1
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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to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies.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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2
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Huisjes NM, Retzer TM, Scherr MJ, Agarwal R, Rajappa L, Safaric B, Minnen A, Duderstadt KE. Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages. eLife 2022; 11:75899. [PMID: 36098381 PMCID: PMC9470159 DOI: 10.7554/elife.75899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.
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Affiliation(s)
- Nadia M Huisjes
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas M Retzer
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Rohit Agarwal
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anita Minnen
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
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3
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Rissone P, Bizarro CV, Ritort F. Stem-loop formation drives RNA folding in mechanical unzipping experiments. Proc Natl Acad Sci U S A 2022; 119:e2025575119. [PMID: 35022230 PMCID: PMC8784153 DOI: 10.1073/pnas.2025575119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force-distance curves (FDCs) exhibit strong irreversible effects with hysteresis and several intermediates, precluding the extraction of the NNBP energies with currently available methods. The combination of a suitable RNA synthesis with a tailored pulling protocol allowed us to obtain the fully reversible FDCs necessary to derive the NNBP energies. We demonstrate the equivalence of sodium and magnesium free-energy salt corrections at the level of individual NNBP. To characterize the irreversibility of the unzipping-rezipping process, we introduce a barrier energy landscape of the stem-loop structures forming along the complementary strands, which compete against the formation of the native hairpin. This landscape correlates with the hysteresis observed along the FDCs. RNA sequence analysis shows that base stacking and base pairing stabilize the stem-loops that kinetically trap the long-lived intermediates observed in the FDC. Stem-loops formation appears as a general mechanism to explain a wide range of behaviors observed in RNA folding.
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Affiliation(s)
- Paolo Rissone
- Small Biosystems Laboratory, Condensed Matter Physics Department, University of Barcelona, Barcelona 08028, Spain
| | - Cristiano V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90616-900 Porto Alegre, Brazil
| | - Felix Ritort
- Small Biosystems Laboratory, Condensed Matter Physics Department, University of Barcelona, Barcelona 08028, Spain;
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4
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Zosel F, Holla A, Schuler B. Labeling of Proteins for Single-Molecule Fluorescence Spectroscopy. Methods Mol Biol 2022; 2376:207-233. [PMID: 34845612 DOI: 10.1007/978-1-0716-1716-8_12] [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: 06/13/2023]
Abstract
Single-molecule fluorescence spectroscopy has become an important technique for studying the conformational dynamics and folding of proteins. A key step for performing such experiments is the availability of high-quality samples. This chapter describes a simple and widely applicable strategy for preparing proteins that are site-specifically labeled with a donor and an acceptor dye for single-molecule Förster resonance energy transfer (FRET) experiments. The method is based on introducing two cysteine residues that are labeled with maleimide-functionalized fluorophores, combined with high-resolution chromatography. We discuss how to optimize site-specific labeling even in the absence of orthogonal coupling chemistry and present purification strategies that are suitable for samples ranging from intrinsically disordered proteins to large folded proteins. We also discuss common problems in protein labeling, how to avoid them, and how to stringently control sample quality.
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Affiliation(s)
- Franziska Zosel
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Novo Nordisk A/S, Måløv, Denmark
| | - Andrea Holla
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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5
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Wang Z, Mothi N, Muñoz V. Single-Molecule Fluorescence Spectroscopy Approaches for Probing Fast Biomolecular Dynamics and Interactions. Methods Mol Biol 2022; 2376:235-246. [PMID: 34845613 DOI: 10.1007/978-1-0716-1716-8_13] [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: 06/13/2023]
Abstract
Single-molecule fluorescence spectroscopy, and particularly its Förster resonance energy transfer implementation (SM-FRET), provides the opportunity to resolve the stochastic conformational fluctuations undergone by individual protein molecules while they fold-unfold, bind to their partners, or carry out catalysis. Such information is key to resolve the microscopic pathways and mechanisms underlying such processes, and cannot be obtained from bulk experiments. To fully resolve protein conformational dynamics, SM-FRET experiments need to reach microsecond, and even sub-microsecond, time resolutions. The key to reach such resolution lies in increasing the efficiency at which photons emitted by a single molecule are collected and detected by the instrument (photon count rates). In this chapter, we describe basic procedures that an end user can follow to optimize the confocal microscope optics in order to maximize the photon count rates. We also discuss the use of photoprotection cocktails specifically designed to reduce fluorophore triplet buildup at high irradiance (the major cause of limiting photon emission rates) while improving the mid-term photostability of the fluorophores. Complementary strategies based on the data analysis are discussed in depth by other authors in Chap. 14 .
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Affiliation(s)
- Zifan Wang
- Department of Bioengineering, University of California at Merced, Merced, CA, USA
- NSF CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, CA, USA
| | - Nivin Mothi
- Chemistry and Chemical Biology Graduate Program, University of California at Merced, Merced, CA, USA
- NSF CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, CA, USA
| | - Victor Muñoz
- Department of Bioengineering and Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA, USA.
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6
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Opatovski N, Shalev Ezra Y, Weiss LE, Ferdman B, Orange-Kedem R, Shechtman Y. Multiplexed PSF Engineering for Three-Dimensional Multicolor Particle Tracking. NANO LETTERS 2021; 21:5888-5895. [PMID: 34213332 DOI: 10.1021/acs.nanolett.1c02068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Three-dimensional spatiotemporal tracking of microscopic particles in multiple colors is a challenging optical imaging task. Existing approaches require a trade-off between photon efficiency, field of view, mechanical complexity, spectral specificity, and speed. Here, we introduce multiplexed point-spread-function engineering that achieves photon-efficient, 3D multicolor particle tracking over a large field of view. This is accomplished by first chromatically splitting the emission path of a microscope to different channels, engineering the point-spread function of each, and then recombining them onto the same region of the camera. We demonstrate our technique for simultaneously tracking five types of emitters in vitro as well as colocalization of DNA loci in live yeast cells.
