51
|
Chen Z, Kuang T, Han X, Li G, Zeng W, Xiong W, Xiao G, Luo H. Differential displacement measurement of the levitated particle using D-shaped mirrors in the optical tweezers. OPTICS EXPRESS 2022; 30:30791-30798. [PMID: 36242176 DOI: 10.1364/oe.468264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Displacement measurement using a D-shaped mirror is a key technology in optical tweezers, which have emerged as an important tool for precision measurement. In this paper, we first study the influences of installation errors for the D-shaped mirror on the displacement measurement. The calibration factor and sensitivity of the different installation parameters are quantified. The results show that the variation of the calibration factor obeys the cosine curve with the angle error, and the sensitivity increases exponentially with the translation error. Besides, we find that the translation error will also lead to crosstalk between transverse and axial displacement. Our work will contribute to improving the performance of optical tweezers for the application in precision measurement and basic physics.
Collapse
|
52
|
Shen Y, Weitz DA, Forde NR, Shayegan M. Line optical tweezers as controllable micromachines: techniques and emerging trends. SOFT MATTER 2022; 18:5359-5365. [PMID: 35819100 DOI: 10.1039/d2sm00259k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the past three decades, the technology of optical tweezers has made significant contributions in various scientific areas, including optics, photonics, and nanosciences. Breakthroughs include manipulating particles in both static and dynamic ways, particle sorting, and constructing controllable micromachines. Advances in shaping and controlling the laser beam profile enable control over the position and location of the trap, which has many possible applications. A line optical tweezer (LOT) can be created by rapidly moving a spot optical tweezer using a tool such as a galvanometer mirror or an acousto-optic modulator. By manipulating the intensity profile along the beam line to be asymmetric or non-uniform, the technique can be adapted to various specific applications. Among the many exciting applications of line optical tweezers, in this work, we discuss in detail applications of LOT, including probing colloidal interactions, transporting and sorting of colloidal microspheres, self-propelled motions, trapping anisotropic particles, exploring colloidal interactions at fluid-fluid interfaces, and building optical thermal ratchets. We further discuss prospective applications in each of these areas of soft matter, including polymeric and biological soft materials.
Collapse
Affiliation(s)
- Yinan Shen
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
| | - David A Weitz
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Marjan Shayegan
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
| |
Collapse
|
53
|
Yadav S, Devi A, De AK. Enhanced optical force on multilayered dielectric nanoparticles by tuning material properties and nature of excitation: a theoretical investigation. NANOSCALE ADVANCES 2022; 4:2979-2987. [PMID: 36133514 PMCID: PMC9419164 DOI: 10.1039/d2na00280a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/06/2022] [Indexed: 06/16/2023]
Abstract
Using dipole approximation, a comparative study of trapping force/potential on different types of dielectric nanoparticles is presented. The trapping force for multilayered nanoparticles, i.e. core-shell-shell type nanoparticles, is found to be enhanced compared with both core-only type and core-shell type nanoparticles. It is shown that an appropriate choice of material and thickness of the middle layer results in tuning the polarizability, thereby playing a vital role in determining the trapping efficiency for core-shell-shell type nanoparticles. Further, the effect of optical nonlinearity under femtosecond pulsed excitation is investigated and it is elucidated that depending on the specific need (i.e. high force versus long confinement time), the nature of excitation (i.e. pulsed excitation or continuous-wave excitation) can be judiciously chosen. These findings are promised to open up new prospects for controlled nanoscale trapping and manipulation across different fields of nanoscience and nanotechnology.
Collapse
Affiliation(s)
- Sumit Yadav
- Condensed Phase Dynamics Group, Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Sector 81 SAS Nagar Punjab 140306 India
| | - Anita Devi
- Condensed Phase Dynamics Group, Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Sector 81 SAS Nagar Punjab 140306 India
| | - Arijit K De
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Sector 81 SAS Nagar Punjab 140306 India
| |
Collapse
|
54
|
Manca M, Zhang C, Scheffold F, Salentinig S. Optical tweezer platform for the characterization of pH-triggered colloidal transformations in the oleic acid/water system. J Colloid Interface Sci 2022; 627:610-620. [PMID: 35872418 DOI: 10.1016/j.jcis.2022.07.028] [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: 04/29/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 10/17/2022]
Abstract
HYPOTHESIS Soft colloidal particles that respond to their environment have innovative potential for many fields ranging from food and health to biotechnology and oil recovery. The in situ characterisation of colloidal transformations that triggers the functional response remain a challenge. EXPERIMENTS This study demonstrates the combination of an optical micromanipulation platform, polarized optical video microscopy and microfluidics in a comprehensive approach for the analysis of pH-driven structural transformations in emulsions. The new platform, together with synchrotron small angle X-ray scattering, was then applied to research the food-relevant, pH-responsive, oleic acid in water system. FINDINGS The experiments demonstrate structural transformations in individual oleic acid particles from micron-sized onion-type multilamellar oleic acid vesicles at pH 8.6, to nanostructured emulsions at pH < 8.0, and eventually oil droplets at pH < 6.5. The smooth particle-water interface of the onion-type vesicles at pH 8.6 was transformed into a rough particle surface at pH below 7.5. The pH-triggered changes of the interfacial tension at the droplet-water interface together with mass transport owing to structural transformations induced a self-propelled motion of the particle. The results of this study contribute to the fundamental understanding of the structure-property relationship in pH-responsive emulsions for nutrient and drug delivery applications.
Collapse
Affiliation(s)
- Marco Manca
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700 Fribourg, Switzerland
| | - Chi Zhang
- Department of Physics, University of Fribourg, Chemin du Musée 3, 1700 Fribourg, Switzerland
| | - Frank Scheffold
- Department of Physics, University of Fribourg, Chemin du Musée 3, 1700 Fribourg, Switzerland.
| | - Stefan Salentinig
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700 Fribourg, Switzerland.
| |
Collapse
|
55
|
Buck S, Pekarek L, Caliskan N. POTATO: Automated pipeline for batch analysis of optical tweezers data. Biophys J 2022; 121:2830-2839. [PMID: 35778838 PMCID: PMC9388390 DOI: 10.1016/j.bpj.2022.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/22/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Optical tweezers are a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein-nucleic acid interactions, and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (practical optical tweezers analysis tool). POTATO automatically processes the high-frequency raw data generated by force-ramp experiments and identifies (un)folding events using predefined parameters. After segmentation of the force-distance trajectories at the identified (un)folding events, sections of the curve can be fitted independently to a worm-like chain and freely jointed chain models, and the work applied on the molecule can be calculated by numerical integration. Furthermore, the tool allows plotting of constant force data and fitting of the Gaussian distance distribution over time. All these features are wrapped in a user-friendly graphical interface, which allows researchers without programming knowledge to perform sophisticated data analysis.
