1
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Sharma N, van Oijen AM, Spenkelink LM, Mueller SH. Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:595-614. [PMID: 39328428 PMCID: PMC11423410 DOI: 10.1021/cbmi.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 09/28/2024]
Abstract
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
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Affiliation(s)
- Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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2
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Singh V, Singh V. Inferring Interaction Networks from Transcriptomic Data: Methods and Applications. Methods Mol Biol 2024; 2812:11-37. [PMID: 39068355 DOI: 10.1007/978-1-0716-3886-6_2] [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: 07/30/2024]
Abstract
Transcriptomic data is a treasure trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilized to infer biomolecular interaction networks that can provide insights into the complex regulatory mechanisms underpinning the dynamic cellular processes. Gene regulatory networks and protein-protein interaction networks are two major classes of such networks. This chapter thoroughly investigates the wide range of methodologies used for distilling insightful revelations from transcriptomic data that include association-based methods (based on correlation among expression vectors), probabilistic models (using Bayesian and Gaussian models), and interologous methods. We reviewed different approaches for evaluating the significance of interactions based on the network topology and biological functions of the interacting molecules and discuss various strategies for the identification of functional modules. The chapter concludes with highlighting network-based techniques of prioritizing key genes, outlining the centrality-based, diffusion- based, and subgraph-based methods. The chapter provides a meticulous framework for investigating transcriptomic data to uncover assembly of complex molecular networks for their adaptable analyses across a broad spectrum of biological domains.
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Affiliation(s)
- Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh, India.
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3
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Taris KKH, Kamsma D, Wuite GJL. Single-Cell Measurements Using Acoustic Force Spectroscopy (AFS). Methods Mol Biol 2024; 2694:467-477. [PMID: 37824018 DOI: 10.1007/978-1-0716-3377-9_22] [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: 10/13/2023]
Abstract
Single-molecule force spectroscopy is a powerful tool to investigate the forces and motions related to interactions of biological molecules. Acoustic force spectroscopy (AFS) is a developed measurement tool to study single molecules or cells making use of acoustic standing waves. AFS permits high experimental throughput because many individual molecules can be manipulated and tracked in parallel. Moreover, a wide range of forces can be applied as well as a force loading rate with range of six orders of magnitude. At the same time, AFS stands out because of its simplicity and the compactness of the experimental setup. Even though the AFS setup is simple, it can still be challenging to perform high-quality measurements. Here we describe, in detail, how to setup, perform, and analyze an AFS measurement to determine cell adhesion.
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Affiliation(s)
- Kees-Karel H Taris
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Kamsma
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- LUMICKS B.V, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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4
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Pérez-García L, Selin M, Ciarlo A, Magazzù A, Pesce G, Sasso A, Volpe G, Pérez Castillo I, Arzola AV. Optimal calibration of optical tweezers with arbitrary integration time and sampling frequencies: a general framework [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:6442-6469. [PMID: 38420310 PMCID: PMC10898575 DOI: 10.1364/boe.495468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 03/02/2024]
Abstract
Optical tweezers (OT) have become an essential technique in several fields of physics, chemistry, and biology as precise micromanipulation tools and microscopic force transducers. Quantitative measurements require the accurate calibration of the trap stiffness of the optical trap and the diffusion constant of the optically trapped particle. This is typically done by statistical estimators constructed from the position signal of the particle, which is recorded by a digital camera or a quadrant photodiode. The finite integration time and sampling frequency of the detector need to be properly taken into account. Here, we present a general approach based on the joint probability density function of the sampled trajectory that corrects exactly the biases due to the detector's finite integration time and limited sampling frequency, providing theoretical formulas for the most widely employed calibration methods: equipartition, mean squared displacement, autocorrelation, power spectral density, and force reconstruction via maximum-likelihood-estimator analysis (FORMA). Our results, tested with experiments and Monte Carlo simulations, will permit users of OT to confidently estimate the trap stiffness and diffusion constant, extending their use to a broader set of experimental conditions.
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Affiliation(s)
- Laura Pérez-García
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Martin Selin
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Antonio Ciarlo
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte Sant’Angelo, Via Cintia, I- 80126, Naples, Italy
| | - Alessandro Magazzù
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Giuseppe Pesce
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte Sant’Angelo, Via Cintia, I- 80126, Naples, Italy
| | - Antonio Sasso
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte Sant’Angelo, Via Cintia, I- 80126, Naples, Italy
| | - Giovanni Volpe
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Isaac Pérez Castillo
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - Alejandro V. Arzola
- Departamento de Física Cuántica y Fotónica, Instituto de Física, Universidad Nacional Autónoma de México, C.P. 04510, Cd. de México, Mexico
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5
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Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J. Theoretical and computational tools to model multistable gene regulatory networks. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023; 86:10.1088/1361-6633/acec88. [PMID: 37531952 PMCID: PMC10521208 DOI: 10.1088/1361-6633/acec88] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/02/2023] [Indexed: 08/04/2023]
Abstract
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the use of theoretical modeling to describe genetic and biochemical circuits becomes more widespread, theoreticians with mathematical and physical backgrounds routinely apply concepts from statistical physics, non-linear dynamics, and network theory to biological systems. This review aims at providing a clear overview of the most important methodologies applied in the field while highlighting current and future challenges. It also includes hands-on tutorials to solve and simulate some of the archetypical biological system models used in the field. Furthermore, we provide concrete examples from the existing literature for theoreticians that wish to explore this fast-developing field. Whenever possible, we highlight the similarities and differences between biochemical and regulatory networks and 'classical' systems typically studied in non-equilibrium statistical and quantum mechanics.
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Affiliation(s)
- Federico Bocci
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
- Department of Mathematics, University of California, Irvine, CA 92697, USA
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Qing Nie
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
- Department of Mathematics, University of California, Irvine, CA 92697, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - José Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
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6
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Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J. Theoretical and computational tools to model multistable gene regulatory networks. ARXIV 2023:arXiv:2302.07401v2. [PMID: 36824430 PMCID: PMC9949162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the use of theoretical modeling to describe genetic and biochemical circuits becomes more widespread, theoreticians with mathematical and physical backgrounds routinely apply concepts from statistical physics, non-linear dynamics, and network theory to biological systems. This review aims at providing a clear overview of the most important methodologies applied in the field while highlighting current and future challenges. It also includes hands-on tutorials to solve and simulate some of the archetypical biological system models used in the field. Furthermore, we provide concrete examples from the existing literature for theoreticians that wish to explore this fast-developing field. Whenever possible, we highlight the similarities and differences between biochemical and regulatory networks and 'classical' systems typically studied in non-equilibrium statistical and quantum mechanics.
