201
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Zimny P, Juncker D, Reisner W. Hydrogel droplet single-cell processing: DNA purification, handling, release, and on-chip linearization. BIOMICROFLUIDICS 2018; 12:024107. [PMID: 30867855 PMCID: PMC6404942 DOI: 10.1063/1.5020571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The preparation and handling of mammalian single-cell genomic DNA is limited by the complexity bottleneck inherent to performing multi-step, multi-reagent operations in a microfluidic environment. We have developed a method for benchtop preparation of high-molecular weight, intact, single-cell genomes and demonstrate the extraction of long nucleic acid molecules in a microfluidic system. Lymphoblasts are encapsulated inside of alginate microparticles using a droplet microfluidics, and cells are lysed in bulk. The purified genomes are then delivered to and imaged on a dedicated microfluidic device. High-molecular weight DNA is protected from shear and retains its original cellular identity. Using this encapsulation protocol, we were able to extract individual nucleic acid strands on the millimeter scale inside of a microfluidic channel.
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Affiliation(s)
| | - David Juncker
- Authors to whom correspondence should be addressed: ,
| | - Walter Reisner
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
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202
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Pollari R, Milstein JN. Accounting for polarization in the calibration of a donut beam axial optical tweezers. PLoS One 2018; 13:e0193402. [PMID: 29474494 PMCID: PMC5825067 DOI: 10.1371/journal.pone.0193402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 02/09/2018] [Indexed: 11/18/2022] Open
Abstract
Advances in light shaping techniques are leading to new tools for optical trapping and micromanipulation. For example, optical tweezers made from Laguerre-Gaussian or donut beams display an increased axial trap strength and can impart angular momentum to rotate a specimen. However, the application of donut beam optical tweezers to precision, biophysical measurements remains limited due to a lack of methods for calibrating such devices sufficiently. For instance, one notable complication, not present when trapping with a Gaussian beam, is that the polarization of the trap light can significantly affect the tweezers’ strength as well as the location of the trap. In this article, we show how to precisely calibrate the axial trap strength as a function of height above the coverslip surface while accounting for focal shifts in the trap position arising from radiation pressure, mismatches in the index of refraction, and polarization induced intensity variations. This provides a foundation for implementing a donut beam optical tweezers capable of applying precise axial forces.
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Affiliation(s)
- Russell Pollari
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Physics, University of Toronto, Toronto, ON, Canada
| | - Joshua N. Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Physics, University of Toronto, Toronto, ON, Canada
- * E-mail:
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203
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Zhang Y, Ha T, Marqusee S. Editorial Overview: Single-Molecule Approaches up to Difficult Challenges in Folding and Dynamics. J Mol Biol 2018; 430:405-408. [PMID: 29288633 PMCID: PMC5858691 DOI: 10.1016/j.jmb.2017.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, United States.
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Howard Hughes Medical Institute, Baltimore, MD 21205, United States; Department of Biophysics, Johns Hopkins University, Howard Hughes Medical Institute, Baltimore, MD 21205, United States; Department of Biomedical Engineering, Johns Hopkins University, Howard Hughes Medical Institute, Baltimore, MD 21205, United States.
| | - Susan Marqusee
- Department of Molecular & Cell Biology, Institute for Quantitative Biosciences (QB3)-Berkeley, University of California, Berkeley, Berkeley, CA 94720, United States.
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204
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Habibi M, Plotkin SS, Rottler J. Soft Vibrational Modes Predict Breaking Events during Force-Induced Protein Unfolding. Biophys J 2018; 114:562-569. [PMID: 29414701 PMCID: PMC5985024 DOI: 10.1016/j.bpj.2017.11.3781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/04/2017] [Accepted: 11/27/2017] [Indexed: 01/03/2023] Open
Abstract
We investigate the correlation between soft vibrational modes and unfolding events in simulated force spectroscopy of proteins. Unfolding trajectories are obtained from molecular dynamics simulations of a Gō model of a monomer of a mutant of superoxide dismutase 1 protein containing all heavy atoms in the protein, and a normal mode analysis is performed based on the anisotropic network model. We show that a softness map constructed from the superposition of the amplitudes of localized soft modes correlates with unfolding events at different stages of the unfolding process. Soft residues are up to eight times more likely to undergo disruption of native structure than the average amino acid. The memory of the softness map is retained for extensions of up to several nanometers, but decorrelates more rapidly during force drops.
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Affiliation(s)
- Mona Habibi
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada.
| | - Jörg Rottler
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada; Quantum Matter Institute, University of British Columbia, Vancouver, Canada
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205
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Nautiyal P, Alam F, Balani K, Agarwal A. The Role of Nanomechanics in Healthcare. Adv Healthc Mater 2018; 7. [PMID: 29193838 DOI: 10.1002/adhm.201700793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/18/2017] [Indexed: 12/21/2022]
Abstract
Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.
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Affiliation(s)
- Pranjal Nautiyal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
| | - Fahad Alam
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Kantesh Balani
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Arvind Agarwal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
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206
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Almendarez-Rangel P, Morales-Cruzado B, Sarmiento-Gómez E, Pérez-Gutiérrez FG. Finding trap stiffness of optical tweezers using digital filters. APPLIED OPTICS 2018; 57:652-658. [PMID: 29400734 DOI: 10.1364/ao.57.000652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/26/2017] [Indexed: 06/07/2023]
Abstract
Obtaining trap stiffness and calibration of the position detection system is the basis of a force measurement using optical tweezers. Both calibration quantities can be calculated using several experimental methods available in the literature. In most cases, stiffness determination and detection system calibration are performed separately, often requiring procedures in very different conditions, and thus confidence of calibration methods is not assured due to possible changes in the environment. In this work, a new method to simultaneously obtain both the detection system calibration and trap stiffness is presented. The method is based on the calculation of the power spectral density of positions through digital filters to obtain the harmonic contributions of the position signal. This method has the advantage of calculating both trap stiffness and photodetector calibration factor from the same dataset in situ. It also provides a direct method to avoid unwanted frequencies that could greatly affect calibration procedure, such as electric noise, for example.
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207
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Dorfman KD. The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics. J Biomech Eng 2018; 140:2653367. [PMID: 28857114 PMCID: PMC5816256 DOI: 10.1115/1.4037790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/16/2017] [Indexed: 12/28/2022]
Abstract
The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.
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Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and
Materials Science,
University of Minnesota—Twin Cities,
421 Washington Ave SE,
Minneapolis, MN 55455
e-mail:
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208
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Probing DNA-DNA Interactions with a Combination of Quadruple-Trap Optical Tweezers and Microfluidics. Methods Mol Biol 2018; 1486:275-293. [PMID: 27844432 DOI: 10.1007/978-1-4939-6421-5_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA metabolism and DNA compaction in vivo involve frequent interactions of remote DNA segments, mediated by proteins. In order to gain insight into such interactions, quadruple-trap optical tweezers have been developed. This technique provides an unprecedented degree of control through the ability to independently manipulate two DNA molecules in three dimensions. In this way, discrete regions of different DNA molecules can be brought into contact with one another, with a well-defined spatial configuration. At the same time, the tension and extension of the DNA molecules can be monitored. Furthermore, combining quadruple-trap optical tweezers with microfluidics makes fast buffer exchange possible, which is important for in situ generation of the dual DNA-protein constructs needed for these kinds of experiments. In this way, processes such as protein-mediated inter-DNA bridging can be studied with unprecedented control. This chapter provides a step-by-step description of how to perform a dual DNA manipulation experiment using combined quadruple-trap optical tweezers and microfluidics.