Collapse
Affiliation(s)
- Stefan Buck
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Lukas Pekarek
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany; Medical Faculty, Julius-Maximilians University Würzburg, Würzburg, Germany.
| |
Collapse
|
56
|
Feng H, Jin S, Chen X, Xiong W, Yang K, Xiao G, Luo H. Customizable trajectory of trapped particle in quadruple-beam optical trap. OPTICS EXPRESS 2022; 30:17221-17229. [PMID: 36221549 DOI: 10.1364/oe.456697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/26/2022] [Indexed: 06/16/2023]
Abstract
We have presented and demonstrated a customizable trajectory of a trapped particle in the Quadruple-beam optical trap. The orbital motion of the trapped microsphere was realized by modulating the trapping power. The motion trajectories could be designed by adjusting the modulation frequency, amplitude, and phase. By using this method, we have realized the triangle, bowknot, ellipse, straight line, and hooklike trajectories. The motion frequencies and circumferences were also modulated. The customizable trajectory in the optical trap may result in more possibilities for directional movement, microfluidic mixing, driven machines, and even painting freely.
Collapse
|
57
|
Bell NAW, Molloy JE. Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging. Nucleic Acids Res 2022; 50:e77. [PMID: 35489063 PMCID: PMC9303394 DOI: 10.1093/nar/gkac300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 03/18/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023] Open
Abstract
Single-molecule techniques such as optical tweezers and fluorescence imaging are powerful tools for probing the biophysics of DNA and DNA-protein interactions. The application of these methods requires efficient approaches for creating designed DNA structures with labels for binding to a surface or microscopic beads. In this paper, we develop a simple and fast technique for making a diverse range of such DNA constructs by combining PCR amplicons and synthetic oligonucleotides using golden gate assembly rules. We demonstrate high yield fabrication of torsionally-constrained duplex DNA up to 10 kbp in length and a variety of DNA hairpin structures. We also show how tethering to a cross-linked antibody substrate significantly enhances measurement lifetime under high force. This rapid and adaptable fabrication method streamlines the assembly of DNA constructs for single molecule biophysics.
Collapse
|
58
|
Abstract
Single-molecule magnetic tweezers deliver magnetic force and torque to single target molecules, permitting the study of dynamic changes in biomolecular structures and their interactions. Because the magnetic tweezer setups can generate magnetic fields that vary slowly over tens of millimeters-far larger than the nanometer scale of the single molecule events being observed-this technique can maintain essentially constant force levels during biochemical experiments while generating a biologically meaningful force on the order of 1-100 pN. When using bead-tether constructs to pull on single molecules, smaller magnetic beads and shorter submicrometer tethers improve dynamic response times and measurement precision. In addition, employing high-speed cameras, stronger light sources, and a graphics programming unit permits true high-resolution single-molecule magnetic tweezers that can track nanometer changes in target molecules on a millisecond or even submillisecond time scale. The unique force-clamping capacity of the magnetic tweezer technique provides a way to conduct measurements under near-equilibrium conditions and directly map the energy landscapes underlying various molecular phenomena. High-resolution single-molecule magnetic tweezers can thus be used to monitor crucial conformational changes in single-protein molecules, including those involved in mechanotransduction and protein folding. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Hyun-Kyu Choi
- Wallace H. Coulter Department of Biomedical Engineering and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Hyun Gyu Kim
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea;
| | - Min Ju Shon
- Department of Physics and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science & Technology (POSTECH), Pohang, South Korea;
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea;
| |
Collapse
|
59
|
Xie Y, Liu X. Multifunctional manipulation of red blood cells using optical tweezers. JOURNAL OF BIOPHOTONICS 2022; 15:e202100315. [PMID: 34773382 DOI: 10.1002/jbio.202100315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Serving as natural vehicles to deliver oxygen throughout the whole body, red blood cells (RBCs) have been regarded as important indicators for biomedical analysis and clinical diagnosis. Various diseases can be induced due to the dysfunction of RBCs. Hence, a flexible tool is required to perform precise manipulation and quantitative characterization of their physiological mechanisms and viscoelastic properties. Optical tweezers have emerged as potential candidates due to their noncontact manipulation and femtonewton-precision measurements. This review aimed to highlight the recent advances in the multifunctional manipulation of RBCs using optical tweezers, including controllable deformation, dynamic stretching, RBC aggregation, blood separation and Raman characterization. Further, great attentions have been focused on the precise assembly of functional biophotonics devices with trapped RBCs, and a brief overview was offered for the growing interests to manipulate RBCs in vivo.
Collapse
Affiliation(s)
- Yanzheng Xie
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Xiaoshuai Liu
- Institute of Nanophotonics, Jinan University, Guangzhou, China
| |
Collapse
|
60
|
Sun W, Gao X, Lei H, Wang W, Cao Y. Biophysical Approaches for Applying and Measuring Biological Forces. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105254. [PMID: 34923777 PMCID: PMC8844594 DOI: 10.1002/advs.202105254] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 05/13/2023]
Abstract
Over the past decades, increasing evidence has indicated that mechanical loads can regulate the morphogenesis, proliferation, migration, and apoptosis of living cells. Investigations of how cells sense mechanical stimuli or the mechanotransduction mechanism is an active field of biomaterials and biophysics. Gaining a further understanding of mechanical regulation and depicting the mechanotransduction network inside cells require advanced experimental techniques and new theories. In this review, the fundamental principles of various experimental approaches that have been developed to characterize various types and magnitudes of forces experienced at the cellular and subcellular levels are summarized. The broad applications of these techniques are introduced with an emphasis on the difficulties in implementing these techniques in special biological systems. The advantages and disadvantages of each technique are discussed, which can guide readers to choose the most suitable technique for their questions. A perspective on future directions in this field is also provided. It is anticipated that technical advancement can be a driving force for the development of mechanobiology.
Collapse
Affiliation(s)
- Wenxu Sun
- School of SciencesNantong UniversityNantong226019P. R. China
| | - Xiang Gao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Hai Lei
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
| | - Wei Wang
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Yi Cao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- MOE Key Laboratory of High Performance Polymer Materials and TechnologyDepartment of Polymer Science & EngineeringCollege of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
| |
Collapse
|
61
|
Weerakoon D, Carbajo RJ, De Maria L, Tyrchan C, Zhao H. Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex. J Chem Inf Model 2022; 62:340-349. [PMID: 35018781 DOI: 10.1021/acs.jcim.1c01036] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The conformational behavior of a small molecule free in solution is important to understand the free energy of binding to its target. This could be of special interest for proteolysis-targeting chimeras (PROTACs) due to their often flexible and lengthy linkers and the need to induce a ternary complex. Here, we report on the molecular dynamics (MD) simulations of two PROTACs, MZ1 and dBET6, revealing different linker conformational behaviors. The simulation of MZ1 in dimethyl sulfoxide (DMSO) agrees well with the nuclear magnetic resonance study, providing strong support for the relevance of our simulations. To further understand the role of linker plasticity in the formation of a ternary complex, the dissociation of the complex von Hippel-Lindau-MZ1-BRD4 is investigated in detail by steered simulations and is shown to follow a two-step pathway. Interestingly, both MZ1 and dBET6 display in water, a tendency toward an intramolecular lipophilic interaction between the two warheads. The hydrophobic contact of the two warheads would prevent them from binding to their respective proteins and might have an effect on the efficacy of induced cellular protein degradation. However, conformations featuring this hydrophobic contact of the two warheads are calculated to be marginally more favorable.