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7
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Paul T, Ha T, Myong S. Regeneration of PEG slide for multiple rounds of single-molecule measurements. Biophys J 2021; 120:1788-1799. [PMID: 33675764 DOI: 10.1016/j.bpj.2021.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022] Open
Abstract
Single-molecule fluorescence detection of protein and other biomolecules requires a polyethylene glycol (PEG)-passivated surface. Individual channels on a PEG-passivated slide are typically used only a few times, limiting the number of experiments per slide. Here, we report several strategies for regenerating PEG surfaces for multiple rounds of experiments. First, we show regeneration of DNA- or RNA-tethered surfaces by washing out the bound protein by 0.1% sodium dodecyl sulfate, which is significantly more effective than 6 M urea, 6 M GdmCl, or 100 μM proteinase K. Strikingly, 10 consecutive experiments in five different systems produced indistinguishable results both in molecule count and protein activity. Second, duplexed DNA unwound by helicase or denatured by 50 mM NaOH was reannealed with a complementary strand to regenerate the duplexed substrate with an exceptionally high recovery rate. Third, the biotin-PEG layer was regenerated by using 7 M NaOH to strip off NeutrAvidin, which can be reapplied for additional experiments. We demonstrate five cycles of regenerating antibody immobilized surface by which three different protein activity was measured. Altogether, our methods represent reliable and reproducible yet simple and rapid strategies that will enhance the efficiency of single-molecule experiments.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois.
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8
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Real-Time 3D Single Particle Tracking: Towards Active Feedback Single Molecule Spectroscopy in Live Cells. Molecules 2019; 24:molecules24152826. [PMID: 31382495 PMCID: PMC6695621 DOI: 10.3390/molecules24152826] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/27/2019] [Accepted: 08/01/2019] [Indexed: 01/25/2023] Open
Abstract
Single molecule fluorescence spectroscopy has been largely implemented using methods which require tethering of molecules to a substrate in order to make high temporal resolution measurements. However, the act of tethering a molecule requires that the molecule be removed from its environment. This is especially perturbative when measuring biomolecules such as enzymes, which may rely on the non-equilibrium and crowded cellular environment for normal function. A method which may be able to un-tether single molecule fluorescence spectroscopy is real-time 3D single particle tracking (RT-3D-SPT). RT-3D-SPT uses active feedback to effectively lock-on to freely diffusing particles so they can be measured continuously with up to photon-limited temporal resolution over large axial ranges. This review gives an overview of the various active feedback 3D single particle tracking methods, highlighting specialized detection and excitation schemes which enable high-speed real-time tracking. Furthermore, the combination of these active feedback methods with simultaneous live-cell imaging is discussed. Finally, the successes in real-time 3D single molecule tracking (RT-3D-SMT) thus far and the roadmap going forward for this promising family of techniques are discussed.
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9
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Hanspach G, Trucks S, Hengesbach M. Strategic labelling approaches for RNA single-molecule spectroscopy. RNA Biol 2019; 16:1119-1132. [PMID: 30874475 DOI: 10.1080/15476286.2019.1593093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Most single-molecule techniques observing RNA in vitro or in vivo require fluorescent labels that have to be connected to the RNA of interest. In recent years, a plethora of methods has been developed to achieve site-specific labelling, in many cases under near-native conditions. Here, we review chemical as well as enzymatic labelling methods that are compatible with single-molecule fluorescence spectroscopy or microscopy and show how these can be combined to offer a large variety of options to site-specifically place one or more labels in an RNA of interest. By either chemically forming a covalent bond or non-covalent hybridization, these techniques are prerequisites to perform state-of-the-art single-molecule experiments.
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Affiliation(s)
- Gerd Hanspach
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
| | - Sven Trucks
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
| | - Martin Hengesbach
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
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10
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Abstract
The past decades have witnessed tremendous developments in our understanding of RNA biology. At the core of these advances have been studies aimed at discerning RNA structure and at understanding the forces that influence the RNA folding process. It is easy to take the present state of understanding for granted, but there is much to be learned by considering the path to our current understanding, which has been tortuous, with the birth and death of models, the adaptation of experimental tools originally developed for characterization of protein structure and catalysis, and the development of novel tools for probing RNA. In this review we tour the stages of RNA folding studies, considering them as "epochs" that can be generalized across scientific disciplines. These epochs span from the discovery of catalytic RNA, through biophysical insights into the putative primordial RNA World, to characterization of structured RNAs, the building and testing of models, and, finally, to the development of models with the potential to yield generalizable predictive and quantitative models for RNA conformational, thermodynamic, and kinetic behavior. We hope that this accounting will aid others as they navigate the many fascinating questions about RNA and its roles in biology, in the past, present, and future.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
- Department of Chemistry, Stanford University, Stanford, California 94305
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford, California 94305
| | - Steve Bonilla
- Department of Biochemistry, Stanford University, Stanford, California 94305
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Namita Bisaria
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
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11
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Sharma KK, Marzinek JK, Tantirimudalige SN, Bond PJ, Wohland T. Single-molecule studies of flavivirus envelope dynamics: Experiment and computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:38-51. [PMID: 30223001 DOI: 10.1016/j.pbiomolbio.2018.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022]
Abstract
Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that are employed to investigate flaviviruses. In particular, we review how (i) time-resolved Förster resonance energy transfer (trFRET) was applied to probe dengue envelope conformations; (ii) FRET-fluorescence correlation spectroscopy to investigate dengue envelope intrinsic dynamics and (iii) single particle tracking to follow the path of dengue viruses in cells. We also discuss how such methods may be supported by molecular dynamics (MD) simulations over a range of spatio-temporal scales, to provide complementary data on the structure and dynamics of flaviviral systems. We describe recent improvements in multiscale MD approaches that allowed the simulation of dengue particle envelopes in near-atomic resolution. We hope this review is an incentive for setting up and applying similar single-molecule studies and combine them with MD simulations to investigate structural dynamics of entire flavivirus particles over the nanosecond-to-millisecond time-scale and follow viruses during infection in cells over milliseconds to minutes.
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Affiliation(s)
- Kamal Kant Sharma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Jan K Marzinek
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Sarala Neomi Tantirimudalige
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.