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209
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Polymer Mechanochemistry: A New Frontier for Physical Organic Chemistry. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2018. [DOI: 10.1016/bs.apoc.2018.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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210
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Keller N, delToro DJ, Smith DE. Single-Molecule Measurements of Motor-Driven Viral DNA Packaging in Bacteriophages Phi29, Lambda, and T4 with Optical Tweezers. Methods Mol Biol 2018; 1805:393-422. [PMID: 29971729 DOI: 10.1007/978-1-4939-8556-2_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Viral DNA packaging is a required step in the assembly of many dsDNA viruses. A molecular motor fueled by ATP hydrolysis packages the viral genome to near crystalline density inside a preformed prohead shell in ~5 min at room temperature. We describe procedures for measuring the packaging of single DNA molecules into single viral proheads with optical tweezers. Three viral packaging systems are described in detail: bacteriophages phi29 (φ29), lambda (λ), and T4. Two different approaches are described: (1) With φ29 and T4, prohead-motor complexes can be preassembled in bulk and packaging can be initiated in the optical tweezers by "feeding" a single DNA molecule to one of the complexes; (2) With φ29 and λ, packaging can be initiated in bulk then stalled, and a single prohead-motor-DNA complex can then be captured with optical tweezers and restarted. In both cases, the prohead is ultimately attached to one trapped microsphere and the end of the DNA being packaged is attached to a second trapped microsphere such that packaging of the DNA pulls the two microspheres together and the rate of packaging and force generated by the motor is directly measured in real time. These protocols allow for the effect of many experimental parameters on packaging dynamics to be studied such as temperature, ATP concentration, ionic conditions, structural changes to the DNA substrate, and mutations in the motor proteins. Procedures for capturing microspheres with the optical traps and different measurement modes are also described.
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Affiliation(s)
- Nicholas Keller
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Damian J delToro
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Douglas E Smith
- Department of Physics, University of California San Diego, La Jolla, CA, USA.
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211
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van Mameren J, Wuite GJL, Heller I. Introduction to Optical Tweezers: Background, System Designs, and Commercial Solutions. Methods Mol Biol 2018; 1665:3-23. [PMID: 28940061 DOI: 10.1007/978-1-4939-7271-5_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, while forces on the trapped objects can be accurately measured and exerted. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes them excellently suited to study biological processes from the single-cell down to the single-molecule level. In this chapter, we will provide an introduction on the use of optical tweezers in single-molecule approaches. We will introduce the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next we describe the components of an optical tweezers setup and their experimental relevance in single-molecule approaches. Finally, we provide a concise overview of commercial optical tweezers systems. Commercial systems are becoming increasingly available and provide access to single-molecule optical tweezers experiments without the need for a thorough background in physics.
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Affiliation(s)
- Joost van Mameren
- Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Iddo Heller
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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212
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Scherr MJ, Safaric B, Duderstadt KE. Noise in the Machine: Alternative Pathway Sampling is the Rule During DNA Replication. Bioessays 2017; 40. [PMID: 29282758 DOI: 10.1002/bies.201700159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/01/2017] [Indexed: 11/07/2022]
Abstract
The astonishing efficiency and accuracy of DNA replication has long suggested that refined rules enforce a single highly reproducible sequence of molecular events during the process. This view was solidified by early demonstrations that DNA unwinding and synthesis are coupled within a stable molecular factory, known as the replisome, which consists of conserved components that each play unique and complementary roles. However, recent single-molecule observations of replisome dynamics have begun to challenge this view, revealing that replication may not be defined by a uniform sequence of events. Instead, multiple exchange pathways, pauses, and DNA loop types appear to dominate replisome function. These observations suggest we must rethink our fundamental assumptions and acknowledge that each replication cycle may involve sampling of alternative, sometimes parallel, pathways. Here, we review our current mechanistic understanding of DNA replication while highlighting findings that exemplify multi-pathway aspects of replisome function and considering the broader implications.
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Affiliation(s)
- Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
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213
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Polotsky AA, Birshtein TM, Mercurieva AA, Leermakers FAM, Borisov OV. Unfolding of a comb-like polymer in a poor solvent: translation of macromolecular architecture in the force-deformation spectra. SOFT MATTER 2017; 13:9147-9161. [PMID: 29177317 DOI: 10.1039/c7sm01589e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A numerical self-consistent field modeling approach was employed to study the mechanical unfolding of a globule made by comb-like polymers in a poor solvent with the aim of unraveling how the macromolecular architecture affects the shape of the single-molecule force-deformation curves. We demonstrate that the dependence of the restoring force on the imposed extension of the main chain of the comb-like polymer exhibits a characteristic oscillatory shape in the intermediate deformation range. Theoretical arguments are developed that enable us to relate the shape of the patterns on the force-deformation curves to the molecular architecture (grafting density and length of the side chains) and interaction parameters. Thus, the results of our study suggest a new approach for the determination of macromolecular topology from single-molecule mechanical unfolding experiments.
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Affiliation(s)
- Alexey A Polotsky
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr, 199004 Saint Petersburg, Russia.
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214
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Sikora G, Wyłomańska A, Gajda J, Solé L, Akin EJ, Tamkun MM, Krapf D. Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis. Phys Rev E 2017; 96:062404. [PMID: 29347346 DOI: 10.1103/physreve.96.062404] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Indexed: 01/08/2023]
Abstract
Protein and lipid nanodomains are prevalent on the surface of mammalian cells. In particular, it has been recently recognized that ion channels assemble into surface nanoclusters in the soma of cultured neurons. However, the interactions of these molecules with surface nanodomains display a considerable degree of heterogeneity. Here, we investigate this heterogeneity and develop statistical tools based on the recurrence of individual trajectories to identify subpopulations within ion channels in the neuronal surface. We specifically study the dynamics of the K^{+} channel Kv1.4 and the Na^{+} channel Nav1.6 on the surface of cultured hippocampal neurons at the single-molecule level. We find that both these molecules are expressed in two different forms with distinct kinetics with regards to surface interactions, emphasizing the complex proteomic landscape of the neuronal surface. Further, the tools presented in this work provide new methods for the analysis of membrane nanodomains, transient confinement, and identification of populations within single-particle trajectories.