Collapse
Affiliation(s)
- Dhanushka Weerakoon
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Rodrigo J Carbajo
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United Kingdom
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| |
Collapse
|
62
|
Manipulation of free-floating objects using Faraday flows and deep reinforcement learning. Sci Rep 2022; 12:335. [PMID: 35013455 PMCID: PMC8748864 DOI: 10.1038/s41598-021-04204-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/17/2021] [Indexed: 11/08/2022] Open
Abstract
The ability to remotely control a free-floating object through surface flows on a fluid medium can facilitate numerous applications. Current studies on this problem have been limited to uni-directional motion control due to the challenging nature of the control problem. Analytical modelling of the object dynamics is difficult due to the high-dimensionality and mixing of the surface flows while the control problem is hard due to the nonlinear slow dynamics of the fluid medium, underactuation, and chaotic regions. This study presents a methodology for manipulation of free-floating objects using large-scale physical experimentation and recent advances in deep reinforcement learning. We demonstrate our methodology through the open-loop control of a free-floating object in water using a robotic arm. Our learned control policy is relatively quick to obtain, highly data efficient, and easily scalable to a higher-dimensional parameter space and/or experimental scenarios. Our results show the potential of data-driven approaches for solving and analyzing highly complex nonlinear control problems.
Collapse
|
63
|
Mennillo L, Bendkowski C, Elsayed M, Edwards H, Zhang S, Pawar V, Wheeler AR, Stoyanov D, Shaw M. Adaptive Autonomous Navigation of Multiple Optoelectronic Microrobots in Dynamic Environments. IEEE Robot Autom Lett 2022. [DOI: 10.1109/lra.2022.3194308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | - Shuailong Zhang
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing, China
| | | | | | - Danail Stoyanov
- Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS), University College London, London, United Kingdom
| | | |
Collapse
|
64
|
Hao Y, Maillard R. Using Optical Tweezers to Dissect Allosteric Communication Networks in Protein Kinases. Methods Mol Biol 2022; 2394:485-498. [PMID: 35094342 PMCID: PMC8884448 DOI: 10.1007/978-1-0716-1811-0_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mutations in protein kinases are often associated with the development of cancer, and application of mutant-specific inhibitors as therapeutic measures have shown a remarkable improvement in prolonging patient survival. However, it has also been observed that tumors bearing certain mutation types are more resistant to current approved drugs. Importantly, many resistant mutations are located in regions outside substrate or inhibitor binding sites, indicating allosteric effects. Understanding how mutations trigger effects over a distant site of the protein requires a deeper investigation of the molecular origin of allosteric regulation networks in kinases. In this chapter, we show the application of single-molecule optical tweezers to selectively manipulate specific regions of proteins to trace allosteric signals, thereby allowing the elucidation of allosteric communication networks. We illustrate this approach using as model system the regulatory subunit of protein kinase A. This single-molecule optical tweezers approach, however, can be readily applicable to study other kinases, and can be further expanded to screen potential allosteric drugs for future therapeutics.
Collapse
Affiliation(s)
- Yuxin Hao
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Rodrigo Maillard
- Department of Chemistry, Georgetown University, Washington, DC, USA.
| |
Collapse
|
65
|
Sudhakar S, Rajendran P, Schäffer E. Synthesis of Germanium Nanospheres as High-Precision Optical Tweezers Probes. Methods Mol Biol 2022; 2478:25-35. [PMID: 36063317 DOI: 10.1007/978-1-0716-2229-2_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Force spectroscopy on single molecular machines generating piconewton forces is often performed using optical tweezers. Since trapping forces scale with the particle volume, piconewton-force measurements so far required micron-sized probes practically limiting the spatiotemporal resolution. Here, we have overcome this limit by developing high-refractive index germanium nanospheres as ultraresolution trapping probes. With a refractive index of 4.4, their trapping efficiency and maximum force per power is more than 10-fold higher compared to silica spheres of equal size. Therefore, the use of germanium allows piconewton-force measurements with nanometer sized probes. Using 70-nm-diameter germanium nanospheres as trappable optical probes (GeNTOPs), we could show that kinesin-1 walks with 4-nm-center-of-mass steps. In the long-term, the application of these novel high-precision GeNTOPs will provide new insight into the working mechanism of molecular machines and are promising candidates for other applications in microscopy, optoelectronics, and nanophotonics.
Collapse
Affiliation(s)
- Swathi Sudhakar
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Tübingen, Germany
| | - Pasupathi Rajendran
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Tübingen, Germany
| | - Erik Schäffer
- Eberhard Karls Universität Tübingen, Cellular Nanoscience (ZMBP), Tübingen, Germany.
| |
Collapse
|
66
|
Thin film breakage in oil–in–water emulsions, a multidisciplinary study. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.127808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
67
|
King GA, Spakman D, Peterman EJG, Wuite GJL. Generating Negatively Supercoiled DNA Using Dual-Trap Optical Tweezers. Methods Mol Biol 2022; 2478:243-272. [PMID: 36063323 DOI: 10.1007/978-1-0716-2229-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many genomic processes lead to the formation of underwound (negatively supercoiled) or overwound (positively supercoiled) DNA. These DNA topological changes regulate the interactions of DNA-binding proteins, including transcription factors, architectural proteins and topoisomerases. In order to advance our understanding of the structure and interactions of supercoiled DNA, we recently developed a single-molecule approach called Optical DNA Supercoiling (ODS). This method enables rapid generation of negatively supercoiled DNA (with between <5% and 70% lower helical twist than nonsupercoiled DNA) using a standard dual-trap optical tweezers instrument. ODS is advantageous as it allows for combined force spectroscopy, fluorescence imaging, and spatial control of the supercoiled substrate, which is difficult to achieve with most other approaches. Here, we describe how to generate negatively supercoiled DNA using dual-trap optical tweezers. To this end, we provide detailed instructions on the design and preparation of suitable DNA substrates, as well as a step-by-step guide for how to control and calibrate the supercoiling density produced.
Collapse
Affiliation(s)
- Graeme A King
- Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Dian Spakman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Gijs J L Wuite
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
68
|
Meijering AEC, Bakx JAM, Man T, Heller I, Wuite GJL, Peterman EJG. Implementation of 3D Multi-Color Fluorescence Microscopy in a Quadruple Trap Optical Tweezers System. Methods Mol Biol 2022; 2478:75-100. [PMID: 36063319 DOI: 10.1007/978-1-0716-2229-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent advances in the design and measurement capabilities of optical tweezers instruments, and especially the combination with multi-color fluorescence detection, have accommodated a dramatic increase in the versatility of optical trapping. Quadruple (Q)-trap optical tweezers are an excellent example of such an advance, by providing three-dimensional control over two constructs and thereby enabling for example DNA-DNA braiding. However, the implementation of fluorescence detection in such a Q-trapping system poses several challenges: (1) since typical samples span a distance in the order of tens of micrometers, it requires imaging of a large field of view, (2) in order to capture fast molecular dynamics, fast imaging with single-molecule sensitivity is desired, (3) in order to study three-dimensional objects, it could be needed to detect emission light at different axial heights while keeping the objective lens and thus the optically trapped microspheres in a fixed position. In this chapter, we describe design guidelines for a fluorescence imaging module on a Q-trap system that overcomes these challenges and provide a step-by-step description for construction and alignment of such a system. Finally, we present detailed instructions for proof-of-concept experiments that can be used to validate and highlight the capabilities of the instruments.