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7
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Nandel V, Scadden J, Baker MAB. Ion-Powered Rotary Motors: Where Did They Come from and Where They Are Going? Int J Mol Sci 2023; 24:10601. [PMID: 37445779 PMCID: PMC10341847 DOI: 10.3390/ijms241310601] [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] [Received: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Molecular motors are found in many living organisms. One such molecular machine, the ion-powered rotary motor (IRM), requires the movement of ions across a membrane against a concentration gradient to drive rotational movement. The bacterial flagellar motor (BFM) is an example of an IRM which relies on ion movement through the stator proteins to generate the rotation of the flagella. There are many ions which can be used by the BFM stators to power motility and different ions can be used by a single bacterium expressing multiple stator variants. The use of ancestral sequence reconstruction (ASR) and functional analysis of reconstructed stators shows promise for understanding how these proteins evolved and when the divergence in ion use may have occurred. In this review, we discuss extant BFM stators and the ions that power them as well as recent examples of the use of ASR to study ion-channel selectivity and how this might be applied to further study of the BFM stator complex.
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Affiliation(s)
| | | | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW 2033, Australia; (V.N.); (J.S.)
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8
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Tsan VH, Fan D, Caneva S, Smith CS, Verbiest GJ. Low-cost acoustic force trap in a microfluidic channel. HARDWAREX 2023; 14:e00428. [PMID: 37275951 PMCID: PMC10232849 DOI: 10.1016/j.ohx.2023.e00428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A low-cost glass-based microfluidic flow cell with a piezo actuator is built using off-the-shelf parts (total cost €9 per device) to apply acoustophoretic force on polystyrene micro-beads. The main challenge in the fabrication of these devices was to ensure their leak tightness, which we solved using double-sided tape and nail polish. Beads with 1.5 μm diameter flowing in a 100 μm deep channel were trapped at 7.5 MHz using a 23.7 peak-to-peak voltage (V pp ) sinusoidal input. The trap located at 50 ± 0.1 μm depth was measured to have a stiffness of approximately 0.6 pN/μm. With this simple device we can trap and control the axial position of micrometer scale objects, which allows for the manipulation of beads and cells. We intend to use the device for force spectroscopy on micro-bead tethered DNA. This can be combined with super-resolution imaging techniques to study mechanics and binding of protein structures along a DNA strand as a function of induced tension.
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Affiliation(s)
- Vi-hung Tsan
- Faculty of Mechanical, Materials, and Maritime Engineering, Technische Universiteit Delft, Delft 2628CD, The Netherlands
| | - Daniel Fan
- Faculty of Mechanical, Materials, and Maritime Engineering, Technische Universiteit Delft, Delft 2628CD, The Netherlands
| | - Sabina Caneva
- Faculty of Mechanical, Materials, and Maritime Engineering, Technische Universiteit Delft, Delft 2628CD, The Netherlands
| | - Carlas S. Smith
- Faculty of Mechanical, Materials, and Maritime Engineering, Technische Universiteit Delft, Delft 2628CD, The Netherlands
| | - Gerard J. Verbiest
- Faculty of Mechanical, Materials, and Maritime Engineering, Technische Universiteit Delft, Delft 2628CD, The Netherlands
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9
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Capera-Aragones P, Tyson RC, Foxall E. The maximum entropy principle to predict forager spatial distributions: an alternate perspective for movement ecology. THEOR ECOL-NETH 2023. [DOI: 10.1007/s12080-023-00552-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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10
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Shivalkar S, Chowdhary P, Afshan T, Chaudhary S, Roy A, Samanta SK, Sahoo AK. Nanoengineering of biohybrid micro/nanobots for programmed biomedical applications. Colloids Surf B Biointerfaces 2023; 222:113054. [PMID: 36446238 DOI: 10.1016/j.colsurfb.2022.113054] [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: 02/24/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022]
Abstract
Biohybrid micro/nanobots have emerged as an innovative resource to be employed in the biomedical field due to their biocompatible and biodegradable properties. These are tiny nanomaterial-based integrated structures engineered in a way that they can move autonomously and perform the programmed tasks efficiently even at hard-to-reach organ/tissues/cellular sites. The biohybrid micro/nanobots can either be cell/bacterial/enzyme-based or may mimic the properties of an active molecule. It holds the potential to change the landscape in various areas of biomedical including early diagnosis of disease, therapeutics, imaging, or precision surgery. The propulsion mechanism of the biohybrid micro/nanobots can be both fuel-based and fuel-free, but the most effective and easiest way to propel these micro/nanobots is via enzymes. Micro/nanobots possess the feature to adsorb/functionalize chemicals or drugs at their surfaces thus offering the scope of delivering drugs at the targeted locations. They also have shown immense potential in intracellular sensing of biomolecules and molecular events. Moreover, with recent progress in the material development and processing is required for enhanced activity and robustness the fabrication is done via various advanced techniques to avoid self-degradation and cause cellular toxicity during autonomous movement in biological medium. In this review, various approaches of design, architecture, and performance of such micro/nanobots have been illustrated along with their potential applications in controlled cargo release, therapeutics, intracellular sensing, and bioimaging. Furthermore, it is also foregrounding their advancement offering an insight into their future scopes, opportunities, and challenges involved in advanced biomedical applications.
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Affiliation(s)
- Saurabh Shivalkar
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India.
| | - Pallabi Chowdhary
- Department of Biotechnology, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Tayyaba Afshan
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India
| | - Shrutika Chaudhary
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Anwesha Roy
- Department of Biotechnology, Heritage Institute of Technology, Kolkata, West Bengal, India
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India.
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11
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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12
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Luo Y, Chang J, Yang D, Bryan JS, MacIsaac M, Pressé S, Wong WP. Resolving Molecular Heterogeneity with Single-Molecule Centrifugation. J Am Chem Soc 2023; 145:3276-3282. [PMID: 36716175 PMCID: PMC9936575 DOI: 10.1021/jacs.2c11450] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
For many classes of biomolecules, population-level heterogeneity is an essential aspect of biological function─from antibodies produced by the immune system to post-translationally modified proteins that regulate cellular processes. However, heterogeneity is difficult to fully characterize for multiple reasons: (i) single-molecule approaches are needed to avoid information lost by ensemble-level averaging, (ii) sufficient statistics must be gathered on both a per-molecule and per-population level, and (iii) a suitable analysis framework is required to make sense of a potentially limited number of intrinsically noisy measurements. Here, we introduce an approach that overcomes these difficulties by combining three techniques: a DNA nanoswitch construct to repeatedly interrogate the same molecule, a benchtop centrifuge force microscope (CFM) to obtain thousands of statistics in a highly parallel manner, and a Bayesian nonparametric (BNP) inference method to resolve separate subpopulations with distinct kinetics. We apply this approach to characterize commercially available antibodies and find that polyclonal antibody from rabbit serum is well-modeled by a mixture of three subpopulations. Our results show how combining a spatially and temporally multiplexed nanoswitch-CFM assay with BNP analysis can help resolve complex biomolecular interactions in heterogeneous samples.