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Affiliation(s)
- Grzegorz Sikora
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.,Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Agnieszka Wyłomańska
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, 50-370 Wrocław, Poland
| | - Janusz Gajda
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, 50-370 Wrocław, Poland
| | - Laura Solé
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Elizabeth J Akin
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Michael M Tamkun
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523, USA.,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
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215
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Burgos-Bravo F, Figueroa NL, Casanova-Morales N, Quest AFG, Wilson CAM, Leyton L. Single-molecule measurements of the effect of force on Thy-1/αvβ3-integrin interaction using nonpurified proteins. Mol Biol Cell 2017; 29:326-338. [PMID: 29212879 PMCID: PMC5996956 DOI: 10.1091/mbc.e17-03-0133] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 10/10/2017] [Accepted: 12/01/2017] [Indexed: 12/11/2022] Open
Abstract
Single-molecule measurements combined with a novel mathematical strategy were applied to accurately characterize how bimolecular interactions respond to mechanical force, especially when protein purification is not possible. Specifically, we studied the effect of force on Thy-1/αvβ3 integrin interaction, a mediator of neuron-astrocyte communication. Thy-1 and αvβ3 integrin mediate bidirectional cell-to-cell communication between neurons and astrocytes. Thy-1/αvβ3 interactions stimulate astrocyte migration and the retraction of neuronal prolongations, both processes in which internal forces are generated affecting the bimolecular interactions that maintain cell–cell adhesion. Nonetheless, how the Thy-1/αvβ3 interactions respond to mechanical cues is an unresolved issue. In this study, optical tweezers were used as a single-molecule force transducer, and the Dudko-Hummer-Szabo model was applied to calculate the kinetic parameters of Thy-1/αvβ3 dissociation. A novel experimental strategy was implemented to analyze the interaction of Thy-1-Fc with nonpurified αvβ3-Fc integrin, whereby nonspecific rupture events were corrected by using a new mathematical approach. This methodology permitted accurately estimating specific rupture forces for Thy-1-Fc/αvβ3-Fc dissociation and calculating the kinetic and transition state parameters. Force exponentially accelerated Thy-1/αvβ3 dissociation, indicating slip bond behavior. Importantly, nonspecific interactions were detected even for purified proteins, highlighting the importance of correcting for such interactions. In conclusion, we describe a new strategy to characterize the response of bimolecular interactions to forces even in the presence of nonspecific binding events. By defining how force regulates Thy-1/αvβ3 integrin binding, we provide an initial step towards understanding how the neuron–astrocyte pair senses and responds to mechanical cues.
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Affiliation(s)
- Francesca Burgos-Bravo
- Cellular Communication Laboratory, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, 838-0453 Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Center for Studies of Exercise, Metabolism and Cancer, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, 838-0453 Santiago, Chile
| | - Nataniel L Figueroa
- Physics Department, Pontificia Universidad Católica de Chile, 782-0436 Santiago, Chile
| | - Nathalie Casanova-Morales
- Biochemistry and Molecular Biology Department, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, 838-0494 Santiago, Chile
| | - Andrew F G Quest
- Cellular Communication Laboratory, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, 838-0453 Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Center for Studies of Exercise, Metabolism and Cancer, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, 838-0453 Santiago, Chile
| | - Christian A M Wilson
- Biochemistry and Molecular Biology Department, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, 838-0494 Santiago, Chile
| | - Lisette Leyton
- Cellular Communication Laboratory, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, 838-0453 Santiago, Chile .,Advanced Center for Chronic Diseases (ACCDiS), Center for Studies of Exercise, Metabolism and Cancer, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, 838-0453 Santiago, Chile
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216
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Sukhov S, Dogariu A. Non-conservative optical forces. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:112001. [PMID: 28762956 DOI: 10.1088/1361-6633/aa834e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Undoubtedly, laser tweezers are the most recognized application of optically induced mechanical action. Their operation is usually described in terms of conservative forces originating from intensity gradients. However, the fundamental optical action on matter is non-conservative. We will review different manifestations of non-conservative optical forces (NCF) and discuss their dependence on the specific spatial properties of optical fields that generate them. New developments relevant to the NCF such as tractor beams and transversal forces are also discussed.
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Affiliation(s)
- Sergey Sukhov
- CREOL, The College of Optics and Photonics, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States of America
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217
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Revealing dynamics of helicase translocation on single-stranded DNA using high-resolution nanopore tweezers. Proc Natl Acad Sci U S A 2017; 114:11932-11937. [PMID: 29078357 DOI: 10.1073/pnas.1711282114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes that operate on DNA or RNA perform the core functions of replication and expression in all of biology. To gain high-resolution access to the detailed mechanistic behavior of these enzymes, we developed single-molecule picometer-resolution nanopore tweezers (SPRNT), a single-molecule technique in which the motion of polynucleotides through an enzyme is measured by a nanopore. SPRNT reveals two mechanical substates of the ATP hydrolysis cycle of the superfamily 2 helicase Hel308 during translocation on single-stranded DNA (ssDNA). By analyzing these substates at millisecond resolution, we derive a detailed kinetic model for Hel308 translocation along ssDNA that sheds light on how superfamily 1 and 2 helicases turn ATP hydrolysis into motion along DNA. Surprisingly, we find that the DNA sequence within Hel308 affects the kinetics of helicase translocation.
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218
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Zhao X, Zeng X, Lu C, Yan J. Studying the mechanical responses of proteins using magnetic tweezers. NANOTECHNOLOGY 2017; 28:414002. [PMID: 28766506 DOI: 10.1088/1361-6528/aa837e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mechanical stability of proteins has been extensively studied using AFM as a single-molecule force spectroscopy method. While this has led to many important results, these studies have been mainly limited to fast unfolding at a high-force regime due to the rapid mechanical drift in most AFM stretching experiments. Therefore, there is a gap between the knowledge obtained at a high-force regime and the mechanical properties of proteins at a lower force regime which is often more physiologically relevant. Recent studies have demonstrated that this gap can be addressed by stretching single protein molecules using magnetic tweezers, due to the excellent mechanical stability this technology offers. Here we review magnetic tweezers technology and its current application in studies of the force-dependent stability and interactions of proteins.
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Affiliation(s)
- Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
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219
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Vilhena JG, Gnecco E, Pawlak R, Moreno-Herrero F, Meyer E, Pérez R. Stick-Slip Motion of ssDNA over Graphene. J Phys Chem B 2017; 122:840-846. [PMID: 28945092 DOI: 10.1021/acs.jpcb.7b06952] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have performed molecular dynamics simulations of nanomanipulation experiments on short single-stranded DNA chains elastically driven on a graphene surface. After a brief transient, reproducible stick-slip cycles are observed on chains made by 10 units of thymine, cytosine, adenine, and guanine. The cycles have the periodicity of the graphene substrate, and take place via an intermediate stage, appearing as a dip in the sawtooth variations of lateral force recorded while the chains are manipulated. Guanine presents remarkable differences from the other bases, since a lower number of nucleotides are prone to stick to the substrate in this case. Nevertheless, the magnitudes of static friction and lateral stiffness are similar for all chains (30 pN and 0.7 N/m per adsorbed nucleotide respectively).
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Affiliation(s)
- J G Vilhena
- Department of Macromolecular Structures, Centro Nacional de Biotecnologa, Consejo Superior de Investigaciones Cientficas , 28049 Cantoblanco, Madrid, Spain.,Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid , E-28049 Madrid, Spain
| | - Enrico Gnecco
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena , D-07742 Jena, Germany
| | - Rémy Pawlak
- Department of Physics, University of Basel , Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnologa, Consejo Superior de Investigaciones Cientficas , 28049 Cantoblanco, Madrid, Spain
| | - Ernst Meyer
- Department of Physics, University of Basel , Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid , E-28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , E-28049 Madrid, Spain
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220
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Pirrotta A, Solomon GC, Franco I, Troisi A. Excitonic Coupling Modulated by Mechanical Stimuli. J Phys Chem Lett 2017; 8:4326-4332. [PMID: 28837767 DOI: 10.1021/acs.jpclett.7b01828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding energy transfer is of vital importance in a diverse range of applications from biological systems to photovoltaics. The ability to tune excitonic coupling in any of these systems, however, is generally limited. In this work, we have simulated a new class of single-molecule spectroscopy in which force microscopy is used to control the excitonic coupling between chromophores. Here we demonstrate that the excitonic coupling can be controlled by mechanical manipulation of the molecule (perylenediimide dimers and terrylenediimide-perylenediimide heterodimers) and can be tuned over a broad range of values (0.02-0.15 eV) that correspond to different regimes of exciton dynamics going from the folded to the elongated structure of the dimer. In all of the systems considered here, the switching from high to low coupling takes place simultaneously with the mechanical deformation detected by a strong increase and subsequent decay of the force. These simulations suggest that single-molecule force spectroscopy can be used to understand and eventually aid the design of excitonic devices.