Collapse
Affiliation(s)
- Anna E C Meijering
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Julia A M Bakx
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Tianlong Man
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
69
|
Man T, Geldhof JJ, Peterman EJG, Wuite GJL, Heller I. One-Dimensional STED Microscopy in Optical Tweezers. Methods Mol Biol 2022; 2478:101-122. [PMID: 36063320 DOI: 10.1007/978-1-0716-2229-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Optical tweezers and fluorescence microscopy are powerful methods for investigating the mechanical and structural properties of biomolecules and for studying the dynamics of the biomolecular processes that these molecules are involved in. Here we provide an outline of the concurrent use of optical tweezers and fluorescence microscopy for analyzing biomolecular processes. In particular, we focus on the use of super-resolution microscopy in optical tweezers, which allows visualization of molecules at the higher molecular densities that are typically encountered in living systems. We provide specific details on the alignment procedures of the optical pathways for confocal fluorescence microscopy and 1D-STED microscopy and elaborate on how to diagnose and correct optical aberrations and STED phase plate misalignments.
Collapse
Affiliation(s)
- Tianlong Man
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joost J Geldhof
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
70
|
Abstract
Upconversion nanoparticles are a class of luminescent materials that convert longer-wavelength near-infrared photons into visible and ultraviolet emissions. They can respond to various external stimuli, which underpins many opportunities for developing the next generation of sensing technologies. In this perspective, the unique stimuli-responsive properties of upconverting nanoparticles are introduced, and their recent implementations in sensing are summarized. Promising material development strategies for enhancing the key sensing merits, including intrinsic sensitivity, biocompatibility and modality, are identified and discussed. The outlooks on future technological developments, novel sensing concepts, and applications of nanoscale upconversion sensors are provided.
Collapse
Affiliation(s)
- Gungun Lin
- Institute for Biomedical Materials & Devices, Faculty of Science, The University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Dayong Jin
- Institute for Biomedical Materials & Devices, Faculty of Science, The University of Technology Sydney, Ultimo, New South Wales 2007, Australia
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, Nanshan, Shenzhen, Guangdong 518055, China
| |
Collapse
|
71
|
Carlstrom LP, Eltanahy A, Perry A, Rabinstein AA, Elder BD, Morris JM, Meyer FB, Graffeo CS, Lundgaard I, Burns TC. A clinical primer for the glymphatic system. Brain 2021; 145:843-857. [PMID: 34888633 DOI: 10.1093/brain/awab428] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 11/14/2022] Open
Abstract
The complex and dynamic system of fluid flow through the perivascular and interstitial spaces of the central nervous system has new-found implications for neurological diseases. Cerebrospinal fluid movement throughout the CNS parenchyma is more dynamic than could be explained via passive diffusion mechanisms alone. Indeed, a semi-structured glial-lymphatic (glymphatic) system of astrocyte-supported extracellular perivascular channels serves to directionally channel extracellular fluid, clearing metabolites and peptides to optimize neurologic function. Clinical studies of the glymphatic network has to date proven challenging, with most data gleaned from rodent models and post-mortem investigations. However, increasing evidence suggests that disordered glymphatic function contributes to the pathophysiology of CNS aging, neurodegenerative disease, and CNS injuries, as well as normal pressure hydrocephalus. Unlocking such pathophysiology could provide important avenues toward novel therapeutics. We here provide a multidisciplinary overview of glymphatics and critically review accumulating evidence regarding its structure, function, and hypothesized relevance to neurological disease. We highlight emerging technologies of relevance to the longitudinal evaluation of glymphatic function in health and disease. Finally, we discuss the translational opportunities and challenges of studying glymphatic science.
Collapse
Affiliation(s)
- Lucas P Carlstrom
- Departments of Neurologic Surgery, Mayo Clinic, Rochester, MN 55905 USA
| | - Ahmed Eltanahy
- Departments of Neurologic Surgery, Mayo Clinic, Rochester, MN 55905 USA
| | - Avital Perry
- Departments of Neurologic Surgery, Mayo Clinic, Rochester, MN 55905 USA
| | | | - Benjamin D Elder
- Departments of Neurologic Surgery, Mayo Clinic, Rochester, MN 55905 USA
| | | | - Fredric B Meyer
- Departments of Neurologic Surgery, Mayo Clinic, Rochester, MN 55905 USA
| | | | - Iben Lundgaard
- Departments of Experimental Medical Science, Lund University, Lund 228 11 Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund 228 11 Sweden
| | - Terry C Burns
- Departments of Neurologic Surgery, Mayo Clinic, Rochester, MN 55905 USA
| |
Collapse
|
72
|
Pandey S, Xiang Y, Friedrich D, Leng Y, Mao H. Direct Measurement of Intermolecular Mechanical Force for Nonspecific Interactions between Small Molecules. J Phys Chem Lett 2021; 12:11316-11322. [PMID: 34780182 PMCID: PMC8778946 DOI: 10.1021/acs.jpclett.1c03142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mechanical force can evaluate intramolecular interactions in macromolecules. Because of the rapid motion of small molecules, it is extremely challenging to measure mechanical forces of nonspecific intermolecular interactions. Here, we used optical tweezers to directly examine the intermolecular mechanical force (IMMF) of nonspecific interactions between two cholesterols. We found that IMMFs of dimeric cholesterol complexes were dependent on the orientation of the interaction. The surprisingly high IMMF in cholesterol dimers (∼30 pN) is comparable to the mechanical stability of DNA secondary structures. Using Hess-like cycles, we quantified that changes in free energy of solubilizing cholesterol (ΔGsolubility) by β-cyclodextrin (βCD) and methylated βCD (Me-βCD) were as low as -16 and -27 kcal/mol, respectively. Compared to the ΔGsolubility of cholesterols in water (5.1 kcal/mol), these values indicated that cyclodextrins can easily solubilize cholesterols. Our results demonstrated that the IMMF can serve as a generic and multipurpose variable to dissect nonspecific intermolecular interactions among small molecules into orientational components.
Collapse
Affiliation(s)
- Shankar Pandey
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yuan Xiang
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052, USA
| | - Dirk Friedrich
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yongsheng Leng
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| |
Collapse
|
73
|
Kong M, Greene EC. Mechanistic Insights From Single-Molecule Studies of Repair of Double Strand Breaks. Front Cell Dev Biol 2021; 9:745311. [PMID: 34869333 PMCID: PMC8636147 DOI: 10.3389/fcell.2021.745311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/28/2021] [Indexed: 01/01/2023] Open
Abstract
DNA double strand breaks (DSBs) are among some of the most deleterious forms of DNA damage. Left unrepaired, they are detrimental to genome stability, leading to high risk of cancer. Two major mechanisms are responsible for the repair of DSBs, homologous recombination (HR) and nonhomologous end joining (NHEJ). The complex nature of both pathways, involving a myriad of protein factors functioning in a highly coordinated manner at distinct stages of repair, lend themselves to detailed mechanistic studies using the latest single-molecule techniques. In avoiding ensemble averaging effects inherent to traditional biochemical or genetic methods, single-molecule studies have painted an increasingly detailed picture for every step of the DSB repair processes.