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12
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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13
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Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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14
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Teeling-Smith RM, Jung YW, Scozzaro N, Cardellino J, Rampersaud I, North JA, Šimon M, Bhallamudi VP, Rampersaud A, Johnston-Halperin E, Poirier MG, Hammel PC. Electron Paramagnetic Resonance of a Single NV Nanodiamond Attached to an Individual Biomolecule. Biophys J 2017; 110:2044-52. [PMID: 27166812 DOI: 10.1016/j.bpj.2016.03.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/19/2016] [Accepted: 03/07/2016] [Indexed: 11/26/2022] Open
Abstract
Electron paramagnetic resonance (EPR), an established and powerful methodology for studying atomic-scale biomolecular structure and dynamics, typically requires in excess of 10(12) labeled biomolecules. Single-molecule measurements provide improved insights into heterogeneous behaviors that can be masked in ensemble measurements and are often essential for illuminating the molecular mechanisms behind the function of a biomolecule. Here, we report EPR measurements of a single labeled biomolecule. We selectively label an individual double-stranded DNA molecule with a single nanodiamond containing nitrogen-vacancy centers, and optically detect the paramagnetic resonance of nitrogen-vacancy spins in the nanodiamond probe. Analysis of the spectrum reveals that the nanodiamond probe has complete rotational freedom and that the characteristic timescale for reorientation of the nanodiamond probe is slow compared with the transverse spin relaxation time. This demonstration of EPR spectroscopy of a single nanodiamond-labeled DNA provides the foundation for the development of single-molecule magnetic resonance studies of complex biomolecular systems.
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Affiliation(s)
| | - Young Woo Jung
- Samsung Electronics, San #24 Nongseo-Dong, Giheung-Gu, Yongin-City, Gyonggi-Do, Korea
| | - Nicolas Scozzaro
- Department of Physics, The Ohio State University, Columbus, Ohio
| | | | | | - Justin A North
- Department of Physics, The Ohio State University, Columbus, Ohio
| | - Marek Šimon
- Department of Physics, The Ohio State University, Columbus, Ohio
| | | | | | | | | | - P Chris Hammel
- Department of Physics, The Ohio State University, Columbus, Ohio.
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15
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Conformational dynamics of dynamin-like MxA revealed by single-molecule FRET. Nat Commun 2017; 8:15744. [PMID: 28548099 PMCID: PMC5458555 DOI: 10.1038/ncomms15744] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/25/2017] [Indexed: 12/14/2022] Open
Abstract
Human myxovirus resistance protein 1 (MxA) restricts a wide range of viruses and is closely related to the membrane-remodelling GTPase dynamin. The functions of MxA rely on domain rearrangements coupled with GTP hydrolysis cycles. To gain insight into this process, we studied real-time domain dynamics of MxA by single-molecule fluorescence resonance energy transfer. We find that the GTPase domain-bundle-signalling-element (BSE) region can adopt either an ‘open' or a ‘closed' conformation in all nucleotide-loading conditions. Whereas the open conformation is preferred in nucleotide-free, GDP·AlF4−-bound and GDP-bound forms, loading of GTP activates the relative movement between the two domains and alters the conformational preference to the ‘closed' state. Moreover, frequent relative movement was observed between BSE and stalk via hinge 1. On the basis of these results, we suggest how MxA molecules within a helical polymer collectively generate a stable torque through random GTP hydrolysis cycles. Our study provides mechanistic insights into fundamental cellular events such as viral resistance and endocytosis. MxA (myxovirus resistance protein A) is a viral restriction factor whose activity depends on self-assembly into polymeric rings and helical filaments. Here the authors reveal the conformational movements involved in generating torque within polymeric MxA molecules and the dynamic conformational changes that occur upon GTP loading and hydrolysis.
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16
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Xu H, Plaut B, Zhu X, Chen M, Mavinkurve U, Maiti A, Song G, Murari K, Mandal M. Direct Observation of Folding Energy Landscape of RNA Hairpin at Mechanical Loading Rates. J Phys Chem B 2017; 121:2220-2229. [PMID: 28248503 DOI: 10.1021/acs.jpcb.6b10362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By applying a controlled mechanical load using optical tweezers, we measured the diffusive barrier crossing in a 49 nt long P5ab RNA hairpin. We find that in the free-energy landscape the barrier height (G‡) and transition distance (x‡) are dependent on the loading rate (r) along the pulling direction, x, as predicted by Bell. The barrier shifted toward the initial state, whereas ΔG‡ reduced significantly from 50 to 5 kT, as r increased from 0 to 32 pN/s. However, the equilibrium work (ΔG) during strand separation, as estimated by Crook's fluctuation theorem, remained unchanged at different rates. Previously, helix formation and denaturation have been described as two-state (F ↔ U) transitions for P5ab. Herein, we report three intermediate states I1, I, and I2 located at 4, 11, and 16 nm respectively, from the folded conformation. The intermediates were observed only when the hairpin was subjected to an optimal r, 7.6 pN/s. The results indicate that the complementary strands in P5ab can zip and unzip through complex routes, whereby mismatches act as checkpoints and often impose barriers. The study highlights the significance of loading rates in force-spectroscopy experiments that are increasingly being used to measure the folding properties of biomolecules.
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Affiliation(s)
- Huizhong Xu
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Benjamin Plaut
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Xiran Zhu
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Maverick Chen
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Udit Mavinkurve
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Anindita Maiti
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Guangtao Song
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Krishna Murari
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Maumita Mandal
- Department of Physics, ‡Department of Mathematical Sciences, §Department of Computer Science, and ∥Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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Rakshit S, Moulik SP, Bhattacharya SC. Understanding the effect of size and shape of gold nanomaterials on nanometal surface energy transfer. J Colloid Interface Sci 2016; 491:349-357. [PMID: 28056444 DOI: 10.1016/j.jcis.2016.12.052] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/30/2022]
Abstract
Gold Nanomaterials (GNMs) interact with fluorophores via electromagnetic coupling under excitation. In this particular work we carried out (to the best of our knowledge for the first time) a comprehensive study of systematic quenching of a blue emitter 2-Anthracene Sulfonate (2-AS) in the presence of gold nanoparticles of different size and shape. We synthesized gold nanomaterials of four different dimensions [nanoparticle (0D), nanorod (1D), nanotriangle (2D) and nanobipyramids (3D)] and realized the underlying effect on the emitting dipole in terms of steady and time resolved fluorescence. Nanometal Surface Energy Transfer (NSET) has already been proved to be the best long range spectroscopic ruler so far. Many attempts have been made to understand the interaction between a fluorescent molecule and gold nanomaterials. But not a single model can interpret alone the interaction phenomena. We have opted three different models to compare the experimental and theoretical data. Due to the presence of size dependent absorptivity and dielectric function, modified CPS-Kuhn model was proved to be the worthiest to comprehend variance of behavior of an emitting dipole in close proximity to nanometal surface by coupling with the image dipole of gold nanomaterials.