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Affiliation(s)
- Yi Luo
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jeffrey Chang
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Darren Yang
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - J. Shepard Bryan
- Department
of Physics, Arizona State University, Tempe, Arizona 85287, United States,Center
for
Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Molly MacIsaac
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steve Pressé
- Department
of Physics, Arizona State University, Tempe, Arizona 85287, United States,Center
for
Biological Physics, Arizona State University, Tempe, Arizona 85287, United States,School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Wesley P. Wong
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States,
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13
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Mishra RK, Maganti L. Antitumor drugs effect on the stability of double-stranded DNA: steered molecular dynamics analysis. J Biomol Struct Dyn 2022; 40:11373-11382. [PMID: 34355668 DOI: 10.1080/07391102.2021.1960193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Denaturation of the DNA double helix inside the cell is essential for cellular processes such as replication and transcription for the growth of the cells. However, the growth of unwanted cells, which are responsible for cancerous kind of disease, is one of the biggest challenges of modern therapeutics. DNA cross-linking agents may kill cancer cells by damaging their DNA and stopping them from dividing. In the present study, we have carried out steered molecular dynamics simulations to study the effects of rupture and unzipping forces on the stability of dsDNA in the absence and presence of covalently bonded drugs. We have found that the stability of dsDNA increases strongly in the presence of covalently bonded drugs. The microscopic study of disruption of hydrogen-bonds associated with base-pairs of the dsDNA and the study of the variation of stacking overlap parameters gives evidence of symmetry during the rupture and asymmetry in the unzip event. The significance of the mechanism of force-induced melting study of the dsDNA in the absence and presence of antitumor drugs might have a biological relevance as it provides a pathway to open the double helix in a specific position and may help for the pharmaceutical design of drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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14
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Akbari E, Shahhosseini M, Robbins A, Poirier MG, Song JW, Castro CE. Low cost and massively parallel force spectroscopy with fluid loading on a chip. Nat Commun 2022; 13:6800. [PMID: 36357383 PMCID: PMC9649742 DOI: 10.1038/s41467-022-34212-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 10/18/2022] [Indexed: 11/12/2022] Open
Abstract
Current approaches for single molecule force spectroscopy are typically constrained by low throughput and high instrumentation cost. Herein, a low-cost, high throughput technique is demonstrated using microfluidics for multiplexed mechanical manipulation of up to ~4000 individual molecules via molecular fluid loading on-a-chip (FLO-Chip). The FLO-Chip consists of serially connected microchannels with varying width, allowing for simultaneous testing at multiple loading rates. Molecular force measurements are demonstrated by dissociating Biotin-Streptavidin and Digoxigenin-AntiDigoxigenin interactions along with unzipping of double stranded DNA of varying sequence under different dynamic loading rates and solution conditions. Rupture force results under varying loading rates and solution conditions are in good agreement with prior studies, verifying a versatile approach for single molecule biophysics and molecular mechanobiology. FLO-Chip enables straightforward, rapid, low-cost, and portable mechanical testing of single molecules that can be implemented on a wide range of microscopes to broaden access and may enable new applications of molecular force spectroscopy.
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Affiliation(s)
- Ehsan Akbari
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Melika Shahhosseini
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Ariel Robbins
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Jonathan W Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Comprehensive Cancer Center, 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.
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15
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Arias-Gonzalez JR. Fluctuation relations for irreversible emergence of information. Sci Rep 2022; 12:17230. [PMID: 36241690 PMCID: PMC9568592 DOI: 10.1038/s41598-022-21729-9] [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: 06/03/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
Information theory and Thermodynamics have developed closer in the last years, with a growing application palette in which the formal equivalence between the Shannon and Gibbs entropies is exploited. The main barrier to connect both disciplines is the fact that information does not imply a dynamics, whereas thermodynamic systems unfold with time, often away from equilibrium. Here, we analyze chain-like systems comprising linear sequences of physical objects carrying symbolic meaning. We show that, after defining a reading direction, both reversible and irreversible informations emerge naturally from the principle of microscopic reversibility in the evolution of the chains driven by a protocol. We find fluctuation equalities that relate entropy, the relevant concept in communication, and energy, the thermodynamically significant quantity, examined along sequences whose content evolves under writing and revision protocols. Our results are applicable to nanoscale chains, where information transfer is subject to thermal noise, and extendable to virtually any communication system.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Centro de Tecnologías Físicas, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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16
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Jiang T. Identification of the genetic central dogma in osteogenic differentiation of MSCs by osteoinductive medium from transcriptional data sets. Chronic Dis Transl Med 2022; 8:218-228. [PMID: 36161200 PMCID: PMC9481875 DOI: 10.1002/cdt3.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Background The genetic central dogma (GCD) has been demonstrated its essential function in many biological processes and diseases. However, its roles in the process of osteogenic differentiation of mesenchymal stem cells (MSCs) remain unclear. Methods In this project, we analyzed an online database of osteogenic differentiation of MSCs after 14 days and 28 days by osteoinductive medium (GSE83770). The differentially expressed genes were screened by GEO2R, with further conducting of KEGG pathways using DAVID. In addition, protein-protein interactions of the enriched pathways were performed using STRING with marked hub genes measured by the CytoHubba. Hub genes were verified by quantitative reverse-transcription polymerase chain reaction. Results Results showed that six pathways related to GCD, including DNA replication, Aminoacyl-tRNA biosynthesis, Mismatch repair, Ribosome, Spliceosome, and RNA degradation pathways enriched in the early stage (14 days vs. undifferentiated MSCs) of osteogenesis. The Lysosome pathway was highly enriched in the late stage (28 vs. 14 days) of osteogenesis, and Ribosome pathway plays a key role throughout the entire process (28 days vs. undifferentiated MSCs) of osteogenesis. Conclusion Both DNA replication and protein translation were functionally worked in the early stage of osteogenesis, whereas the Lysosome pathway was the only GCD-related one in the late stage of osteogenesis. The GCD-related Ribosome pathway occupied the entire process of osteogenesis.