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Affiliation(s)
- Alessandro Pirrotta
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Gemma C Solomon
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Ignacio Franco
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool , L69 7DZ Liverpool, United Kingdom
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221
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Chen Z, Chen L, Zhang W. Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level. Front Microbiol 2017; 8:1831. [PMID: 28979258 PMCID: PMC5611438 DOI: 10.3389/fmicb.2017.01831] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/06/2017] [Indexed: 12/16/2022] Open
Abstract
Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.
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Affiliation(s)
- Zixi Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China.,Center for Biosafety Research and Strategy, Tianjin UniversityTianjin, China
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223
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Hao Y, Canavan C, Taylor SS, Maillard RA. Integrated Method to Attach DNA Handles and Functionally Select Proteins to Study Folding and Protein-Ligand Interactions with Optical Tweezers. Sci Rep 2017; 7:10843. [PMID: 28883488 PMCID: PMC5589850 DOI: 10.1038/s41598-017-11214-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/21/2017] [Indexed: 12/15/2022] Open
Abstract
Optical tweezers has emerged as a powerful tool to study folding, ligand binding, and motor enzymes. The manipulation of proteins with optical tweezers requires attaching molecular handles to the protein of interest. Here, we describe a novel method that integrates the covalent attachment of DNA handles to target proteins with a selection step for functional and properly folded molecules. In addition, this method enables obtaining protein molecules in different liganded states and can be used with handles of different lengths. We apply this method to study the cAMP binding domain A (CBD-A) of Protein kinase A. We find that the functional selection step drastically improves the reproducibility and homogeneity of the single molecule data. In contrast, without a functional selection step, proteins often display misfolded conformations. cAMP binding stabilizes the CBD-A against a denaturing force, and increases the folded state lifetime. Data obtained with handles of 370 and 70 base pairs are indistinguishable, but at low forces short handles provide a higher spatial resolution. Altogether, this method is flexible, selects for properly folded molecules in different liganded states, and can be readily applicable to study protein folding or protein-ligand interactions with force spectroscopy that require molecular handles.
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Affiliation(s)
- Yuxin Hao
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - Clare Canavan
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - Susan S Taylor
- Department of Pharmacology & Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodrigo A Maillard
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
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224
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Kastelik JC, Dupont S, Yushkov KB, Molchanov VY, Gazalet J. Double acousto-optic deflector system for increased scanning range of laser beams. ULTRASONICS 2017; 80:62-65. [PMID: 28500905 DOI: 10.1016/j.ultras.2017.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
A new laser scanning system is presented based on two wide-band acousto-optic deflectors. The interaction medium is tellurium dioxide. Anisotropic interactions take place under two different tangential phase matching configurations in such a way that the acousto-optic bandwidths add up. We demonstrate the feasibility of such a cascade deflection system for the wavelength of λ=514nm. The total frequency bandwidth is Δf=100MHz, equally distributed between the two acousto-optic deflectors. The total angular scan at the output is Δθ=4.4° leading to 125 resolvable spots for a 1mm truncated Gaussian beam.
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Affiliation(s)
- J-C Kastelik
- Université Lille Nord de France, 59000 Lille, France; Université de Valenciennes et du Hainaut-Cambrésis, IEMN-DOAE, Le Mont Houy, 59313 Valenciennes Cedex 9, France; CNRS, UMR 8520, 59650 Villeneuve d'Ascq, France.
| | - S Dupont
- Université Lille Nord de France, 59000 Lille, France; Université de Valenciennes et du Hainaut-Cambrésis, IEMN-DOAE, Le Mont Houy, 59313 Valenciennes Cedex 9, France; CNRS, UMR 8520, 59650 Villeneuve d'Ascq, France
| | - K B Yushkov
- Acousto-Optical Research Center, National University of Science and Technology "MISIS", 4 Leninsky prospect, 119049 Moscow, Russia
| | - V Ya Molchanov
- Acousto-Optical Research Center, National University of Science and Technology "MISIS", 4 Leninsky prospect, 119049 Moscow, Russia
| | - J Gazalet
- Université Lille Nord de France, 59000 Lille, France; Université de Valenciennes et du Hainaut-Cambrésis, IEMN-DOAE, Le Mont Houy, 59313 Valenciennes Cedex 9, France; CNRS, UMR 8520, 59650 Villeneuve d'Ascq, France
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225
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Gao D, Ding W, Nieto-Vesperinas M, Ding X, Rahman M, Zhang T, Lim C, Qiu CW. Optical manipulation from the microscale to the nanoscale: fundamentals, advances and prospects. LIGHT, SCIENCE & APPLICATIONS 2017; 6:e17039. [PMID: 30167291 PMCID: PMC6062326 DOI: 10.1038/lsa.2017.39] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/28/2017] [Accepted: 03/07/2017] [Indexed: 05/07/2023]
Abstract
Since the invention of optical tweezers, optical manipulation has advanced significantly in scientific areas such as atomic physics, optics and biological science. Especially in the past decade, numerous optical beams and nanoscale devices have been proposed to mechanically act on nanoparticles in increasingly precise, stable and flexible ways. Both the linear and angular momenta of light can be exploited to produce optical tractor beams, tweezers and optical torque from the microscale to the nanoscale. Research on optical forces helps to reveal the nature of light-matter interactions and to resolve the fundamental aspects, which require an appropriate description of momenta and the forces on objects in matter. In this review, starting from basic theories and computational approaches, we highlight the latest optical trapping configurations and their applications in bioscience, as well as recent advances down to the nanoscale. Finally, we discuss the future prospects of nanomanipulation, which has considerable potential applications in a variety of scientific fields and everyday life.