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Affiliation(s)
- Soumyadipta Rakshit
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India; Centre for Surface Science, Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Satya Priya Moulik
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India; Centre for Surface Science, Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Subhash Chandra Bhattacharya
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India; Centre for Surface Science, Department of Chemistry, Jadavpur University, Kolkata 700 032, India.
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18
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19
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van Oijen AM, Dixon NE. Probing molecular choreography through single-molecule biochemistry. Nat Struct Mol Biol 2015; 22:948-52. [DOI: 10.1038/nsmb.3119] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/06/2015] [Indexed: 01/09/2023]
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20
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Poongavanam MV, Kisley L, Kourentzi K, Landes CF, Willson RC. Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:154-64. [PMID: 26307469 DOI: 10.1016/j.bbapap.2015.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/09/2015] [Accepted: 08/18/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND The IgE-binding DNA aptamer 17.4 is known to inhibit the interaction of IgE with the high-affinity IgE Fc receptor FcεRI. While this and other aptamers have been widely used and studied, there has been relatively little investigation of the kinetics and energetics of their interactions with their targets, by either single-molecule or ensemble methods. METHODS The dissociation kinetics of the D17.4/IgE complex and the effects of temperature and ionic strength were studied using fluorescence anisotropy and single-molecule spectroscopy, and activation parameters calculated. RESULTS The dissociation of D17.4/IgE complex showed a strong dependence on temperature and salt concentration. The koff of D17.4/IgE complex was calculated to be (2.92±0.18)×10(-3) s(-1) at 50 mM NaCl, and (1.44±0.02)×10(-2) s(-1) at 300 mM NaCl, both in 1 mM MgCl2 and 25°C. The dissociation activation energy for the D17.4/IgE complex, Ea, was 16.0±1.9 kcal mol(-1) at 50 mM NaCl and 1 mM MgCl2. Interestingly, we found that the C19A mutant of D17.4 with stabilized stem structure showed slower dissociation kinetics compared to D17.4. Single-molecule observations of surface-immobilized D17.4/IgE showed much faster dissociation kinetics, and heterogeneity not observable by ensemble techniques. CONCLUSIONS The increasing koff value with increasing salt concentration is attributed to the electrostatic interactions between D17.4/IgE. We found that both the changes in activation enthalpy and activation entropy are insignificant with increasing NaCl concentration. The slower dissociation of the mutant C19A/IgE complex is likely due to the enhanced stability of the aptamer. GENERAL SIGNIFICANCE The activation parameters obtained by applying transition state analysis to kinetic data can provide details on mechanisms of molecular recognition and have applications in drug design. Single-molecule dissociation kinetics showed greater kinetic complexity than was observed in the ensemble in-solution systems, potentially reflecting conformational heterogeneity of the aptamer. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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Affiliation(s)
| | - Lydia Kisley
- Department of Chemistry, Rice University, Houston, TX77005-1827, USA
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, TX 77204-4004, USA
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, TX77005-1827, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005-1827, USA.
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, TX 77204-5001, USA; Department of Chemical and Biomolecular Engineering, University of Houston, TX 77204-4004, USA; Houston Methodist Research Institute, Houston, TX 77030, USA; Centro de Biotecnología FEMSA, Departamento de Biotecnología e Ingeniería de Alimentos, Tecnológico de Monterrey, Monterrey 64849, Mexico.
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21
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Ray PC, Fan Z, Crouch RA, Sinha SS, Pramanik A. Nanoscopic optical rulers beyond the FRET distance limit: fundamentals and applications. Chem Soc Rev 2015; 43:6370-404. [PMID: 24902784 DOI: 10.1039/c3cs60476d] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the last few decades, Förster resonance energy transfer (FRET) based spectroscopy rulers have served as a key tool for the understanding of chemical and biochemical processes, even at the single molecule level. Since the FRET process originates from dipole-dipole interactions, the length scale of a FRET ruler is limited to a maximum of 10 nm. Recently, scientists have reported a nanomaterial based long-range optical ruler, where one can overcome the FRET optical ruler distance dependence limit, and which can be very useful for monitoring biological processes that occur across a greater distance than the 10 nm scale. Advancement of nanoscopic long range optical rulers in the last ten years indicate that, in addition to their long-range capability, their brightness, long lifetime, lack of blinking, and chemical stability make nanoparticle based rulers a good choice for long range optical probes. The current review discusses the basic concepts and unique light-focusing properties of plasmonic nanoparticles which are useful in the development of long range one dimensional to three dimensional optical rulers. In addition, to provide the readers with an overview of the exciting opportunities within this field, this review discusses the applications of long range rulers for monitoring biological and chemical processes. At the end, we conclude by speculating on the role of long range optical rulers in future scientific research and discuss possible problems, outlooks and future needs in the use of optical rulers for technological applications.
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Affiliation(s)
- Paresh Chandra Ray
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA.
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Pan H, Xia Y, Qin M, Cao Y, Wang W. A simple procedure to improve the surface passivation for single molecule fluorescence studies. Phys Biol 2015; 12:045006. [DOI: 10.1088/1478-3975/12/4/045006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Giambaşu GM, York DM, Case DA. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. RNA (NEW YORK, N.Y.) 2015; 21:963-74. [PMID: 25805858 PMCID: PMC4408802 DOI: 10.1261/rna.047357.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/17/2015] [Indexed: 05/16/2023]
Abstract
RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements.