Collapse
Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, United States
| |
Collapse
|
74
|
A viral genome packaging ring-ATPase is a flexibly coordinated pentamer. Nat Commun 2021; 12:6548. [PMID: 34772936 PMCID: PMC8589836 DOI: 10.1038/s41467-021-26800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/21/2021] [Indexed: 01/13/2023] Open
Abstract
Multi-subunit ring-ATPases carry out a myriad of biological functions, including genome packaging in viruses. Though the basic structures and functions of these motors have been well-established, the mechanisms of ATPase firing and motor coordination are poorly understood. Here, using single-molecule fluorescence, we determine that the active bacteriophage T4 DNA packaging motor consists of five subunits of gp17. By systematically doping motors with an ATPase-defective subunit and selecting single motors containing a precise number of active or inactive subunits, we find that the packaging motor can tolerate an inactive subunit. However, motors containing one or more inactive subunits exhibit fewer DNA engagements, a higher failure rate in encapsidation, reduced packaging velocity, and increased pausing. These findings suggest a DNA packaging model in which the motor, by re-adjusting its grip on DNA, can skip an inactive subunit and resume DNA translocation, suggesting that strict coordination amongst motor subunits of packaging motors is not crucial for function.
Collapse
|
75
|
Bocanegra R, Plaza G A I, Ibarra B. In vitro single-molecule manipulation studies of viral DNA replication. Enzymes 2021; 49:115-148. [PMID: 34696830 DOI: 10.1016/bs.enz.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.
Collapse
Affiliation(s)
- Rebeca Bocanegra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Ismael Plaza G A
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.
| |
Collapse
|
76
|
Li W, Zhang H, Hu M, Zhu Q, Su H, Li N, Hu H. 3D calibration of microsphere position in optical tweezers using the back-focal-plane interferometry method. OPTICS EXPRESS 2021; 29:32271-32284. [PMID: 34615302 DOI: 10.1364/oe.435592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
This paper presents a method to directly calibrate the position of a trapped micro-sphere in optical tweezers utilizing its interference pattern formed at the back focal plane (BFP). Through finite difference time domain (FDTD) and scalar diffraction theorem, the scattering field complex amplitude of the near and far fields can be simulated after interference between the trapped sphere and focus Gaussian beam. The position of the trapped sphere can be recovered and calibrated based on a back focal plane interferometry (BFPI) algorithm. Theoretical results demonstrate that optical tweezers with a larger numerical aperture (NA) Gaussian beam will yield a better detection sensitivity but with a smaller linear range. These results were experimentally validated by trapping a microsphere in a single beam optical tweezer. We used an extra focused laser to manipulate the trapped sphere and then compared its position in the images and that obtained using the BFP method. The interference pattern from simulation and experiments showed good agreement, implying that the calibration factor can be deduced from simulation and requires no intermediate calculation process. These results provide a pathway to obtain the calibration factor, enable a faster and direct measurement of the sphere position, and show possibilities for adjusting the crosstalk and nonlinearity inside an optical trap.
Collapse
|
77
|
Obydennov DV, Yushkov KB, Molchanov VY. Ring-shaped optical trap based on an acousto-optic tunable spatial filter. OPTICS LETTERS 2021; 46:4494-4497. [PMID: 34525030 DOI: 10.1364/ol.435485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
We report on a novel, to the best of our knowledge, optical scheme of an annular optical trap based on an acousto-optic tunable spatial filter. Design of the optical trap is proposed and validated. Experimental demonstration with polystyrene microspheres includes controllable arrangement of freely floating particles into a circular pattern, aggregation, and disaggregation of the particles. Dynamical adjustment of the trapping field potential diameter is achieved by programmable frequency-swept controlling of the acousto-optic filter.
Collapse
|
78
|
Wang Y, Le JV, Crocker K, Darcy MA, Halley PD, Zhao D, Andrioff N, Croy C, Poirier MG, Bundschuh R, Castro CE. A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules. Nucleic Acids Res 2021; 49:8987-8999. [PMID: 34358322 PMCID: PMC8421221 DOI: 10.1093/nar/gkab656] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/30/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.
Collapse
Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny V Le
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A Darcy
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick D Halley
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Dengke Zhao
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Nick Andrioff
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Cassie Croy
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
79
|
Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
Collapse
Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
| |
Collapse
|
80
|
Kamit A, Tseng C, Kudo T, Sugiyama T, Hofkens J, Bresolí‐Obach R, Masuhara H. Unraveling the three‐dimensional morphology and dynamics of the optically evolving polystyrene nanoparticle assembly using dual‐objective lens microscopy. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Abdullah Kamit
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
| | - Ching‐Shiang Tseng
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
| | - Tetsuhiro Kudo
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
- Laser Science Laboratory Toyota Technological University Nagoya Japan
| | - Teruki Sugiyama
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
- Division of Materials Science, Graduate School of Science and Technology Nara Institute of Science and Technology Ikoma Nara Japan
| | - Johan Hofkens
- Department of Chemistry Katholieke Universiteit Leuven Leuven Belgium
- Max‐Planck‐Institute for Polymer Research Mainz Germany
| | - Roger Bresolí‐Obach
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
- Department of Chemistry Katholieke Universiteit Leuven Leuven Belgium
| | - Hiroshi Masuhara
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
| |
Collapse
|
81
|
Kolesnik K, Xu M, Lee PVS, Rajagopal V, Collins DJ. Unconventional acoustic approaches for localized and designed micromanipulation. LAB ON A CHIP 2021; 21:2837-2856. [PMID: 34268539 DOI: 10.1039/d1lc00378j] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Acoustic fields are ideal for micromanipulation, being biocompatible and with force gradients approaching the scale of single cells. They have accordingly found use in a variety of microfluidic devices, including for microscale patterning, separation, and mixing. The bulk of work in acoustofluidics has been predicated on the formation of standing waves that form periodic nodal positions along which suspended particles and cells are aligned. An evolving range of applications, however, requires more targeted micromanipulation to create unique patterns and effects. To this end, recent work has made important advances in improving the flexibility with which acoustic fields can be applied, impressively demonstrating generating arbitrary arrangements of pressure fields, spatially localizing acoustic fields and selectively translating individual particles in ways that are not achievable via traditional approaches. In this critical review we categorize and examine these advances, each of which open the door to a wide range of applications in which single-cell fidelity and flexible micromanipulation are advantageous, including for tissue engineering, diagnostic devices, high-throughput sorting and microfabrication.
Collapse
Affiliation(s)
- Kirill Kolesnik
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia.
| | - Mingxin Xu
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia.
| | - Peter V S Lee
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia.
| | - Vijay Rajagopal
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia.
| | - David J Collins
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia.
| |
Collapse
|
82
|
Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
Collapse
|
83
|
Hsu CF, Chang KC, Chen YL, Hsieh PS, Lee AI, Tu JY, Chen YT, Wen JD. Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates. Nucleic Acids Res 2021; 49:6941-6957. [PMID: 34161580 PMCID: PMC8266650 DOI: 10.1093/nar/gkab512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Programmed –1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that the intermediates are greatly suppressed, suggesting that mRNA refolding may be modulated by ribosomes. Moreover, masking the first few nucleotides of S1 favors the folding from S2 and yields native pseudoknots, which are stable enough to retrieve the masked nucleotides. We hypothesize that translating ribosomes can remodel an intermediate mRNA structure into a stable conformation, which may in turn stimulate backward slippage of the ribosome. This supports an interactive model of ribosomal frameshifting and gives an insightful account addressing previous experimental observations.