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Affiliation(s)
- Tong‐Meng Jiang
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiang310027China
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17
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The Development of Single Molecule Force Spectroscopy: From Polymer Biophysics to Molecular Machines. Q Rev Biophys 2022; 55:e9. [PMID: 35916314 DOI: 10.1017/s0033583522000087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Nguyen HVT, Jiang Y, Mohapatra S, Wang W, Barnes JC, Oldenhuis NJ, Chen KK, Axelrod S, Huang Z, Chen Q, Golder MR, Young K, Suvlu D, Shen Y, Willard AP, Hore MJA, Gómez-Bombarelli R, Johnson JA. Bottlebrush polymers with flexible enantiomeric side chains display differential biological properties. Nat Chem 2022; 14:85-93. [PMID: 34824461 PMCID: PMC9122101 DOI: 10.1038/s41557-021-00826-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/27/2021] [Indexed: 11/08/2022]
Abstract
Chirality and molecular conformation are central components of life: biological systems rely on stereospecific interactions between discrete (macro)molecular conformers, and the impacts of stereochemistry and rigidity on the properties of small molecules and biomacromolecules have been intensively studied. Nevertheless, how these features affect the properties of synthetic macromolecules has received comparably little attention. Here we leverage iterative exponential growth and ring-opening metathesis polymerization to produce water-soluble, chiral bottlebrush polymers (CBPs) from two enantiomeric pairs of macromonomers of differing rigidity. Remarkably, CBPs with conformationally flexible, mirror image side chains show several-fold differences in cytotoxicity, cell uptake, blood pharmacokinetics and liver clearance; CBPs with comparably rigid, mirror image side chains show no differences. These observations are rationalized with a simple model that correlates greater conformational freedom with enhanced chiral recognition. Altogether, this work provides routes to the synthesis of chiral nanostructured polymers and suggests key roles for stereochemistry and conformational rigidity in the design of future biomaterials.
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Affiliation(s)
- Hung V-T Nguyen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yivan Jiang
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Somesh Mohapatra
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wencong Wang
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan C Barnes
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathan J Oldenhuis
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathleen K Chen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Axelrod
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Zhihao Huang
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qixian Chen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew R Golder
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katherine Young
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dylan Suvlu
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yizhi Shen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam P Willard
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael J A Hore
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Rafael Gómez-Bombarelli
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jeremiah A Johnson
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Yadav R, Senanayake KB, Comstock MJ. High-Resolution Optical Tweezers Combined with Multicolor Single-Molecule Microscopy. Methods Mol Biol 2022; 2478:141-240. [PMID: 36063322 DOI: 10.1007/978-1-0716-2229-2_8] [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
We present an instrument that combines high-resolution optical tweezers and multicolor confocal fluorescence spectroscopy. Biological macromolecules exhibit complex conformation and stoichiometry changes in coordination with their motion and activity. To further our understanding of the complex machinery of life, we need methods that can simultaneously probe more than one degree of freedom of single molecules and complexes. Fluorescence optical tweezers, or "fleezers," combine the capabilities of optical tweezers and single-molecule fluorescence microscopy into a single instrument. Here we present the latest generation of a high-resolution fleezers instrument integrated with multicolor fluorescence spectroscopy. The tweezers portion of the instrument can manipulate biological macromolecules with pN scale forces while measuring subnanometer distances. Simultaneous with tweezers measurements, the multicolor fluorescence capability allows the direct observation of multiple molecules or multiple degrees of freedom which allows, for example, the observation of multiple proteins simultaneously within a complex. The instrument incorporates three fluorescence excitation lasers, all sourced from a single-mode optical fiber allowing a reliable alignment scheme, that allows, for example, three independent fluorescent probes or fluorescence resonance energy transfer (FRET) measurements and also increases flexibility in the choice of fluorescent probes. To avoid photobleaching and improve tweezers stability, the instrument implements a timesharing (using a single trap laser to produce a pair of traps via rapid switching between two locations) and interlacing (turning the trapping beam off when the fluorescence excitation beams are on and vice versa) scheme using acousto-optic modulators (AOM) to rapidly and precisely modulate lasers. Our latest "random phase" trap AOM control method obliterates previous residual trap positioning and bead position measurement errors. Here we present the general design principles and detailed construction and testing protocols for the instrument.
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Affiliation(s)
- Rajeev Yadav
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA
| | - Kasun B Senanayake
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA
| | - Matthew J Comstock
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA.
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20
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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.
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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.
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21
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A Horizontal Magnetic Tweezers for Studying Single DNA Molecules and DNA-Binding Proteins. Molecules 2021; 26:molecules26164781. [PMID: 34443369 PMCID: PMC8398817 DOI: 10.3390/molecules26164781] [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: 06/30/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
We report data from single molecule studies on the interaction between single DNA molecules and core histones using custom-designed horizontal magnetic tweezers. The DNA-core histone complexes were formed using λ-DNA tethers, core histones, and NAP1 and were exposed to forces ranging from ~2 pN to ~74 pN. During the assembly events, we observed the length of the DNA decrease in approximate integer multiples of ~50 nm, suggesting the binding of the histone octamers to the DNA tether. During the mechanically induced disassembly events, we observed disruption lengths in approximate integer multiples of ~50 nm, suggesting the unbinding of one or more octamers from the DNA tether. We also observed histone octamer unbinding events at forces as low as ~2 pN. Our horizontal magnetic tweezers yielded high-resolution, low-noise data on force-mediated DNA-core histone assembly and disassembly processes.
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22
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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.
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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.
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23
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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.
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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.
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24
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Kilic Z, Sgouralis I, Pressé S. Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach. Biophys J 2021; 120:1665-1679. [PMID: 33705761 DOI: 10.1016/j.bpj.2021.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 01/09/2023] Open
Abstract
The time spent by a single RNA polymerase (RNAP) at specific locations along the DNA, termed "residence time," reports on the initiation, elongation, and termination stages of transcription. At the single-molecule level, this information can be obtained from dual ultrastable optical trapping experiments, revealing a transcriptional elongation of RNAP interspersed with residence times of variable duration. Successfully discriminating between long and short residence times was used by previous approaches to learn about RNAP's transcription elongation dynamics. Here, we propose an approach based on the Bayesian sticky hidden Markov model that treats all residence times for an Escherichia coli RNAP on an equal footing without a priori discriminating between long and short residence times. Furthermore, our method has two additional advantages: we provide full distributions around key point statistics and directly treat the sequence dependence of RNAP's elongation rate. By applying our approach to experimental data, we find assigned relative probabilities on long versus short residence times, force-dependent average residence time transcription elongation dynamics, ∼10% drop in the average backtracking durations in the presence of GreB, and ∼20% drop in the average residence time as a function of applied force in the presence of RNaseA.