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Affiliation(s)
- Dongliang Gao
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- College of Physics, Optoelectronics and Energy, Soochow University, Suzhou 215006, China
| | - Weiqiang Ding
- Department of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Manuel Nieto-Vesperinas
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, Madrid 28049, Spain
| | - Xumin Ding
- Department of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Mahdy Rahman
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- Department of Electrical and Computer Engineering, North South University, Dhaka 1229, Bangladesh
| | - Tianhang Zhang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - ChweeTeck Lim
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
- Department of Mechanical Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Cheng-Wei Qiu
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science and Technology, Shenzhen University, Shenzhen 518060, China
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226
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Naranjo T, Cerrón F, Nieto-Ortega B, Latorre A, Somoza Á, Ibarra B, Pérez EM. Mechanical measurement of hydrogen bonded host-guest systems under non-equilibrium, near-physiological conditions. Chem Sci 2017; 8:6037-6041. [PMID: 28989633 PMCID: PMC5625567 DOI: 10.1039/c7sc03044d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 07/29/2017] [Indexed: 11/26/2022] Open
Abstract
Decades after the birth of supramolecular chemistry, there are many techniques to measure noncovalent interactions, such as hydrogen bonding, under equilibrium conditions. As ensembles of molecules rapidly lose coherence, we cannot extrapolate bulk data to single-molecule events under non-equilibrium conditions, more relevant to the dynamics of biological systems. We present a new method that exploits the high force resolution of optical tweezers to measure at the single molecule level the mechanical strength of a hydrogen bonded host-guest pair out of equilibrium and under near-physiological conditions. We utilize a DNA reporter to unambiguously isolate single binding events. The Hamilton receptor-cyanuric acid host-guest system is used as a test bed. The force required to dissociate the host-guest system is ∼17 pN and increases with the pulling rate as expected for a system under non-equilibrium conditions. Blocking one of the hydrogen bonding sites results in a significant decrease of the force-to-break by 1-2 pN, pointing out the ability of the method to resolve subtle changes in the mechanical strength of the binding due to the individual H-bonding components. We believe the method will prove to be a versatile tool to address important questions in supramolecular chemistry.
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Affiliation(s)
- Teresa Naranjo
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Fernando Cerrón
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Belén Nieto-Ortega
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Alfonso Latorre
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Álvaro Somoza
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
- Nanobiotecnología (IMDEA-Nanociencia) , Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 , Madrid , Spain
| | - Borja Ibarra
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
- Nanobiotecnología (IMDEA-Nanociencia) , Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 , Madrid , Spain
| | - Emilio M Pérez
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
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227
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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228
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229
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Stochastic analysis of time series for the spatial positions of particles trapped in optical tweezers. Sci Rep 2017; 7:4832. [PMID: 28684757 PMCID: PMC5500579 DOI: 10.1038/s41598-017-04557-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 04/27/2017] [Indexed: 11/21/2022] Open
Abstract
We propose a nonlinear method for the analysis of the time series for the spatial position of a bead trapped in optical tweezers, which enables us to reconstruct its dynamical equation of motion. The main advantage of the method is that all the functions and parameters of the dynamics are determined directly (non-parametrically) from the measured series. It also allows us to determine, for the first time to our knowledge, the spatial-dependence of the diffusion coefficient of a bead in an optical trap, and to demonstrate that it is not in general constant. This is in contrast with the main assumption of the popularly-used power spectrum calibration method. The proposed method is validated via synthetic time series for the bead position with spatially-varying diffusion coefficients. Our detailed analysis of the measured time series reveals that the power spectrum analysis overestimates considerably the force constant.
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230
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Zhang Y. Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers. Protein Sci 2017; 26:1252-1265. [PMID: 28097727 PMCID: PMC5477538 DOI: 10.1002/pro.3116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/03/2017] [Indexed: 01/17/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are universal molecular engines that drive membrane fusion. Particularly, synaptic SNAREs mediate fast calcium-triggered fusion of neurotransmitter-containing vesicles with plasma membranes for synaptic transmission, the basis of all thought and action. During membrane fusion, complementary SNAREs located on two apposed membranes (often called t- and v-SNAREs) join together to assemble into a parallel four-helix bundle, releasing the energy to overcome the energy barrier for fusion. A long-standing hypothesis suggests that SNAREs act like a zipper to draw the two membranes into proximity and thereby force them to fuse. However, a quantitative test of this SNARE zippering hypothesis was hindered by difficulties to determine the energetics and kinetics of SNARE assembly and to identify the relevant folding intermediates. Here, we first review different approaches that have been applied to study SNARE assembly and then focus on high-resolution optical tweezers. We summarize the folding energies, kinetics, and pathways of both wild-type and mutant SNARE complexes derived from this new approach. These results show that synaptic SNAREs assemble in four distinct stages with different functions: slow N-terminal domain association initiates SNARE assembly; a middle domain suspends and controls SNARE assembly; and rapid sequential zippering of the C-terminal domain and the linker domain directly drive membrane fusion. In addition, the kinetics and pathway of the stagewise assembly are shared by other SNARE complexes. These measurements prove the SNARE zippering hypothesis and suggest new mechanisms for SNARE assembly regulated by other proteins.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale School of MedicineYale UniversityNew HavenConnecticut06511
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231
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Shrestha P, Jonchhe S, Emura T, Hidaka K, Endo M, Sugiyama H, Mao H. Confined space facilitates G-quadruplex formation. NATURE NANOTECHNOLOGY 2017; 12:582-588. [PMID: 28346457 DOI: 10.1038/nnano.2017.29] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 02/06/2017] [Indexed: 05/25/2023]
Abstract
Molecular simulations suggest that the stability of a folded macromolecule increases in a confined space due to entropic effects. However, due to the interactions between the confined molecular structure and the walls of the container, clear-cut experimental evidence for this prediction is lacking. Here, using DNA origami nanocages, we show the pure effect of confined space on the property of individual human telomeric DNA G-quadruplexes. We induce targeted mechanical unfolding of the G-quadruplex while leaving the nanocage unperturbed. We find that the mechanical and thermodynamic stabilities of the G-quadruplex inside the nanocage increase with decreasing cage size. Compared to the case of diluted or molecularly crowded buffer solutions, the G-quadruplex inside the nanocage is significantly more stable, showing a 100 times faster folding rate. Our findings suggest the possibility of co-replicational or co-transcriptional folding of G-quadruplex inside the polymerase machinery in cells.
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Affiliation(s)
- Prakash Shrestha
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA
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232
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Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics. Proc Natl Acad Sci U S A 2017. [PMID: 28634300 DOI: 10.1073/pnas.1705642114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules' interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.
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233
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Yasuda M, Takei K, Arie T, Akita S. Direct measurement of optical trapping force gradient on polystyrene microspheres using a carbon nanotube mechanical resonator. Sci Rep 2017; 7:2825. [PMID: 28588196 PMCID: PMC5460215 DOI: 10.1038/s41598-017-03068-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/21/2017] [Indexed: 11/10/2022] Open
Abstract
Optical tweezers based on optical radiation pressure are widely used to manipulate nanoscale to microscale particles. This study demonstrates direct measurement of the optical force gradient distribution acting on a polystyrene (PS) microsphere using a carbon nanotube (CNT) mechanical resonator, where a PS microsphere with 3 μm diameter is welded at the CNT tip using laser heating. With the CNT mechanical resonator with PS microsphere, we measured the distribution of optical force gradient with resolution near the thermal noise limit of 0.02 pN/μm in vacuum, in which condition enables us to high accuracy measurement using the CNT mechanical resonator because of reduced mechanical damping from surrounding fluid. The obtained force gradient and the force gradient distribution agree well with theoretical values calculated using Lorenz–Mie theory.
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Affiliation(s)
- Masaaki Yasuda
- Department of Physics and Electronics, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Japan
| | - Kuniharu Takei
- Department of Physics and Electronics, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Japan
| | - Takayuki Arie
- Department of Physics and Electronics, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Japan
| | - Seiji Akita
- Department of Physics and Electronics, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Japan.