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Affiliation(s)
- George M Giambaşu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Darrin M York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - David A Case
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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24
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Perez-Gonzalez DC, Penedo JC. Single-Molecule Strategies for DNA and RNA Diagnostics. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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25
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Single molecule studies of RNA-RNA interactions. Methods Mol Biol 2014; 1240:97-112. [PMID: 25352139 DOI: 10.1007/978-1-4939-1896-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Non-coding RNAs including microRNAs, siRNAs, and snoRNAs interact with their targets directly through RNA-RNA interactions by base-paring (van Himbergen et al., Nucleic Acids Res 21(8):1713-1717, 1993). RNA-RNA interactions play important roles in gene transcription and protein translation, which can be investigated with several experimental techniques including single molecule methods. Here, we describe how single molecule Förster resonance energy transfer (FRET) can be used to study RNA-RNA interactions in vitro by either surface immobilization or vesicle encapsulation.
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26
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Juette MF, Terry DS, Wasserman MR, Zhou Z, Altman RB, Zheng Q, Blanchard SC. The bright future of single-molecule fluorescence imaging. Curr Opin Chem Biol 2014; 20:103-11. [PMID: 24956235 DOI: 10.1016/j.cbpa.2014.05.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 05/09/2014] [Indexed: 11/13/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is an essential and maturing tool to probe biomolecular interactions and conformational dynamics in vitro and, increasingly, in living cells. Multi-color smFRET enables the correlation of multiple such events and the precise dissection of their order and timing. However, the requirements for good spectral separation, high time resolution, and extended observation times place extraordinary demands on the fluorescent labels used in such experiments. Together with advanced experimental designs and data analysis, the development of long-lasting, non-fluctuating fluorophores is therefore proving key to progress in the field. Recently developed strategies for obtaining ultra-stable organic fluorophores spanning the visible spectrum are underway that will enable multi-color smFRET studies to deliver on their promise of previously unachievable biological insights.
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Affiliation(s)
- Manuel F Juette
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Michael R Wasserman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Qinsi Zheng
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States; Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States; Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States.
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27
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Paudel B, Rueda D. RNA folding dynamics using laser-assisted single-molecule refolding. Methods Mol Biol 2014; 1086:289-307. [PMID: 24136611 DOI: 10.1007/978-1-62703-667-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
RNA folding pathways can be complex and even include kinetic traps or misfolded intermediates that can be slow to resolve. Characterizing these pathways is critical to understanding how RNA molecules acquire their biological function. We have previously developed a novel approach to help characterize such misfolded intermediates. Laser-assisted single-molecule refolding (LASR) is a powerful technique that combines temperature-jump (T-jump) kinetics with single-molecule detection. In a typical LASR experiment, the temperature is rapidly increased and conformational dynamics are characterized, in real-time, at the single-molecule level using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide detailed protocols for performing LASR experiments including sample preparation, temperature calibration, and data analysis.
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Affiliation(s)
- Bishnu Paudel
- Department of Medicine, Section of Virology, Imperial College, London, UK
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28
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Abstract
Riboswitches are structured noncoding RNA elements that control the expression of their embedding messenger RNAs by sensing the intracellular concentration of diverse metabolites. As the name suggests, riboswitches are dynamic in nature so that studying their inherent conformational dynamics and ligand-mediated folding is important for understanding their mechanism of action. Single-molecule fluorescence energy transfer (smFRET) microscopy is a powerful and versatile technique for studying the folding pathways and intra- and intermolecular dynamics of biological macromolecules, especially RNA. The ability of smFRET to monitor intramolecular distances and their temporal evolution make it a particularly insightful tool for probing the structure and dynamics of riboswitches. Here, we detail the general steps for using prism-based total internal reflection fluorescence microscopy for smFRET studies of the structure, dynamics, and ligand-binding mechanisms of riboswitches.
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29
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Abstract
Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.
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Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109;
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30
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Abstract
Single-molecule spectroscopy has developed into a widely used method for probing the structure, dynamics, and mechanisms of biomolecular systems, especially in combination with Förster resonance energy transfer (FRET). In this introductory tutorial, essential concepts and methods will be outlined, from the FRET process and the basic considerations for sample preparation and instrumentation to some key elements of data analysis and photon statistics. Different approaches for obtaining dynamic information over a wide range of timescales will be explained and illustrated with examples, including the quantitative analysis of FRET efficiency histograms, correlation spectroscopy, fluorescence trajectories, and microfluidic mixing.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057
Zurich, Switzerland
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Chen P, Keller AM, Joshi CP, Martell DJ, Andoy NM, Benítez JJ, Chen TY, Santiago AG, Yang F. Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones. Biochemistry 2013; 52:7170-83. [PMID: 24053279 DOI: 10.1021/bi400597v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.
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Affiliation(s)
- Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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Affiliation(s)
- Jens Michaelis
- Biophysics
Institute, Faculty of Natural Sciences, Ulm University, Albert-Einstein-Allee
11, 89081 Ulm, Germany
- Center
for Integrated Protein Science Munich (CIPSM), Department
of Chemistry and Biochemistry, Munich University, Butenandtstrasse 5-13, 81377 München, Germany
| | - Barbara Treutlein
- Department
of Bioengineering, Stanford University, James H. Clark Center, E-300, 318
Campus Drive, Stanford, California 94305-5432, United States
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Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes. Nat Protoc 2013; 8:1459-74. [PMID: 23845960 DOI: 10.1038/nprot.2013.082] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microfluidic mixing in combination with single-molecule spectroscopy allows the investigation of complex biomolecular processes under non-equilibrium conditions. Here we present a protocol for building, installing and operating microfluidic mixing devices optimized for this purpose. The mixer is fabricated by replica molding with polydimethylsiloxane (PDMS), which allows the production of large numbers of devices at a low cost using a single microfabricated silicon mold. The design is based on hydrodynamic focusing combined with diffusive mixing and allows single-molecule kinetics to be recorded over five orders of magnitude in time, from 1 ms to ∼100 s. Owing to microfabricated particle filters incorporated in the inlet channels, the devices provide stable flow for many hours to days without channel blockage, which allows reliable collection of high-quality data. Modular design enables rapid exchange of samples and mixing devices, which are mounted in a specifically designed holder for use with a confocal microscopy detection system. Integrated Peltier elements provide temperature control from 4 to 37 °C. The protocol includes the fabrication of a silicon master, production of the microfluidic devices, instrumentation setup and data acquisition. Once a silicon master is available, devices can be produced and experiments started within ∼1 d of preparation. We demonstrate the performance of the system with single-molecule Förster resonance energy transfer (FRET) measurements of kinetics of protein folding and conformational changes. The dead time of 1 ms, as predicted from finite element calculations, was confirmed by the measurements.