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Affiliation(s)
- Zeliha Kilic
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Steve Pressé
- Center for Biological Physics, Department of Physics and School of Molecular Sciences, Arizona State University, Tempe, Arizona. spresse@%20asu.edu
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25
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Theory of optical tweezing of dielectric microspheres in chiral host media and its applications. Sci Rep 2020; 10:16481. [PMID: 33020577 PMCID: PMC7536396 DOI: 10.1038/s41598-020-73530-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022] Open
Abstract
We report for the first time the theory of optical tweezers of spherical dielectric particles embedded in a chiral medium. We develop a partial-wave (Mie) expansion to calculate the optical force acting on a dielectric microsphere illuminated by a circularly-polarized, highly focused laser beam. When choosing a polarization with the same handedness of the medium, the axial trap stability is improved, thus allowing for tweezing of high-refractive-index particles. When the particle is displaced off-axis by an external force, its equilibrium position is rotated around the optical axis by the mechanical effect of an optical torque. Both the optical torque and the angle of rotation are greatly enhanced in the presence of a chiral host medium when considering radii a few times larger than the wavelength. In this range, the angle of rotation depends strongly on the microsphere radius and the chirality parameter of the host medium, opening the way for a quantitative characterization of both parameters. Measurable angles are predicted even in the case of naturally occurring chiral solutes, allowing for a novel all-optical method to locally probe the chiral response at the nanoscale.
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26
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Affiliation(s)
- Ryota Iino
- Institute for Molecular Science and The Graduate University for
Advanced Studies (SOKENDAI)
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27
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Gutiérrez-Mejía FA, Moerland CP, van IJzendoorn LJ, Prins MWJ. Conformation switching of single native proteins revealed by nanomechanical probing without a pulling force. NANOSCALE 2019; 11:19933-19942. [PMID: 31599908 DOI: 10.1039/c9nr01448a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein conformational changes are essential to biological function, and the heterogeneous nature of the corresponding protein states provokes an interest to measure conformational changes at the single molecule level. Here we demonstrate that conformational changes in single native proteins can be revealed by non-covalent antibody-targeting of specific domains within the protein, using nanomechanical probing without an applied pulling force. The protein of interest was captured between a particle and a substrate and three properties were quantified: the twist amplitude related to an applied torque, torsional compliance related to rotational Brownian motion, and translational Brownian displacement. Calcium-dependent conformation switching was studied in native human cardiac troponin, a heterotrimer protein complex that regulates the contraction and relaxation of heart muscle cells and is also a key biomarker for diagnosing myocardial infarction. The data reveal a change in mechanical properties upon conformation switching from the non-saturated to the calcium-saturated state, which in cardiomyocytes gives myosin motor proteins access to actin filaments. A clear increase was observed in the molecular stiffness for the calcium-saturated protein conformation. Using libraries of monoclonal antibodies, the nanomechanical probing of conformation by antibody targeting opens avenues for characterizing single native protein complexes for research as well as for diagnostic applications.
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Affiliation(s)
- Fabiola A Gutiérrez-Mejía
- Department of Applied Physics, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands. and Institute for Complex Molecular Systems (ICMS), TU/e, Eindhoven, The Netherlands
| | - Christian P Moerland
- Department of Applied Physics, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands. and Institute for Complex Molecular Systems (ICMS), TU/e, Eindhoven, The Netherlands
| | - Leo J van IJzendoorn
- Department of Applied Physics, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands. and Institute for Complex Molecular Systems (ICMS), TU/e, Eindhoven, The Netherlands
| | - Menno W J Prins
- Department of Applied Physics, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands. and Institute for Complex Molecular Systems (ICMS), TU/e, Eindhoven, The Netherlands and Department of Biomedical Engineering, TU/e, Eindhoven, The Netherlands
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28
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Chakrabarti S, Jarzynski C, Thirumalai D. Processivity, Velocity, and Universal Characteristics of Nucleic Acid Unwinding by Helicases. Biophys J 2019; 117:867-879. [PMID: 31400912 PMCID: PMC6731385 DOI: 10.1016/j.bpj.2019.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/20/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022] Open
Abstract
Helicases are components of the cellular replisome that are essential for unwinding double-strand nucleic acids during the process of replication. Intriguingly, most helicases are inefficient and require either oligomerization or assistance from other partner proteins to increase the processivity of unwinding in the presence of the replication fork, which acts as a barrier to progress. Single-molecule force spectroscopy has emerged as a promising experimental technique to probe how relieving this barrier on the helicase can allow for increased efficiency of unwinding. However, there exists no comprehensive theoretical framework to provide unique interpretations of the underlying helicase kinetics from the force spectroscopy data. This remains a major confounding issue in the field. Here, we develop a mathematical framework and derive analytic expressions for the velocity and run length of a general model of finitely processive helicases, the two most commonly measured experimental quantities. We show that in contrast to the unwinding velocity, the processivity exhibits a universal increase in response to external force, irrespective of the underlying architecture and unwinding kinetics of the helicase. Our work provides the first, to our knowledge, explanation to a wide array of experiments and suggests that helicases may have evolved to maximize processivity rather than speed. To demonstrate the use of our theory on experimental data, we analyze velocity and processivity data on the T7 helicase and provide unique inferences on the kinetics of the helicase. Our results show that T7 is a weakly active helicase that destabilizes the fork ahead by less than 1 kBT and back steps very frequently while unwinding DNA. Our work generates fundamental insights into the force response of helicases and provides a widely applicable method for inferring the underlying helicase kinetics from force spectroscopy data.
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Affiliation(s)
- Shaon Chakrabarti
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.
| | - Christopher Jarzynski
- Department of Chemistry and Biochemistry, Institute for Physical Sciences and Technology, Department of Physics, University of Maryland, College Park, Maryland
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
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29
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Desai VP, Frank F, Lee A, Righini M, Lancaster L, Noller HF, Tinoco I, Bustamante C. Co-temporal Force and Fluorescence Measurements Reveal a Ribosomal Gear Shift Mechanism of Translation Regulation by Structured mRNAs. Mol Cell 2019; 75:1007-1019.e5. [PMID: 31471187 DOI: 10.1016/j.molcel.2019.07.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/12/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022]
Abstract
The movement of ribosomes on mRNA is often interrupted by secondary structures that present mechanical barriers and play a central role in translation regulation. We investigate how ribosomes couple their internal conformational changes with the activity of translocation factor EF-G to unwind mRNA secondary structures using high-resolution optical tweezers with single-molecule fluorescence capability. We find that hairpin opening occurs during EF-G-catalyzed translocation and is driven by the forward rotation of the small subunit head. Modulating the magnitude of the hairpin barrier by force shows that ribosomes respond to strong barriers by shifting their operation to an alternative 7-fold-slower kinetic pathway prior to translocation. Shifting into a slow gear results from an allosteric switch in the ribosome that may allow it to exploit thermal fluctuations to overcome mechanical barriers. Finally, we observe that ribosomes occasionally open the hairpin in two successive sub-codon steps, revealing a previously unobserved translocation intermediate.