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234
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Frenkel I, Niv A. Light generated bubble for microparticle propulsion. Sci Rep 2017; 7:2814. [PMID: 28588312 PMCID: PMC5460221 DOI: 10.1038/s41598-017-03114-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/24/2017] [Indexed: 11/25/2022] Open
Abstract
Light activated motion of micron-sized particles with effective forces in the range of micro-Newtons is hereby proposed and demonstrated. Our investigation shows that this exceptional amount of force results from accumulation of light-generated heat by a micron-sized particle that translates into motion due to a phase transition in the nearby water. High-speed imagery indicates the role of bubble expansion and later collapse in this event. Comparing observations with known models reveals a dynamic behavior controlled by polytropic trapped vapor and the inertia of the surrounding liquid. The potential of the proposed approach is demonstrated by realization of disordered optical media with binary light-activated switching from opacity to high transparency.
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Affiliation(s)
- Ido Frenkel
- Swiss Institute for Dryland Environmental and Energy Research, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel.,The Unit of Energy Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Avi Niv
- Swiss Institute for Dryland Environmental and Energy Research, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel.
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235
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Chen YT, Chang KC, Hu HT, Chen YL, Lin YH, Hsu CF, Chang CF, Chang KY, Wen JD. Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot. Nucleic Acids Res 2017; 45:6011-6022. [PMID: 28334864 PMCID: PMC5449628 DOI: 10.1093/nar/gkx134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 12/28/2022] Open
Abstract
Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes. We found that the first ribosome target stem was resistant to unwinding when the neighboring loop was confined along the stem; such constrained conformation was dependent on the presence of consecutive adenosines in this loop. Mutations that disrupted the distal base triples abolished all remaining tertiary base pairs. Changes in frameshifting efficiency correlated with the stem unwinding resistance. Our results demonstrate that various tertiary base pairs are coordinated inside a highly efficient frameshift-stimulating RNA pseudoknot and suggest a mechanism by which mechanical resistance of the pseudoknot may persistently act on translocating ribosomes.
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Affiliation(s)
- Yu-Ting Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Teng Hu
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Yi-Lan Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - You-Hsin Lin
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chiung-Fang Hsu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Fu Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Kung-Yao Chang
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
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236
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237
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Collins DJ, Khoo BL, Ma Z, Winkler A, Weser R, Schmidt H, Han J, Ai Y. Selective particle and cell capture in a continuous flow using micro-vortex acoustic streaming. LAB ON A CHIP 2017; 17:1769-1777. [PMID: 28394386 DOI: 10.1039/c7lc00215g] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Acoustic streaming has emerged as a promising technique for refined microscale manipulation, where strong rotational flow can give rise to particle and cell capture. In contrast to hydrodynamically generated vortices, acoustic streaming is rapidly tunable, highly scalable and requires no external pressure source. Though streaming is typically ignored or minimized in most acoustofluidic systems that utilize other acoustofluidic effects, we maximize the effect of acoustic streaming in a continuous flow using a high-frequency (381 MHz), narrow-beam focused surface acoustic wave. This results in rapid fluid streaming, with velocities orders of magnitude greater than that of the lateral flow, to generate fluid vortices that extend the entire width of a 400 μm wide microfluidic channel. We characterize the forces relevant for vortex formation in a combined streaming/lateral flow system, and use these acoustic streaming vortices to selectively capture 2 μm from a mixed suspension with 1 μm particles and human breast adenocarcinoma cells (MDA-231) from red blood cells.
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Affiliation(s)
- David J Collins
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore 487372, Singapore.
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238
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Huang Q, Lee J, Arce FT, Yoon I, Angsantikul P, Liu J, Shi Y, Villanueva J, Thamphiwatana S, Ma X, Zhang L, Chen S, Lal R, Sirbuly DJ. Nanofibre optic force transducers with sub-piconewton resolution via near-field plasmon-dielectric interactions. NATURE PHOTONICS 2017; 11:352-355. [PMID: 29576804 PMCID: PMC5863742 DOI: 10.1038/nphoton.2017.74] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 04/12/2017] [Indexed: 05/31/2023]
Abstract
Ultrasensitive nanomechanical instruments, including the atomic force microscope (AFM)1-4 and optical and magnetic tweezers5-8, have helped shed new light on the complex mechanical environments of biological processes. However, it is difficult to scale down the size of these instruments due to their feedback mechanisms9, which, if overcome, would enable high-density nanomechanical probing inside materials. A variety of molecular force probes including mechanophores10, quantum dots11, fluorescent pairs12,13 and molecular rotors14-16 have been designed to measure intracellular stresses; however, fluorescence-based techniques can have short operating times due to photo-instability and it is still challenging to quantify the forces with high spatial and mechanical resolution. Here, we develop a compact nanofibre optic force transducer (NOFT) that utilizes strong near-field plasmon-dielectric interactions to measure local forces with a sensitivity of <200 fN. The NOFT system is tested by monitoring bacterial motion and heart-cell beating as well as detecting infrasound power in solution.
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Affiliation(s)
- Qian Huang
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Joon Lee
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Fernando Teran Arce
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Ilsun Yoon
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Pavimol Angsantikul
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Justin Liu
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Yuesong Shi
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Josh Villanueva
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Soracha Thamphiwatana
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Xuanyi Ma
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Liangfang Zhang
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Shaochen Chen
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Ratnesh Lal
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Donald J. Sirbuly
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
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239
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Cuculis L, Schroeder CM. A Single-Molecule View of Genome Editing Proteins: Biophysical Mechanisms for TALEs and CRISPR/Cas9. Annu Rev Chem Biomol Eng 2017; 8:577-597. [PMID: 28489428 DOI: 10.1146/annurev-chembioeng-060816-101603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Exciting new advances in genome engineering have unlocked the potential to radically alter the treatment of human disease. In this review, we discuss the application of single-molecule techniques to uncover the mechanisms behind two premier classes of genome editing proteins: transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas). These technologies have facilitated a striking number of gene editing applications in a variety of organisms; however, we are only beginning to understand the molecular mechanisms governing the DNA editing properties of these systems. Here, we discuss the DNA search and recognition process for TALEs and Cas9 that have been revealed by recent single-molecule experiments.
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Affiliation(s)
- Luke Cuculis
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801;
| | - Charles M Schroeder
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; .,Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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240
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Jiang C, Kaul N, Campbell J, Meyhofer E. A novel dual-color bifocal imaging system for single-molecule studies. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:053705. [PMID: 28571404 DOI: 10.1063/1.4983648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this paper, we report the design and implementation of a dual-color bifocal imaging (DBI) system that is capable of acquiring two spectrally distinct, spatially registered images of objects located in either same or two distinct focal planes. We achieve this by separating an image into two channels with distinct chromatic properties and independently focusing both images onto a single CCD camera. The two channels in our device are registered with subpixel accuracy, and long-term stability of the registered images with nanometer-precision was accomplished by reducing the drift of the images to ∼5 nm. We demonstrate the capabilities of our DBI system by imaging biomolecules labeled with spectrally distinct dyes and micro- and nano-sized spheres located in different focal planes.
