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States
| | - Brad L. Corso
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
| | - Mytrang N. Dang
- Department of Chemistry, University of California, Irvine, CA 92697, United States
| | - Gregory A. Weiss
- Department of Chemistry, University of California, Irvine, CA 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States
- Corresponding Author: G.A.W. () or P.G.C. ()
| | - Philip G. Collins
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
- Corresponding Author: G.A.W. () or P.G.C. ()
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