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Affiliation(s)
- Varsha P Desai
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Filipp Frank
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Antony Lee
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maurizio Righini
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Laura Lancaster
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Harry F Noller
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Bustamante
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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30
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Abstract
The 2018 Nobel Prize in Physics has been awarded jointly to Arthur Ashkin for the discovery and development of optical tweezers and their applications to biological systems and to Gérard Mourou and Donna Strickland for the invention of laser chirped pulse amplification. Here we focus on Arthur Ashkin and how his revolutionary work opened a window into the world of molecular mechanics and spurred the rise of single-molecule biophysics.
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Wasserman MR, Liu S. A Tour de Force on the Double Helix: Exploiting DNA Mechanics To Study DNA-Based Molecular Machines. Biochemistry 2019; 58:4667-4676. [PMID: 31251042 DOI: 10.1021/acs.biochem.9b00346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA is both a fundamental building block of life and a fascinating natural polymer. The advent of single-molecule manipulation tools made it possible to exert controlled force on individual DNA molecules and measure their mechanical response. Such investigations elucidated the elastic properties of DNA and revealed its distinctive structural configurations across force regimes. In the meantime, a detailed understanding of DNA mechanics laid the groundwork for single-molecule studies of DNA-binding proteins and DNA-processing enzymes that bend, stretch, and twist DNA. These studies shed new light on the metabolism and transactions of nucleic acids, which constitute a major part of the cell's operating system. Furthermore, the marriage of single-molecule fluorescence visualization and force manipulation has enabled researchers to directly correlate the applied tension to changes in the DNA structure and the behavior of DNA-templated complexes. Overall, experimental exploitation of DNA mechanics has been and will continue to be a unique and powerful strategy for understanding how molecular machineries recognize and modify the physical state of DNA to accomplish their biological functions.
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Affiliation(s)
- Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
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Abstract
While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold.
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Affiliation(s)
- Holger Flechsig
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan
| | - Alexander S Mikhailov
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan.,2 Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin , Germany
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33
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Boël G, Danot O, de Lorenzo V, Danchin A. Omnipresent Maxwell's demons orchestrate information management in living cells. Microb Biotechnol 2019; 12:210-242. [PMID: 30806035 PMCID: PMC6389857 DOI: 10.1111/1751-7915.13378] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information-managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.
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Affiliation(s)
- Grégory Boël
- UMR 8261 CNRS‐University Paris DiderotInstitut de Biologie Physico‐Chimique13 rue Pierre et Marie Curie75005ParisFrance
| | - Olivier Danot
- Institut Pasteur25‐28 rue du Docteur Roux75724Paris Cedex 15France
| | - Victor de Lorenzo
- Molecular Environmental Microbiology LaboratorySystems Biology ProgrammeCentro Nacional de BiotecnologiaC/Darwin n° 3, Campus de Cantoblanco28049MadridEspaña
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
- The School of Biomedical SciencesLi Kashing Faculty of MedicineHong Kong University21, Sassoon RoadPokfulamSAR Hong Kong
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Kotnala A, Zheng Y, Fu J, Cheng W. Back-focal-plane interferometric detection of nanoparticles in spatially confined microfluidic channels. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:023107. [PMID: 30831709 PMCID: PMC6382495 DOI: 10.1063/1.5074194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/01/2019] [Indexed: 05/08/2023]
Abstract
Nanoparticles are important in several areas of modern biomedical research. However, detection and characterization of nanoparticles is challenging due to their small size. Back-focal-plane interferometry (BFPI) is a highly sensitive technique that has been used in laser tweezers for quantitative measurement of force and displacement. The utility of BFPI for detection and characterization of nanoparticles, however, has not yet been achieved. Here we show that BFPI can be used for rapid probing of a suspension of nanoparticles in a spatially confined microfluidic channel. We show that the Gaussian Root-mean-squared noise of the BFPI signal is highly sensitive to the nanoparticle size and can be used as a parameter for rapid detection of nanoparticles at a single-particle level and characterization of particle heterogeneities in a suspension. By precisely aligning the optical trap relative to the channel boundaries, individual polystyrene particles with a diameter as small as 63 nm can be detected using BFPI with a high signal-to-noise ratio.
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Affiliation(s)
- Abhay Kotnala
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, USA
| | - Yi Zheng
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, Michigan 48109, USA
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, Michigan 48109, USA
| | - Wei Cheng
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, USA
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35
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Leveille MP, Tran T, Dingillo G, Cannon B. Detection of Mg 2+-dependent, coaxial stacking rearrangements in a bulged three-way DNA junction by single-molecule FRET. Biophys Chem 2018; 245:25-33. [PMID: 30551070 DOI: 10.1016/j.bpc.2018.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 12/15/2022]
Abstract
Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) approaches. The 3WJs varied according to the GC content and sequence of the junction core as well as the pyrimidine content of the internal bulge. Mg2+ titration experiments by ensemble FRET show that both stacking conformations have similar Mg2+ requirements for folding. Strikingly, smFRET experiments reveal that a specific junction sequence can populate both conformers and that this junction undergoes continual interconversion between the two stacked conformers. These findings will support the development of folding principles for the rational design of functional DNA nanostructures.
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Affiliation(s)
| | - Thao Tran
- Department of Physics, Loyola University Chicago, Chicago, IL, USA
| | - Gianna Dingillo
- Department of Physics, Loyola University Chicago, Chicago, IL, USA
| | - Brian Cannon
- Department of Physics, Loyola University Chicago, Chicago, IL, USA.