Collapse
Affiliation(s)
- Chiung-Fang Hsu
- 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
| | - Yi-Lan Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Po-Szu Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - An-I Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jui-Yun Tu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ting Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, 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
| |
Collapse
|
84
|
Niina T, Matsunaga Y, Takada S. Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure. PLoS Comput Biol 2021; 17:e1009215. [PMID: 34283829 PMCID: PMC8323932 DOI: 10.1371/journal.pcbi.1009215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/30/2021] [Accepted: 06/26/2021] [Indexed: 12/01/2022] Open
Abstract
Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological condition, but the observed data are limited to the surface height of specimens. Since the AFM images highly depend on the probe tip shape, for successful inference of molecular structures from the measurement, the knowledge of the probe shape is required, but is often missing. Here, we developed a method of the rigid-body fitting to AFM images, which simultaneously finds the shape of the probe tip and the placement of the molecular structure via an exhaustive search. First, we examined four similarity scores via twin-experiments for four test proteins, finding that the cosine similarity score generally worked best, whereas the pixel-RMSD and the correlation coefficient were also useful. We then applied the method to two experimental high-speed-AFM images inferring the probe shape and the molecular placement. The results suggest that the appropriate similarity score can differ between target systems. For an actin filament image, the cosine similarity apparently worked best. For an image of the flagellar protein FlhAC, we found the correlation coefficient gave better results. This difference may partly be attributed to the flexibility in the target molecule, ignored in the rigid-body fitting. The inferred tip shape and placement results can be further refined by other methods, such as the flexible fitting molecular dynamics simulations. The developed software is publicly available. Observation of functional dynamics of individual biomolecules is important to understand molecular mechanisms of cellular phenomena. High-speed (HS) atomic force microscopy (AFM) is a powerful tool that enables us to visualize the real-time dynamics of working biomolecules under near-physiological conditions. However, the information available by the AFM images is limited to the two-dimensional surface shape detected via the force to the probe. While the surface information is affected by the shape of the probe tip, the probe shape itself cannot be directly measured before each AFM measurement. To overcome this problem, we have developed a computational method to simultaneously infer the probe tip shape and the molecular placement from an AFM image. We show that our method successfully estimates the effective AFM tip shape and visualizes a structure with a more accurate placement. The estimation of a molecular placement with the correct probe tip shape enables us to obtain more insights into functional dynamics of the molecule from HS-AFM images.
Collapse
Affiliation(s)
- Toru Niina
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yasuhiro Matsunaga
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail:
| |
Collapse
|
85
|
Kolb P, Schundner A, Frick M, Gottschalk KE. In Vitro Measurements of Cellular Forces and their Importance in the Lung-From the Sub- to the Multicellular Scale. Life (Basel) 2021; 11:691. [PMID: 34357063 PMCID: PMC8307149 DOI: 10.3390/life11070691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
Throughout life, the body is subjected to various mechanical forces on the organ, tissue, and cellular level. Mechanical stimuli are essential for organ development and function. One organ whose function depends on the tightly connected interplay between mechanical cell properties, biochemical signaling, and external forces is the lung. However, altered mechanical properties or excessive mechanical forces can also drive the onset and progression of severe pulmonary diseases. Characterizing the mechanical properties and forces that affect cell and tissue function is therefore necessary for understanding physiological and pathophysiological mechanisms. In recent years, multiple methods have been developed for cellular force measurements at multiple length scales, from subcellular forces to measuring the collective behavior of heterogeneous cellular networks. In this short review, we give a brief overview of the mechanical forces at play on the cellular level in the lung. We then focus on the technological aspects of measuring cellular forces at many length scales. We describe tools with a subcellular resolution and elaborate measurement techniques for collective multicellular units. Many of the technologies described are by no means restricted to lung research and have already been applied successfully to cells from various other tissues. However, integrating the knowledge gained from these multi-scale measurements in a unifying framework is still a major future challenge.
Collapse
Affiliation(s)
- Peter Kolb
- Institute of Experimental Physics, Ulm University, 89069 Ulm, Germany;
| | - Annika Schundner
- Institute of General Physiology, Ulm University, 89069 Ulm, Germany;
| | - Manfred Frick
- Institute of General Physiology, Ulm University, 89069 Ulm, Germany;
| | - Kay-E. Gottschalk
- Institute of Experimental Physics, Ulm University, 89069 Ulm, Germany;
| |
Collapse
|
86
|
Spakman D, Bakx JAM, Biebricher AS, Peterman EJG, Wuite GJL, King GA. Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches. Nucleic Acids Res 2021; 49:5470-5492. [PMID: 33963870 PMCID: PMC8191776 DOI: 10.1093/nar/gkab239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
Topoisomerases are essential enzymes that regulate DNA topology. Type 1A family topoisomerases are found in nearly all living organisms and are unique in that they require single-stranded (ss)DNA for activity. These enzymes are vital for maintaining supercoiling homeostasis and resolving DNA entanglements generated during DNA replication and repair. While the catalytic cycle of Type 1A topoisomerases has been long-known to involve an enzyme-bridged ssDNA gate that allows strand passage, a deeper mechanistic understanding of these enzymes has only recently begun to emerge. This knowledge has been greatly enhanced through the combination of biochemical studies and increasingly sophisticated single-molecule assays based on magnetic tweezers, optical tweezers, atomic force microscopy and Förster resonance energy transfer. In this review, we discuss how single-molecule assays have advanced our understanding of the gate opening dynamics and strand-passage mechanisms of Type 1A topoisomerases, as well as the interplay of Type 1A topoisomerases with partner proteins, such as RecQ-family helicases. We also highlight how these assays have shed new light on the likely functional roles of Type 1A topoisomerases in vivo and discuss recent developments in single-molecule technologies that could be applied to further enhance our understanding of these essential enzymes.
Collapse
Affiliation(s)
- Dian Spakman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Julia A M Bakx
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Graeme A King
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| |
Collapse
|
87
|
Jarillo J, Ibarra B, Cao-García FJ. DNA replication: In vitro single-molecule manipulation data analysis and models. Comput Struct Biotechnol J 2021; 19:3765-3778. [PMID: 34285777 PMCID: PMC8267548 DOI: 10.1016/j.csbj.2021.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/05/2022] Open
Abstract
Data analysis allows to extract information from the noisy single-molecule data. Models provide insight in the underlying biochemical processes. Ligands can activate or inhibit DNA replication and DNA unwinding.
DNA replication is a key biochemical process of the cell cycle. In the last years, analysis of in vitro single-molecule DNA replication events has provided new information that cannot be obtained with ensembles studies. Here, we introduce crucial techniques for the proper analysis and modelling of DNA replication in vitro single-molecule manipulation data. Specifically, we review some of the main methods to analyze and model the real-time kinetics of the two main molecular motors of the replisome: DNA polymerase and DNA helicase. Our goal is to facilitate access to and understanding of these techniques to promotetheir use in the study of DNA replication at the single-molecule level. A proper analysis of single-molecule data is crucial to obtain a detailed picture of, among others, the kinetics rates, equilibrium contants and conformational changes of the system under study. The techniques presented here have been used or can be adapted to study the operation of other proteins involved in nucleic acids metabolism.