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Affiliation(s)
- Chang Jiang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Neha Kaul
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jenna Campbell
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Edgar Meyhofer
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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241
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Ivinskaya A, Petrov MI, Bogdanov AA, Shishkin I, Ginzburg P, Shalin AS. Plasmon-assisted optical trapping and anti-trapping. LIGHT, SCIENCE & APPLICATIONS 2017; 6:e16258. [PMID: 30167251 PMCID: PMC6062188 DOI: 10.1038/lsa.2016.258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/26/2016] [Accepted: 11/23/2016] [Indexed: 05/23/2023]
Abstract
The ability to manipulate small objects with focused laser beams has opened a venue for investigating dynamical phenomena relevant to both fundamental and applied science. Nanophotonic and plasmonic structures enable superior performance in optical trapping via highly confined near-fields. In this case, the interplay between the excitation field, re-scattered fields and the eigenmodes of a structure can lead to remarkable effects; one such effect, as reported here, is particle trapping by laser light in a vicinity of metal surface. Surface plasmon excitation at the metal substrate plays a key role in tailoring the optical forces acting on a nearby particle. Depending on whether the illuminating Gaussian beam is focused above or below the metal-dielectric interface, an order-of-magnitude enhancement or reduction of the trap stiffness is achieved compared with that of standard glass substrates. Furthermore, a novel plasmon-assisted anti-trapping effect (particle repulsion from the beam axis) is predicted and studied. A highly accurate particle sorting scheme based on the new anti-trapping effect is analyzed. The ability to distinguish and configure various electromagnetic channels through the developed analytical theory provides guidelines for designing auxiliary nanostructures and achieving ultimate control over mechanical motion at the micro- and nano-scales.
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Affiliation(s)
- Aliaksandra Ivinskaya
- Department of Nanophotonics and Metamaterials, ITMO University, Birzhevaja Line, 14, 199034 St Petersburg, Russia
| | - Mihail I Petrov
- Department of Nanophotonics and Metamaterials, ITMO University, Birzhevaja Line, 14, 199034 St Petersburg, Russia
| | - Andrey A Bogdanov
- Department of Nanophotonics and Metamaterials, ITMO University, Birzhevaja Line, 14, 199034 St Petersburg, Russia
| | - Ivan Shishkin
- School of Electrical Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Pavel Ginzburg
- Department of Nanophotonics and Metamaterials, ITMO University, Birzhevaja Line, 14, 199034 St Petersburg, Russia
- School of Electrical Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Alexander S Shalin
- Department of Nanophotonics and Metamaterials, ITMO University, Birzhevaja Line, 14, 199034 St Petersburg, Russia
- Kotel’nikov Institute of Radio Engineering and Electronics of Russian Academy of Sciences (Ulyanovsk branch), Goncharova Street 48/2, 432071 Ulyanovsk, Russia
- Ulyanovsk State University, Lev Tolstoy Street 42, 432017 Ulyanovsk, Russia
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242
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Baker JE, Badman RP, Wang MD. Nanophotonic trapping: precise manipulation and measurement of biomolecular arrays. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 10. [PMID: 28439980 DOI: 10.1002/wnan.1477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/20/2017] [Accepted: 03/22/2017] [Indexed: 12/13/2022]
Abstract
Optical trapping is a powerful and widely used laboratory technique in the biological and materials sciences that enables rapid manipulation and measurement at the nanometer scale. However, expanding the analytical throughput of this technique beyond the serial capabilities of established single-trap microscope-based optical tweezers remains a current goal in the field. In recent years, advances in nanotechnology have been leveraged to create innovative optical trapping methods that increase the number of available optical traps and permit parallel manipulation and measurement of arrays of optically trapped targets. In particular, nanophotonic trapping holds significant promise for integration with other lab-on-a-chip technologies to yield compact, robust analytical devices. In this review, we highlight progress in nanophotonic manipulation and measurement, as well as the potential for implementing these on-chip functionalities in biological research and biomedical applications. WIREs Nanomed Nanobiotechnol 2018, 10:e1477. doi: 10.1002/wnan.1477 This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- James E Baker
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA.,Department of Physics - LASSP, Cornell University, Ithaca, NY, USA
| | - Ryan P Badman
- Department of Physics - LASSP, Cornell University, Ithaca, NY, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA.,Department of Physics - LASSP, Cornell University, Ithaca, NY, USA
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243
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Ye F, Soltani M, Inman JT, Wang MD. Tunable nanophotonic array traps with enhanced force and stability. OPTICS EXPRESS 2017; 25:7907-7918. [PMID: 28380908 DOI: 10.1364/oe.25.007907] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A nanophotonic trapping platform based on on-chip tunable optical interference allows parallel processing of biomolecules and holds promise to make single molecule manipulation and precision measurements more easily and broadly available. The nanophotonic standing wave array trap (nSWAT) device [Nat. Nanotechnol. 9, 448 (2014); Nano Lett. 16, 6661 (2016)] represents such a platform and can trap a large array of beads by the evanescent field of the standing wave of a nanophotonic waveguide and reposition them using an integrated microheater. In this paper, by taking a systematic design approach, we present a new generation of nSWAT devices with significant enhancement of the optical trapping force, stiffness, and stability, while the quality of the standing wave trap is resistant to fabrication imperfections. The device is implemented on a silicon nitride photonic platform and operates at 1064 nm wavelength which permits low optical absorption by the aqueous solution. Such performance improvements open a broader range of applications based on these on-chip optical traps.
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244
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Abstract
Telomeres are specialized chromatin structures that protect chromosome ends from dangerous processing events. In most tissues, telomeres shorten with each round of cell division, placing a finite limit on cell growth. In rapidly dividing cells, including the majority of human cancers, cells bypass this growth limit through telomerase-catalyzed maintenance of telomere length. The dynamic properties of telomeres and telomerase render them difficult to study using ensemble biochemical and structural techniques. This review describes single-molecule approaches to studying how individual components of telomeres and telomerase contribute to function. Single-molecule methods provide a window into the complex nature of telomeres and telomerase by permitting researchers to directly visualize and manipulate the individual protein, DNA, and RNA molecules required for telomere function. The work reviewed in this article highlights how single-molecule techniques have been utilized to investigate the function of telomeres and telomerase.
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Affiliation(s)
- Joseph W Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064; .,Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064; .,Center for Molecular Biology of RNA, Santa Cruz, California 95064
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245
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Wan M, Sun D, Wang S, Wu J, Yang Y, Wang K, He Q, Wang G, Bai J. Influence of concentration on distribution properties of stretched-DNA in the MEC studied with fluorescence imaging and drop shape analyzing. Colloids Surf B Biointerfaces 2017; 151:11-18. [PMID: 27939693 DOI: 10.1016/j.colsurfb.2016.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/19/2016] [Accepted: 12/01/2016] [Indexed: 11/28/2022]
Abstract
Stretching and manipulating DNA efficiently is significant for exploring the properties and applications of single DNA molecules. Here, the influence of concentrations of buffer and DNA on properties of stretched DNA molecules in the molecular evaporation combing (MEC) is investigated systematically with the single molecule fluorescence imaging microscopy and the high-precision drop shape analyzing technology. The stretched degree and uniformity of combed DNA molecules decrease as the buffer concentration are increased from 7 to 20mM. When the buffer concentration changes from 12 to 15mM, the stretched DNA molecules are apt to form a ringlike pattern. During the MEC process, there exist two kinds of evaporation modes, i.e., the constant contact angle mode and the constant contact radius mode. The former only takes effect in the lower concentration of buffer and DNA, enabling the uniform stretching. While the latter plays the leading role in the higher concentration, promoting the formation of the ringlike pattern of DNA molecules.