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36
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Hill SA, Gerke C, Hartmann L. Recent Developments in Solid-Phase Strategies towards Synthetic, Sequence-Defined Macromolecules. Chem Asian J 2018; 13:3611-3622. [PMID: 30216690 DOI: 10.1002/asia.201801171] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Indexed: 01/09/2023]
Abstract
Sequence-control in synthetic polymers is an important contemporary research area because it provides the opportunity to create completely novel materials for structure-function studies. This is especially relevant for biomimetic polymers, bioactive and information security materials. The level of control is strongly dependent and inherent upon the polymerization technique utilized. Today, the most established method yielding monodispersity and monomer sequence-definition is solid-phase synthesis. This Focus Review highlights recent advances in solid-phase strategies to access synthetic, sequence-defined macromolecules. Alternatives strategies towards sequence-defined macromolecules are also briefly summarized.
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Affiliation(s)
- Stephen A Hill
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Christoph Gerke
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Laura Hartmann
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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ATPase and Protease Domain Movements in the Bacterial AAA+ Protease FtsH Are Driven by Thermal Fluctuations. J Mol Biol 2018; 430:4592-4602. [PMID: 30044948 DOI: 10.1016/j.jmb.2018.07.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 01/27/2023]
Abstract
AAA+ proteases are essential players in cellular pathways of protein degradation. Elucidating their conformational behavior is key for understanding their reaction mechanism and, importantly, for elaborating our understanding of mutation-induced protease deficiencies. Here, we study the structural dynamics of the Thermotoga maritima AAA+ hexameric ring metalloprotease FtsH (TmFtsH). Using a single-molecule Förster resonance energy transfer approach to monitor ATPase and protease inter-domain conformational changes in real time, we show that TmFtsH-even in the absence of nucleotide-is a highly dynamic protease undergoing sequential transitions between five states on the second timescale. Addition of ATP does not influence the number of states or change the timescale of domain motions but affects the state occupancy distribution leading to an inter-domain compaction. These findings suggest that thermal energy, but not chemical energy, provides the major driving force for conformational switching, while ATP, through a state reequilibration, introduces directionality into this process. The TmFtsH A359V mutation, a homolog of the human pathogenic A510V mutation of paraplegin (SPG7) causing hereditary spastic paraplegia, does not affect the dynamic behavior of the protease but impairs the ATP-coupled domain compaction and, thus, may account for protease malfunctioning and pathogenesis in hereditary spastic paraplegia.
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38
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Arias-Gonzalez JR. Thermodynamic framework for information in nanoscale systems with memory. J Chem Phys 2018; 147:205101. [PMID: 29195281 DOI: 10.1063/1.5004793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia, C/Faraday 9, Cantoblanco, 28049 Madrid, Spain and CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología," Cantoblanco, 28049 Madrid, Spain
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39
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Arias-Gonzalez JR. Writing, Proofreading and Editing in Information Theory. ENTROPY 2018; 20:e20050368. [PMID: 33265458 PMCID: PMC7512888 DOI: 10.3390/e20050368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/04/2018] [Accepted: 05/12/2018] [Indexed: 12/30/2022]
Abstract
Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains. Our formalism expands the thermodynamic analysis of stochastic chains made up of material subunits to abstract strings of symbols. We introduce a non-Markovian treatment of operational rules over the symbols of the chain that parallels the physical interactions responsible for memory effects in material chains. Our theory underlies any communication system, ranging from human languages and computer science to gene evolution.
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Affiliation(s)
- J. Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia, C/Faraday 9, Cantoblanco, 28049 Madrid, Spain; ; Tel.: +34-91-299-8860
- CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad de Nanobiotecnología”, Cantoblanco, 28049 Madrid, Spain
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40
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King G, Biebricher AS, Heller I, Peterman EJG, Wuite GJL. Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence. NANO LETTERS 2018; 18:2274-2281. [PMID: 29473755 PMCID: PMC6023266 DOI: 10.1021/acs.nanolett.7b04842] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Indexed: 05/25/2023]
Abstract
The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time, using intercalated DNA fluorescence. This approach can report forces over a range of at least ∼0.5-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope. We demonstrate that the method can be easily implemented to report double-stranded (ds)DNA tension in any single-molecule assay that is compatible with fluorescence microscopy. This is particularly useful for multiplexed techniques, where measuring applied force in parallel is technically challenging. Moreover, tension measurements based on local dye binding offer the unique opportunity to determine how an applied force is distributed locally within biomolecular structures. Exploiting this, we apply our method to quantify the position-dependent force profile along the length of flow-stretched DNA and reveal that stretched and entwined DNA molecules-mimicking catenated DNA structures in vivo-display transient DNA-DNA interactions. The method reported here has obvious and broad applications for the study of DNA and DNA-protein interactions. Additionally, we propose that it could be employed to measure forces in any system to which dsDNA can be tethered, for applications including protein unfolding, chromosome mechanics, cell motility, and DNA nanomachines.
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41
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Yang D, Wong WP. Repurposing a Benchtop Centrifuge for High-Throughput Single-Molecule Force Spectroscopy. Methods Mol Biol 2018; 1665:353-366. [PMID: 28940079 PMCID: PMC5640162 DOI: 10.1007/978-1-4939-7271-5_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We present high-throughput single-molecule manipulation using a benchtop centrifuge, overcoming limitations common in other single-molecule approaches such as high cost, low throughput, technical difficulty, and strict infrastructure requirements. An inexpensive and compact Centrifuge Force Microscope (CFM) adapted to a commercial centrifuge enables use by nonspecialists, and integration with DNA nanoswitches facilitates both reliable measurements and repeated molecular interrogation. Here, we provide detailed protocols for constructing the CFM, creating DNA nanoswitch samples, and carrying out single-molecule force measurements.