Collapse
Affiliation(s)
- Javier Jarillo
- University of Namur, Institute of Life-Earth-Environment, Namur Center for Complex Systems, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain
| | - Francisco Javier Cao-García
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain.,Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
| |
Collapse
|
88
|
Morin JA, Cerrón F, Cao-García FJ, Ibarra B. Optical Tweezers to Investigate the Structure and Energetics of Single-Stranded DNA-Binding Protein-DNA Complexes. Methods Mol Biol 2021; 2281:273-288. [PMID: 33847965 DOI: 10.1007/978-1-0716-1290-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Optical tweezers enable the isolation and mechanical manipulation of individual nucleoprotein complexes. Here, we describe how to use this technique to interrogate the mechanical properties of individual protein-DNA complexes and extract information about their overall structural organization.
Collapse
Affiliation(s)
- José A Morin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Fernando Cerrón
- Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - Francisco J Cao-García
- Departamento Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.
| |
Collapse
|
89
|
Measurements of Real-Time Replication Kinetics of DNA Polymerases on ssDNA Templates Coated with Single-Stranded DNA-Binding Proteins. Methods Mol Biol 2021; 2281:289-301. [PMID: 33847966 DOI: 10.1007/978-1-0716-1290-3_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Optical tweezers can monitor and control the activity of individual DNA polymerase molecules in real time, providing in this way unprecedented insight into the complex dynamics and mechanochemical processes that govern their operation. Here, we describe an optical tweezers-based assay to determine at the single-molecule level the effect of single-stranded DNA-binding proteins (SSB) on the real-time replication kinetics of the human mitochondrial DNA polymerase during the synthesis of the lagging strand.
Collapse
|
90
|
Chang KC, Wen JD. Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes. Comput Struct Biotechnol J 2021; 19:3580-3588. [PMID: 34257837 PMCID: PMC8246090 DOI: 10.1016/j.csbj.2021.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/01/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is a translation mechanism that regulates the relative expression level of two proteins encoded on the same messenger RNA (mRNA). This regulation is commonly used by viruses such as coronaviruses and retroviruses but rarely by host human cells, and for this reason, it has long been considered as a therapeutic target for antiviral drug development. Understanding the molecular mechanism of -1 PRF is one step toward this goal. Minus-one PRF occurs with a certain efficiency when translating ribosomes encounter the specialized mRNA signal consisting of the frameshifting site and a downstream stimulatory structure, which impedes translocation of the ribosome. The impeded ribosome can still undergo profound conformational changes to proceed with translocation; however, some of these changes may be unique and essential to frameshifting. In addition, most stimulatory structures exhibit conformational dynamics and sufficient mechanical strength, which, when under the action of ribosomes, may in turn further promote -1 PRF efficiency. In this review, we discuss how the dynamic features of ribosomes and mRNA stimulatory structures may influence the occurrence of -1 PRF and propose a hypothetical frameshifting model that recapitulates the role of conformational dynamics.
Collapse
Affiliation(s)
- Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, CA 94158, United States
| | - 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
| |
Collapse
|
91
|
Sharma D, Lim RYH, Pfohl T, Ekinci Y. Surface-modified elastomeric nanofluidic devices for single nanoparticle trapping. MICROSYSTEMS & NANOENGINEERING 2021; 7:46. [PMID: 34567759 PMCID: PMC8433227 DOI: 10.1038/s41378-021-00273-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 01/14/2021] [Accepted: 04/15/2021] [Indexed: 06/13/2023]
Abstract
Our work focuses on the development of simpler and effective production of nanofluidic devices for high-throughput charged single nanoparticle trapping in an aqueous environment. Single nanoparticle confinement using electrostatic trapping has been an effective approach to study the fundamental properties of charged molecules under a controlled aqueous environment. Conventionally, geometry-induced electrostatic trapping devices are fabricated using SiOx-based substrates and comprise nanochannels imbedded with nanoindentations such as nanopockets, nanoslits and nanogrids. These geometry-induced electrostatic trapping devices can only trap negatively charged particles, and therefore, to trap positively charged particles, modification of the device surface is required. However, the surface modification process of a nanofluidic device is cumbersome and time consuming. Therefore, here, we present a novel approach for the development of surface-modified geometry-induced electrostatic trapping devices that reduces the surface modification time from nearly 5 days to just a few hours. We utilized polydimethylsiloxane for the development of a surface-modified geometry-induced electrostatic trapping device. To demonstrate the device efficiency and success of the surface modification procedure, a comparison study between a PDMS-based geometry-induced electrostatic trapping device and the surface-modified polydimethylsiloxane-based device was performed. The device surface was modified with two layers of polyelectrolytes (1: poly(ethyleneimine) and 2: poly(styrenesulfonate)), which led to an overall negatively charged surface. Our experiments revealed the presence of a homogeneous surface charge density inside the fluidic devices and equivalent trapping strengths for the surface-modified and native polydimethylsiloxane-based geometry-induced electrostatic trapping devices. This work paves the way towards broader use of geometry-induced electrostatic trapping devices in the fields of biosensing, disease diagnosis, molecular analysis, fluid quality control and pathogen detection.
Collapse
Affiliation(s)
- Deepika Sharma
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Laboratory for Micro and Nanotechnology, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Roderick Y. H. Lim
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Thomas Pfohl
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
- Institute of Physics, University of Freiburg, D-79104 Freiburg, Germany
| | - Yasin Ekinci
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
- Laboratory for Micro and Nanotechnology, Paul Scherrer Institut, 5232 Villigen, Switzerland
| |
Collapse
|
92
|
Maksudov F, Jones LK, Barsegov V. Statistical Learning from Single-Molecule Experiments: Support Vector Machines and Expectation-Maximization Approaches to Understanding Protein Unfolding Data. J Phys Chem B 2021; 125:5794-5808. [PMID: 34075752 DOI: 10.1021/acs.jpcb.1c02334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Single-molecule force spectroscopy has become a powerful tool for the exploration of dynamic processes that involve proteins; yet, meaningful interpretation of the experimental data remains challenging. Owing to low signal-to-noise ratio, experimental force-extension spectra contain force signals due to nonspecific interactions, tip or substrate detachment, and protein desorption. Unravelling of complex protein structures results in the unfolding transitions of different types. Here, we test the performance of Support Vector Machines (SVM) and Expectation Maximization (EM) approaches in statistical learning from dynamic force experiments. When the output from molecular modeling in silico (or other studies) is used as a training set, SVM and EM can be applied to understand the unfolding force data. The maximal margin or maximum likelihood classifier can be used to separate experimental test observations into the unfolding transitions of different types, and EM optimization can then be utilized to resolve the statistics of unfolding forces: weights, average forces, and standard deviations. We designed an EM-based approach, which can be directly applied to the experimental data without data classification and division into training and test observations. This approach performs well even when the sample size is small and when the unfolding transitions are characterized by overlapping force ranges.
Collapse
|
93
|
Li J, Chen Z, Liu Y, Kollipara PS, Feng Y, Zhang Z, Zheng Y. Opto-refrigerative tweezers. SCIENCE ADVANCES 2021; 7:7/26/eabh1101. [PMID: 34172454 PMCID: PMC8232904 DOI: 10.1126/sciadv.abh1101] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/12/2021] [Indexed: 05/29/2023]
Abstract
Optical tweezers offer revolutionary opportunities for both fundamental and applied research in materials science, biology, and medical engineering. However, the requirement of a strongly focused and high-intensity laser beam results in potential photon-induced and thermal damages to target objects, including nanoparticles, cells, and biomolecules. Here, we report a new type of light-based tweezers, termed opto-refrigerative tweezers, which exploit solid-state optical refrigeration and thermophoresis to trap particles and molecules at the laser-generated cold region. While laser refrigeration can avoid photothermal heating, the use of a weakly focused laser beam can further reduce the photodamages to the target object. This novel and noninvasive optical tweezing technique will bring new possibilities in the optical control of nanomaterials and biomolecules for essential applications in nanotechnology, photonics, and life science.