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Affiliation(s)
- Mengjiao Wan
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Dan Sun
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Shuang Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jianguo Wu
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yuanyuan Yang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Kaige Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Qingli He
- School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Guiren Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; Mechanical Engineering Department & Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jintao Bai
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
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246
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Conteduca D, Dell'Olio F, Krauss TF, Ciminelli C. Photonic and Plasmonic Nanotweezing of Nano- and Microscale Particles. APPLIED SPECTROSCOPY 2017; 71:367-390. [PMID: 28287314 DOI: 10.1177/0003702816684839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The ability to manipulate and sense biological molecules is important in many life science domains, such as single-molecule biophysics, the development of new drugs and cancer detection. Although the manipulation of biological matter at the nanoscale continues to be a challenge, several types of nanotweezers based on different technologies have recently been demonstrated to address this challenge. In particular, photonic and plasmonic nanotweezers are attracting a strong research effort especially because they are efficient and stable, they offer fast response time, and avoid any direct physical contact with the target object to be trapped, thus preventing its disruption or damage. In this paper, we critically review photonic and plasmonic resonant technologies for biomolecule trapping, manipulation, and sensing at the nanoscale, with a special emphasis on hybrid photonic/plasmonic nanodevices allowing a very strong light-matter interaction. The state-of-the-art of competing technologies, e.g., electronic, magnetic, acoustic and carbon nanotube-based nanotweezers, and a description of their applications are also included.
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247
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Le MT, Kasprzak WK, Kim T, Gao F, Young MYL, Yuan X, Shapiro BA, Seog J, Simon AE. Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch. eLife 2017; 6:e22883. [PMID: 28186489 PMCID: PMC5336357 DOI: 10.7554/elife.22883] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/07/2017] [Indexed: 11/29/2022] Open
Abstract
Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3'UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ3 required five upstream adenylates, and H4a/Ψ3 was necessary for cooperative association of two other hairpins (H5/H4b) in Mg2+. SMD recapitulated the TSS unfolding order in the absence of Mg2+, showed dependence of the resistance to pulling on the 3D orientation and gave structural insights into the measured contour lengths of the TSS structure elements. Adenylate mutations eliminated one-site RdRp binding to the 3'UTR, suggesting that RdRp binding to the adenylates disrupts H4a/Ψ3, leading to loss of H5/H4b interaction and promoting a conformational switch interrupting translation and promoting replication.
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Affiliation(s)
- My-Tra Le
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | - Wojciech K Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Taejin Kim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, United States
| | - Feng Gao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | - Megan YL Young
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | - Xuefeng Yuan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
| | - Bruce A Shapiro
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, United States
| | - Joonil Seog
- Department of Materials Science and Engineering, University of Maryland, College Park, United States
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
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da Silva M, Lenton S, Hughes M, Brockwell DJ, Dougan L. Assessing the Potential of Folded Globular Polyproteins As Hydrogel Building Blocks. Biomacromolecules 2017; 18:636-646. [PMID: 28006103 PMCID: PMC5348097 DOI: 10.1021/acs.biomac.6b01877] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 12/21/2016] [Indexed: 01/14/2023]
Abstract
The native states of proteins generally have stable well-defined folded structures endowing these biomolecules with specific functionality and molecular recognition abilities. Here we explore the potential of using folded globular polyproteins as building blocks for hydrogels. Photochemically cross-linked hydrogels were produced from polyproteins containing either five domains of I27 ((I27)5), protein L ((pL)5), or a 1:1 blend of these proteins. SAXS analysis showed that (I27)5 exists as a single rod-like structure, while (pL)5 shows signatures of self-aggregation in solution. SANS measurements showed that both polyprotein hydrogels have a similar nanoscopic structure, with protein L hydrogels being formed from smaller and more compact clusters. The polyprotein hydrogels showed small energy dissipation in a load/unload cycle, which significantly increased when the hydrogels were formed in the unfolded state. This study demonstrates the use of folded proteins as building blocks in hydrogels, and highlights the potential versatility that can be offered in tuning the mechanical, structural, and functional properties of polyproteins.
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Affiliation(s)
- Marcelo
A. da Silva
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Samuel Lenton
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Matthew Hughes
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David J. Brockwell
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna Dougan
- School of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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249
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Silva EF, Bazoni RF, Ramos EB, Rocha MS. DNA-doxorubicin interaction: New insights and peculiarities. Biopolymers 2017; 107. [PMID: 27718222 DOI: 10.1002/bip.22998] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/25/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
We have investigated the interaction of the DNA molecule with the anticancer drug doxorubicin (doxo) by using three different experimental techniques: single molecule stretching, single molecule imaging, and dynamic light scattering. Such techniques allowed us to get new insights on the mechanical behavior of the DNA-doxo complexes as well as on the physical chemistry of the interaction. First, the contour length data obtained from single molecule stretching were used to extract the physicochemical parameters of the DNA-doxo interaction under different buffer conditions. This analysis has proven that the physical chemistry of such interaction can be modulated by changing the ionic strength of the surrounding buffer. In particular we have found that at low ionc strengths doxo interacts with DNA by simple intercalation (no aggregation) and/or by forming bound dimers. For high ionic strengths, otherwise, doxo-doxo self-association is enhanced, giving rise to the formation of bound doxo aggregates composed by 3 to 4 molecules along the double-helix. On the other hand, the results obtained for the persistence length of the DNA-doxo complexes is strongly force-dependent, presenting different behaviors when measured with stretching or non-stretching techniques.
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Affiliation(s)
- E F Silva
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R F Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E B Ramos
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M S Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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250
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Ryu JK, Jahn R, Yoon TY. Review: Progresses in understanding N-ethylmaleimide sensitive factor (NSF) mediated disassembly of SNARE complexes. Biopolymers 2017; 105:518-31. [PMID: 27062050 DOI: 10.1002/bip.22854] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/19/2016] [Accepted: 04/06/2016] [Indexed: 11/09/2022]
Abstract
N-ethylmaleimide sensitive factor (NSF) is a key protein of intracellular membrane traffic. NSF is a highly conserved protein belonging to the ATPases associated with other activities (AAA+ proteins). AAA+ share common domains and all transduce ATP hydrolysis into major conformational movements that are used to carry out conformational work on client proteins. Together with its cofactor SNAP, NSF is specialized on disassembling highly stable SNARE complexes that form after each membrane fusion event. Although essential for all eukaryotic cells, however, the details of this reaction have long been enigmatic. Recently, major progress has been made in both elucidating the structure of NSF/SNARE complexes and in understanding the reaction mechanism. Advances in both cryo EM and single molecule measurements suggest that NSF, together with its cofactor SNAP, imposes a tight grip on the SNARE complex. After ATP hydrolysis and phosphate release, it then builds up mechanical tension that is ultimately used to rip apart the SNAREs in a single burst. Because the AAA domains are extremely well-conserved, the molecular mechanism elucidated for NSF is presumably shared by many other AAA+ ATPases. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 518-531, 2016.
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Affiliation(s)
- Je-Kyung Ryu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, CJ, 2628, the Netherlands
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Tae-Young Yoon
- Center for Nanomedicine, Institute for Basic Science (IBS) and Y-IBS Institute, Yonsei University, Seoul, 03722, South Korea
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