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Affiliation(s)
- Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Wesley P. Wong
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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42
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Tavakoli M, Taylor JN, Li CB, Komatsuzaki T, Pressé S. Single Molecule Data Analysis: An Introduction. ADVANCES IN CHEMICAL PHYSICS 2017. [DOI: 10.1002/9781119324560.ch4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meysam Tavakoli
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - J. Nicholas Taylor
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Chun-Biu Li
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
- Department of Mathematics; Stockholm University; 106 91 Stockholm Sweden
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Steve Pressé
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Cell and Integrative Physiology; Indiana University School of Medicine; Indianapolis IN 46202 USA
- Department of Physics and School of Molecular Sciences; Arizona State University; Tempe AZ 85287 USA
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43
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Kamsma D, Wuite GJL. Single-Molecule Measurements Using Acoustic Force Spectroscopy (AFS). Methods Mol Biol 2017; 1665:341-351. [PMID: 28940078 DOI: 10.1007/978-1-4939-7271-5_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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44
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Naranjo T, Cerrón F, Nieto-Ortega B, Latorre A, Somoza Á, Ibarra B, Pérez EM. Mechanical measurement of hydrogen bonded host-guest systems under non-equilibrium, near-physiological conditions. Chem Sci 2017; 8:6037-6041. [PMID: 28989633 PMCID: PMC5625567 DOI: 10.1039/c7sc03044d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 07/29/2017] [Indexed: 11/26/2022] Open
Abstract
Decades after the birth of supramolecular chemistry, there are many techniques to measure noncovalent interactions, such as hydrogen bonding, under equilibrium conditions. As ensembles of molecules rapidly lose coherence, we cannot extrapolate bulk data to single-molecule events under non-equilibrium conditions, more relevant to the dynamics of biological systems. We present a new method that exploits the high force resolution of optical tweezers to measure at the single molecule level the mechanical strength of a hydrogen bonded host-guest pair out of equilibrium and under near-physiological conditions. We utilize a DNA reporter to unambiguously isolate single binding events. The Hamilton receptor-cyanuric acid host-guest system is used as a test bed. The force required to dissociate the host-guest system is ∼17 pN and increases with the pulling rate as expected for a system under non-equilibrium conditions. Blocking one of the hydrogen bonding sites results in a significant decrease of the force-to-break by 1-2 pN, pointing out the ability of the method to resolve subtle changes in the mechanical strength of the binding due to the individual H-bonding components. We believe the method will prove to be a versatile tool to address important questions in supramolecular chemistry.
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Affiliation(s)
- Teresa Naranjo
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Fernando Cerrón
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Belén Nieto-Ortega
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Alfonso Latorre
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
| | - Álvaro Somoza
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
- Nanobiotecnología (IMDEA-Nanociencia) , Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 , Madrid , Spain
| | - Borja Ibarra
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
- Nanobiotecnología (IMDEA-Nanociencia) , Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 , Madrid , Spain
| | - Emilio M Pérez
- IMDEA Nanociencia , C/Faraday 9, Ciudad Universitaria de Cantoblanco , 28049 , Madrid , Spain . ;
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46
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A DNA-centered explanation of the DNA polymerase translocation mechanism. Sci Rep 2017; 7:7566. [PMID: 28790383 PMCID: PMC5548866 DOI: 10.1038/s41598-017-08038-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/05/2017] [Indexed: 11/08/2022] Open
Abstract
DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA complex can work against loads greater than 50 pN. It is not known, on the one hand, how chemical energy is transduced into mechanical motion, accounting for such large forces on sub-nanometer steps, and, on the other hand, how energy consumption in fidelity maintenance integrates in this non-equilibrium cycle. Here, we propose a translocation mechanism that points to the flexibility of the DNA, including its overstretching transition, as the principal responsible for the DNA polymerase ratcheting motion. By using thermodynamic analyses, we then find that an external load hardly affects the fidelity of the copying process and, consequently, that translocation and fidelity maintenance are loosely coupled processes. The proposed translocation mechanism is compatible with single-molecule experiments, structural data and stereochemical details of the DNA-protein complex that is formed during replication, and may be extended to RNA transcription.
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47
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Iino R, Iida T, Nakamura A, Saita EI, You H, Sako Y. Single-molecule imaging and manipulation of biomolecular machines and systems. Biochim Biophys Acta Gen Subj 2017; 1862:241-252. [PMID: 28789884 DOI: 10.1016/j.bbagen.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/23/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. SCOPE OF REVIEW We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. MAJOR CONCLUSIONS Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan.
| | - Tatsuya Iida
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Akihiko Nakamura
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Ei-Ichiro Saita
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, China.
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48
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Liu C, Zhai W, Gong H, Liu Y, Chen H. Effect of fluoride ion on the stability of DNA hairpin. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Lisica A, Grill SW. Optical tweezers studies of transcription by eukaryotic RNA polymerases. Biomol Concepts 2017; 8:1-11. [PMID: 28222010 DOI: 10.1515/bmc-2016-0028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/10/2017] [Indexed: 11/15/2022] Open
Abstract
Transcription is the first step in the expression of genetic information and it is carried out by large macromolecular enzymes called RNA polymerases. Transcription has been studied for many years and with a myriad of experimental techniques, ranging from bulk studies to high-resolution transcript sequencing. In this review, we emphasise the advantages of using single-molecule techniques, particularly optical tweezers, to study transcription dynamics. We give an overview of the latest results in the single-molecule transcription field, focusing on transcription by eukaryotic RNA polymerases. Finally, we evaluate recent quantitative models that describe the biophysics of RNA polymerase translocation and backtracking dynamics.
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Affiliation(s)
- Ana Lisica
- BIOTEC, Technical University Dresden, Tatzberg 47/49, D-01307 Dresden, Germany; and Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Stephan W Grill
- BIOTEC, Technical University Dresden, Tatzberg 47/49, D-01307 Dresden, Germany; and Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
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Innocentini GCP, Guiziou S, Bonnet J, Radulescu O. Analytic framework for a stochastic binary biological switch. Phys Rev E 2017; 94:062413. [PMID: 28085300 DOI: 10.1103/physreve.94.062413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Indexed: 11/07/2022]
Abstract
We propose and solve analytically a stochastic model for the dynamics of a binary biological switch, defined as a DNA unit with two mutually exclusive configurations, each one triggering the expression of a different gene. Such a device has the potential to be used as a memory unit for biological computing systems designed to operate in noisy environments. We discuss a recent implementation of this switch in living cells, the recombinase addressable data (RAD) module. In order to understand the behavior of a RAD module we compute the exact time-dependent joint distribution of the two expressed genes starting in one state and evolving to another asymptotic state. We consider two operating regimes of the RAD module, a fast and a slow stochastic switching regime. The fast regime is aggregative and produces unimodal distributions, whereas the slow regime is separative and produces bimodal distributions. Both regimes can serve to prepare pure memory states when all cells are expressing the same gene. The slow regime can also separate mixed states by producing two subpopulations, each one expressing a different gene. Compared to the genetic toggle switch based on positive feedback, the RAD module ensures more rapid memory operations for the same quality of the separation between binary states. Our model provides a simplified phenomenological framework for studying RAD memory devices and our analytic solution can be further used to clarify theoretical concepts in biocomputation and for optimal design in synthetic biology.
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Affiliation(s)
| | - Sarah Guiziou
- CBS, CNRS UMR 5048 - UM - INSERM U 1054, Montpellier, France
| | - Jerome Bonnet
- CBS, CNRS UMR 5048 - UM - INSERM U 1054, Montpellier, France
| | - Ovidiu Radulescu
- DIMNP, UMR CNRS 5235, University of Montpellier, Montpellier, France
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