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Kisley L, Chang WS, Cooper D, Mansur AP, Landes CF. Extending single molecule fluorescence observation time by amplitude-modulated excitation. Methods Appl Fluoresc 2013; 1:037001-37001. [PMID: 24587894 DOI: 10.1088/2050-6120/1/3/037001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a hardware-based method that can improve single molecule fluorophore observation time by up to 1500% and super-localization by 47% for the experimental conditions used. The excitation was modulated using an acousto-optic modulator (AOM) synchronized to the data acquisition and inherent data conversion time of the detector. The observation time and precision in super-localization of four commonly used fluorophores were compared under modulated and traditional continuous excitation, including direct total internal reflectance excitation of Alexa 555 and Cy3, non-radiative Förster resonance energy transfer (FRET) excited Cy5, and direct epi-fluorescence wide field excitation of Rhodamine 6G. The proposed amplitude-modulated excitation does not perturb the chemical makeup of the system or sacrifice signal and is compatible with multiple types of fluorophores. Amplitude-modulated excitation has practical applications for any fluorescent study utilizing an instrumental setup with time-delayed detectors.
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Haenni D, Zosel F, Reymond L, Nettels D, Schuler B. Intramolecular distances and dynamics from the combined photon statistics of single-molecule FRET and photoinduced electron transfer. J Phys Chem B 2013; 117:13015-28. [PMID: 23718771 DOI: 10.1021/jp402352s] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Single-molecule Förster resonance energy transfer (FRET) and photoinduced electron transfer (PET) have developed into versatile and complementary methods for probing distances and dynamics in biomolecules. Here we show that the two methods can be combined in one molecule to obtain both accurate distance information and the kinetics of intramolecular contact formation. In a first step, we show that the fluorescent dyes Alexa 488 and Alexa 594, which are frequently used as a donor and acceptor for single-molecule FRET, are also suitable as PET probes with tryptophan as a fluorescence quencher. We then performed combined FRET/PET experiments with FRET donor- and acceptor-labeled polyproline peptides. The placement of a tryptophan residue into the polyglycylserine tail incorporated in the peptides allowed us to measure both FRET efficiencies and the nanosecond dynamics of contact formation between one of the fluorescent dyes and the quencher. Variation of the linker length between the polyproline and the Alexa dyes and in the position of the tryptophan residue demonstrates the sensitivity of this approach. Modeling of the combined photon statistics underlying the combined FRET and PET process enables the accurate analysis of both the resulting transfer efficiency histograms and the nanosecond fluorescence correlation functions. This approach opens up new possibilities for investigating single biomolecules with high spatial and temporal resolution.
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Affiliation(s)
- Dominik Haenni
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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Dalgarno PA, Bordello J, Morris R, St-Pierre P, Dubé A, Samuel IDW, Lafontaine DA, Penedo JC. Single-molecule chemical denaturation of riboswitches. Nucleic Acids Res 2013; 41:4253-65. [PMID: 23446276 PMCID: PMC3627600 DOI: 10.1093/nar/gkt128] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg2+ ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods.
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Affiliation(s)
- Paul A Dalgarno
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
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Joo C, Ha T. Single-molecule FRET with total internal reflection microscopy. Cold Spring Harb Protoc 2012; 2012:2012/12/pdb.top072058. [PMID: 23209135 DOI: 10.1101/pdb.top072058] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Single-molecule (sm) fluorescence detection is a powerful method for studying biological events without time and population averaging. Förster (fluorescence) resonance energy transfer (FRET) is a spectroscopic technique in which the efficiency of energy transfer from donor to acceptor molecules is used to determine distances between molecules in the 30-80 Å range. Structural changes in biological molecules or relative motion between two interacting molecules can be detected by a change in FRET. This article focuses primarily on smFRET based on total internal reflection (TIR) microscopy. It begins with discussions of dye choice and labeling of nucleic acids and proteins. These are followed by information on surface preparation and data acquisition. Various methods of data analysis are then presented, as is information on setting up TIR microscopy, both the objective and the prism types.
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38
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Giambaşu GM, Lee TS, Scott WG, York DM. Mapping L1 ligase ribozyme conformational switch. J Mol Biol 2012; 423:106-22. [PMID: 22771572 DOI: 10.1016/j.jmb.2012.06.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/21/2012] [Accepted: 06/25/2012] [Indexed: 01/10/2023]
Abstract
L1 ligase (L1L) molecular switch is an in vitro optimized synthetic allosteric ribozyme that catalyzes the regioselective formation of a 5'-to-3' phosphodiester bond, a reaction for which there is no known naturally occurring RNA catalyst. L1L serves as a proof of principle that RNA can catalyze a critical reaction for prebiotic RNA self-replication according to the RNA world hypothesis. L1L crystal structure captures two distinct conformations that differ by a reorientation of one of the stems by around 80Å and are presumed to correspond to the active and inactive state, respectively. It is of great interest to understand the nature of these two states in solution and the pathway for their interconversion. In this study, we use explicit solvent molecular simulation together with a novel enhanced sampling method that utilizes concepts from network theory to map out the conformational transition between active and inactive states of L1L. We find that the overall switching mechanism can be described as a three-state/two-step process. The first step involves a large-amplitude swing that reorients stem C. The second step involves the allosteric activation of the catalytic site through distant contacts with stem C. Using a conformational space network representation of the L1L switch transition, it is shown that the connection between the three states follows different topographical patterns: the stem C swing step passes through a narrow region of the conformational space network, whereas the allosteric activation step covers a much wider region and a more diverse set of pathways through the network.