Collapse
Affiliation(s)
- Jingang Li
- Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zhihan Chen
- Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yaoran Liu
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX 78705, USA
| | | | - Yichao Feng
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Zhenglong Zhang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Yuebing Zheng
- Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA.
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX 78705, USA
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
94
|
Li Q, Apostolidou D, Marszalek PE. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations. Methods 2021; 197:39-53. [PMID: 34020035 DOI: 10.1016/j.ymeth.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/29/2022] Open
Abstract
Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.
Collapse
Affiliation(s)
- Qing Li
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States.
| |
Collapse
|
95
|
Enhanced Signal-to-Noise and Fast Calibration of Optical Tweezers Using Single Trapping Events. MICROMACHINES 2021; 12:mi12050570. [PMID: 34067843 PMCID: PMC8156233 DOI: 10.3390/mi12050570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022]
Abstract
The trap stiffness us the key property in using optical tweezers as a force transducer. Force reconstruction via maximum-likelihood-estimator analysis (FORMA) determines the optical trap stiffness based on estimation of the particle velocity from statistical trajectories. Using a modification of this technique, we determine the trap stiffness for a two micron particle within 2 ms to a precision of ∼10% using camera measurements at 10 kfps with the contribution of pixel noise to the signal being larger the level Brownian motion. This is done by observing a particle fall into an optical trap once at a high stiffness. This type of calibration is attractive, as it avoids the use of a nanopositioning stage, which makes it ideal for systems of large numbers of particles, e.g., micro-fluidics or active matter systems.
Collapse
|
96
|
Zhao X, Chen X, Mi Z, Liu Y, Li W, Shan X, Lu X. Revealing Differential Interaction Forces during Nanopore DNA Sequencing. J Phys Chem B 2021; 125:5045-5051. [PMID: 33955770 DOI: 10.1021/acs.jpcb.1c02296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The interaction between DNA and the nanopore structure plays an important role in nanopore DNA sequencing. Differential interaction forces between each base type and the nanopore structure are obtained by examining the correlation between translocation dwell time and the sequence. The viscous drag force and the intermolecular interaction are identified with single-nucleotide resolution. Active hydrogen donors and acceptors on the inner wall of the nanopore structure are revealed at various offset coordinates. The differential forces as demonstrated in this study have great potential in probing active hydrogen bond interaction in a single protein molecule with subnanometer spatial resolution.
Collapse
Affiliation(s)
- Xinjia Zhao
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu Chen
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Zhuang Mi
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yuru Liu
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Li
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyan Shan
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinghua Lu
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China.,Center for Excellence in Topological Quantum Computation, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| |
Collapse
|
97
|
Loeff L, Kerssemakers JWJ, Joo C, Dekker C. AutoStepfinder: A fast and automated step detection method for single-molecule analysis. PATTERNS 2021; 2:100256. [PMID: 34036291 PMCID: PMC8134948 DOI: 10.1016/j.patter.2021.100256] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 01/05/2023]
Abstract
Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step detection method, AutoStepfinder, that determines steps in large datasets without requiring prior knowledge on the noise contributions and location of steps. The analysis is based on a series of partition events that minimize the difference between the data and the fit. A dual-pass strategy determines the optimal fit and allows AutoStepfinder to detect steps of a wide variety of sizes. We demonstrate step detection for a broad variety of experimental traces. The user-friendly interface and the automated detection of AutoStepfinder provides a robust analysis procedure that enables anyone without programming knowledge to generate step fits and informative plots in less than an hour. Fast, automated, and bias-free detection of steps within single-molecule trajectories Robust step detection without any prior knowledge on the data A dual-pass strategy for the detection of steps over a wide variety of scales A user-friendly interface for a simplified step fitting procedure
Single-molecule techniques have made it possible to track individual protein complexes in real time with a nanometer spatial resolution and a millisecond timescale. Accurate determination of the dynamic states within single-molecule time traces provides valuable kinetic information that underlie the function of biological macromolecules. Here, we present a new automated step detection method called AutoStepfinder, a versatile, robust, and easy-to-use algorithm that allows researchers to determine the kinetic states within single-molecule time trajectories without any bias.
Collapse
Affiliation(s)
- Luuk Loeff
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| |
Collapse
|
98
|
Bocanegra R, Ismael Plaza GA, Pulido CR, Ibarra B. DNA replication machinery: Insights from in vitro single-molecule approaches. Comput Struct Biotechnol J 2021; 19:2057-2069. [PMID: 33995902 PMCID: PMC8085672 DOI: 10.1016/j.csbj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/03/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
The replisome is the multiprotein molecular machinery that replicates DNA. The replisome components work in precise coordination to unwind the double helix of the DNA and replicate the two strands simultaneously. The study of DNA replication using in vitro single-molecule approaches provides a novel quantitative understanding of the dynamics and mechanical principles that govern the operation of the replisome and its components. ‘Classical’ ensemble-averaging methods cannot obtain this information. Here we describe the main findings obtained with in vitro single-molecule methods on the performance of individual replisome components and reconstituted prokaryotic and eukaryotic replisomes. The emerging picture from these studies is that of stochastic, versatile and highly dynamic replisome machinery in which transient protein-protein and protein-DNA associations are responsible for robust DNA replication.
Collapse
Affiliation(s)
- Rebeca Bocanegra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - G A Ismael Plaza
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Carlos R Pulido
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
99
|
Abstract
When an intense 1,064-nm continuous-wave laser is tightly focused at solution surfaces, it exerts an optical force on molecules, polymers, and nanoparticles (NPs). Initially, molecules and NPs are gathered into a single assembly inside the focus, and the laser is scattered and propagated through the assembly. The expanded laser further traps them at the edge of the assembly, producing a single assembly much larger than the focus along the surface. Amino acids and inorganic ionic compounds undergo crystallization and crystal growth, polystyrene NPs form periodic arrays and disklike structures with concentric circles or hexagonal packing, and Au NPs demonstrate assembling and swarming, in which the NPs fluctuate like a group of bees. These phenomena that depend on laser polarization are called optically evolved assembling at solution surfaces, and their dynamics and mechanisms are elucidated in this review. As a promising application in materials science, the optical trapping assembly of lead halide perovskites, supramolecules, and aggregation-induced emission enhancement-active molecules is demonstrated and future directions for fundamental study are discussed.
Collapse
Affiliation(s)
- Hiroshi Masuhara
- Department of Applied Chemistry and Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 30010, Taiwan;
| | - Ken-Ichi Yuyama
- Department of Chemistry, Osaka City University, Osaka 558-8585, Japan;
| |
Collapse
|
100
|
Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT). Essays Biochem 2021; 65:109-127. [PMID: 33491732 DOI: 10.1042/ebc20200027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT's spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT's ability to discern an enzyme's nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.
Collapse
|