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Affiliation(s)
- George M Giambaşu
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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39
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Jung J, Han KY, Koh HR, Lee J, Choi YM, Kim C, Kim SK. Effect of Single-Base Mutation on Activity and Folding of 10-23 Deoxyribozyme Studied by Three-Color Single-Molecule ALEX FRET. J Phys Chem B 2012; 116:3007-12. [DOI: 10.1021/jp2117196] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiwon Jung
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Kyu Young Han
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Hye Ran Koh
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Jihyun Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Yoon Mi Choi
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Christine Kim
- Columbia University Medical Center, New York, New York 10032, United States
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
- WCU Department of Biophysics and
Chemical Biology, Seoul National University, Seoul 151-747, Korea
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40
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Gopal A, Zhou ZH, Knobler CM, Gelbart WM. Visualizing large RNA molecules in solution. RNA (NEW YORK, N.Y.) 2012; 18:284-99. [PMID: 22190747 PMCID: PMC3264915 DOI: 10.1261/rna.027557.111] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 11/12/2011] [Indexed: 05/24/2023]
Abstract
Single-stranded RNAs (ssRNAs) longer than a few hundred nucleotides do not have a unique structure in solution. Their equilibrium properties therefore reflect the average of an ensemble of structures. We use cryo-electron microscopy to image projections of individual long ssRNA molecules and characterize the anisotropy of their ensembles in solution. A flattened prolate volume is found to best represent the shapes of these ensembles. The measured sizes and anisotropies are in good agreement with complementary determinations using small-angle X-ray scattering and coarse-grained molecular dynamics simulations. A long viral ssRNA is compared with shorter noncoding transcripts to demonstrate that prolate geometry and flatness are generic properties independent of sequence length and origin. The anisotropy persists under physiological as well as low-ionic-strength conditions, revealing a direct correlation between secondary structure asymmetry and 3D shape and size. We discuss the physical origin of the generic anisotropy and its biological implications.
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Affiliation(s)
- Ajaykumar Gopal
- Department of Chemistry and Biochemistry, University of California-Los Angeles, CA 90095, USA.
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41
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Abstract
DEAD-box proteins are vitally important to cellular processes and make up the largest class of helicases. Many DEAD-box proteins function as RNA chaperones by accelerating structural transitions of RNA, which can result in the resolution of misfolded conformers or conversion between functional structures. While the biological importance of chaperone proteins is clear, their mechanisms are incompletely understood. Here, we illustrate how the catalytic activity of certain RNAs can be used to measure RNA chaperone activity. By measuring the amount of substrate converted to product, the fraction of catalytically active molecules is measured over time, providing a quantitative measure of the formation or loss of native RNA. The assays are described with references to group I and group II introns and their ribozyme derivatives, and examples are included that illustrate potential complications and indicate how catalytic activity measurements can be combined with physical approaches to gain insights into the mechanisms of DEAD-box proteins as RNA chaperones.
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42
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Cardo L, Karunatilaka KS, Rueda D, Sigel RKO. Single molecule FRET characterization of large ribozyme folding. Methods Mol Biol 2012; 848:227-51. [PMID: 22315073 DOI: 10.1007/978-1-61779-545-9_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A procedure to investigate the folding of group II intron by single molecule Fluorescence Resonance Energy Transfer (smFRET) using total internal reflection fluorescence microscopy (TIRFM) is described in this chapter. Using our previous studies on the folding and dynamics of a large ribozyme in the presence of metal ions (i.e., Mg(2+) and Ca(2+)) and/or the DEAD-box protein Mss116 as an example, we here describe step-by-step procedures to perform experiments. smFRET allows the investigation of individual molecules, thus, providing kinetic and mechanistic information hidden in ensemble averaged experiments.
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Affiliation(s)
- Lucia Cardo
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
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43
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Zhou R, Kunzelmann S, Webb MR, Ha T. Detecting intramolecular conformational dynamics of single molecules in short distance range with subnanometer sensitivity. NANO LETTERS 2011; 11:5482-8. [PMID: 22023515 PMCID: PMC3237907 DOI: 10.1021/nl2032876] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single molecule detection is useful for characterizing nanoscale objects such as biological macromolecules, nanoparticles and nanodevices with nanometer spatial resolution. Fluorescence resonance energy transfer (FRET) is widely used as a single-molecule assay to monitor intramolecular dynamics in the distance range of 3-8 nm. Here we demonstrate that self-quenching of two rhodamine derivatives can be used to detect small conformational dynamics corresponding to subnanometer distance changes in a FRET-insensitive short-range at the single molecule level. A ParM protein mutant labeled with two rhodamines works as a single molecule adenosine 5'-diphosphate (ADP) sensor that has 20 times brighter fluorescence signal in the ADP bound state than the unbound state. Single molecule time trajectories show discrete transitions between fluorescence on and off states that can be directly ascribed to ADP binding and dissociation events. The conformational changes observed with 20:1 contrast are only 0.5 nm in magnitude and are between crystallographic distances of 1.6 and 2.1 nm, demonstrating exquisite sensitivity to short distance scale changes. The systems also allowed us to gain information on the photophysics of self-quenching induced by rhodamine stacking: (1) photobleaching of either of the two rhodamines eliminates quenching of the other rhodamine fluorophore and (2) photobleaching from the highly quenched, stacked state is only 2-fold slower than from the unstacked state.
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Affiliation(s)
- Ruobo Zhou
- Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Illinois 61801, United States
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44
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Biyun S, Cho SS, Thirumalai D. Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations. J Am Chem Soc 2011; 133:20634-43. [DOI: 10.1021/ja2092823] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shi Biyun
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Bio-X Laboratory, Department of Physics and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Samuel S. Cho
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - D. Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemistry, University of Maryland, College Park, Maryland 20742, United States
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45
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KOBITSKI ANDREIYU, NIERTH ALEXANDER, HENGESBACH MARTIN, JÄSCHKE ANDRES, HELM MARK, NIENHAUS GULRICH. EXPLORING THE FOLDING FREE ENERGY LANDSCAPE OF SMALL RNA MOLECULES BY SINGLE-PAIR FÖRSTER RESONANCE ENERGY TRANSFER. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048008000873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Proteins and RNA are biological macromolecules built from linear polymers. The process by which they fold into compact, well-defined, three-dimensional architectures to perform their functional tasks is still not well understood. It can be visualized by Brownian motion of an ensemble of molecules through a rugged energy landscape in search of an energy minimum corresponding to the native state. To explore the conformational energy landscape of small RNAs, single pair Förster resonance energy transfer (spFRET) experiments on solutions as well as on surface-immobilized samples have provided new insights. In this review, we focus on our recent work on two FRET-labeled small RNAs, the Diels-Alderase (DAse) ribozyme and the human mitochondrial tRNA Lys . For both RNAs, three different conformational states can be distinguished, and the associated mean FRET efficiencies provide clues about their structural properties. The systematic variation of their free energies with the concentration of Mg 2+ counterions was analyzed quantitatively by using a thermodynamic model that separates conformational changes from Mg 2+ binding. Furthermore, time-resolved spFRET studies on immobilized DAse reveal slow interconversions between intermediate and folded states on the time scale of ~ 100 ms. The quantitative data obtained from spFRET experiments may likely assist in the further development of theories and models addressing the folding dynamics and (counterion-dependent) energetics of RNA molecules.
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Affiliation(s)
- ANDREI YU. KOBITSKI
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - ALEXANDER NIERTH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARTIN HENGESBACH
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - ANDRES JÄSCHKE
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - MARK HELM
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - G. ULRICH NIENHAUS
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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46
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Goryaynov A, Ma J, Yang W. Single-molecule studies of nucleocytoplasmic transport: from one dimension to three dimensions. Integr Biol (Camb) 2011; 4:10-21. [PMID: 22020388 DOI: 10.1039/c1ib00041a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In eukaryotic cells, the bidirectional trafficking of proteins and genetic materials across the double-membrane nuclear envelope is mediated by nuclear pore complexes (NPCs). A highly selective barrier formed by the phenylalanine-glycine (FG)-nucleoporin (Nup) in the NPC allows for two transport modes: passive diffusion and transport receptor-facilitated translocation. Strict regulation of nucleocytoplasmic transport is crucial for cell survival, differentiation, growth and other essential activities. However, due to the limited knowledge of the native configuration of the FG-Nup barrier and the interactions between the transiting molecules and the barrier in the NPC, the precise nucleocytoplasmic transport mechanism remains unresolved. To refine the transport mechanism, single-molecule fluorescence microscopy methods have been employed to obtain the transport kinetics of individual fluorescent molecules through the NPC and to map the interactions between transiting molecules and the FG-Nup barrier. Important characteristics of nucleocytoplasmic transport, such as transport time, transport efficiency and spatial distribution of single transiting molecules in the NPC, have been obtained that could not be measured by either ensemble average methods or conventional electron microscopy. In this critical review, we discuss the development of various single-molecule techniques and their application to nucleocytoplasmic transport in vitro and in vivo. In particular, we highlight a recent advance from one-dimensional to three-dimensional single-molecule characterization of transport through the NPC and present a comprehensive understanding of the nucleocytoplasmic transport mechanism obtained by this new technical development (105 references).
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Affiliation(s)
- Alexander Goryaynov
- Department of Biological Sciences, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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47
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Abstract
Ribosomal (r-) RNA adopts a well-defined structure within the ribosome, but the role of r-proteins in stabilizing this structure is poorly understood. To address this issue, we use optical tweezers to unfold RNA fragments in the presence or absence of r-proteins. Here, we focus on Escherichia coli r-protein L20, whose globular C-terminal domain (L20C) recognizes an irregular stem in domain II of 23S rRNA. L20C also binds its own mRNA and represses its translation; binding occurs at two different sites--i.e., a pseudoknot and an irregular stem. We find that L20C makes rRNA and mRNA fragments encompassing its binding sites more resistant to mechanical unfolding. The regions of increased resistance correspond within two base pairs to the binding sites identified by conventional methods. While stabilizing specific RNA structures, L20C does not accelerate their formation from alternate conformations--i.e., it acts as a clamp but not as a chaperone. In the ribosome, L20C contacts only one side of its target stem but interacts with both strands, explaining its clamping effect. Other r-proteins bind rRNA similarly, suggesting that several rRNA structures are stabilized by "one-side" clamping.
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48
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Calcium regulation of nucleocytoplasmic transport. Protein Cell 2011; 2:291-302. [PMID: 21528351 DOI: 10.1007/s13238-011-1038-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/27/2011] [Indexed: 10/18/2022] Open
Abstract
Bidirectional trafficking of macromolecules between the cytoplasm and the nucleus is mediated by the nuclear pore complexes (NPCs) embedded in the nuclear envelope (NE) of eukaryotic cell. The NPC functions as the sole pathway to allow for the passive diffusion of small molecules and the facilitated translocation of larger molecules. Evidence shows that these two transport modes and the conformation of NPC can be regulated by calcium stored in the lumen of nuclear envelope and endoplasmic reticulum. However, the mechanism of calcium regulation remains poorly understood. In this review, we integrate data on the observations of calciumregulated structure and function of the NPC over the past years. Furthermore, we highlight challenges in the measurements of dynamic conformational changes and transient transport kinetics in the NPC. Finally, an innovative imaging approach, single-molecule superresolution fluorescence microscopy, is introduced and expected to provide more insights into the mechanism of calcium-regulated nucleocytoplasmic transport.
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49
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van Oijen AM. Single-molecule approaches to characterizing kinetics of biomolecular interactions. Curr Opin Biotechnol 2011; 22:75-80. [DOI: 10.1016/j.copbio.2010.10.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/06/2010] [Indexed: 12/01/2022]
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50
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Abraham BG, Tkachenko NV, Santala V, Lemmetyinen H, Karp M. Bidirectional Fluorescence Resonance Energy Transfer (FRET) in Mutated and Chemically Modified Yellow Fluorescent Protein (YFP). Bioconjug Chem 2011; 22:227-34. [DOI: 10.1021/bc100372u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bobin George Abraham
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Nikolai V. Tkachenko
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Ville Santala
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Helge Lemmetyinen
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Matti Karp
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
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