1
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Morales-Inostroza L, Folz J, Kühnemuth R, Felekyan S, Wieser FF, Seidel CAM, Götzinger S, Sandoghdar V. An optofluidic antenna for enhancing the sensitivity of single-emitter measurements. Nat Commun 2024; 15:2545. [PMID: 38514627 PMCID: PMC10957926 DOI: 10.1038/s41467-024-46730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Many single-molecule investigations are performed in fluidic environments, for example, to avoid unwanted consequences of contact with surfaces. Diffusion of molecules in this arrangement limits the observation time and the number of collected photons, thus, compromising studies of processes with fast or slow dynamics. Here, we introduce a planar optofluidic antenna (OFA), which enhances the fluorescence signal from molecules by about 5 times per passage, leads to about 7-fold more frequent returns to the observation volume, and significantly lengthens the diffusion time within one passage. We use single-molecule multi-parameter fluorescence detection (sm-MFD), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) measurements to characterize our OFAs. The antenna advantages are showcased by examining both the slow (ms) and fast (50 μs) dynamics of DNA four-way (Holliday) junctions with real-time resolution. The FRET trajectories provide evidence for the absence of an intermediate conformational state and introduce an upper bound for its lifetime. The ease of implementation and compatibility with various microscopy modalities make OFAs broadly applicable to a diverse range of studies.
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Affiliation(s)
- Luis Morales-Inostroza
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Julian Folz
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Ralf Kühnemuth
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Suren Felekyan
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Claus A M Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Stephan Götzinger
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91052, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany.
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany.
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2
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Yang J, Kamai H, Wang Y, Xu Y. Nanofluidic Aptamer Nanoarray to Enable Stochastic Capture of Single Proteins at Normal Concentrations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301013. [PMID: 37350189 DOI: 10.1002/smll.202301013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/18/2023] [Indexed: 06/24/2023]
Abstract
Single-molecule experiments allow understanding of the diversity, stochasticity, and heterogeneity of molecular behaviors and properties hidden by conventional ensemble-averaged measurements. They hence have great importance and significant impacts in a wide range of fields. Despite significant advances in single-molecule experiments at ultralow concentrations, the capture of single molecules in solution at normal concentrations within natural biomolecular processes remains a formidable challenge. Here, a high-density, well-defined nanofluidic aptamer nanoarray (NANa) formed via site-specific self-assembly of well-designed aptamer molecules in nanochannels with nano-in-nano gold nanopatterns is presented. The nanofluidic aptamer nanoarray exhibits a high capability to specifically capture target proteins (e.g., platelet-derived growth factor BB; PDGF-BB) to form uniform protein nanoarrays under optimized nanofluidic conditions. Owing to these fundamental features, the nanofluidic aptamer nanoarray enables the stochastic capture of single PDGF-BB molecules at a normal concentration from a sample with an ultrasmall volume equivalent to a single cell by following Poisson statistics, forming a readily addressable single-protein nanoarray. This approach offers a methodology and device to surpass both the concentration and volume limits of single-protein capture in most conventional methodologies of single-molecule experiments, thus opening an avenue to explore the behavior of individual biomolecules in a manner close to their natural forms, which remains largely unexplored to date.
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Affiliation(s)
- Jinbin Yang
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
| | - Hiroki Kamai
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, 26 CBEB, University Park, PA, 16802-6804, USA
| | - Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Metropolitan University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
- Japan Science and Technology Agency (JST), CREST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
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3
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Svirelis J, Adali Z, Emilsson G, Medin J, Andersson J, Vattikunta R, Hulander M, Järlebark J, Kolman K, Olsson O, Sakiyama Y, Lim RYH, Dahlin A. Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates. Nat Commun 2023; 14:5131. [PMID: 37612271 PMCID: PMC10447545 DOI: 10.1038/s41467-023-40889-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.
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Affiliation(s)
- Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Zeynep Adali
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jesper Medin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Radhika Vattikunta
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mats Hulander
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Julia Järlebark
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Krzysztof Kolman
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Oliver Olsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Yusuke Sakiyama
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.
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4
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Irvin EM, Wang H. Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures. DNA Repair (Amst) 2023; 128:103528. [PMID: 37392578 PMCID: PMC10989508 DOI: 10.1016/j.dnarep.2023.103528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.
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Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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5
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The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy. Essays Biochem 2022; 66:875-890. [PMID: 36416865 PMCID: PMC9760427 DOI: 10.1042/ebc20220065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) have emerged as key players across many biological functions and diseases. Differently from structured proteins, disordered proteins lack stable structure and are particularly sensitive to changes in the surrounding environment. Investigation of disordered ensembles requires new approaches and concepts for quantifying conformations, dynamics, and interactions. Here, we provide a short description of the fundamental biophysical properties of disordered proteins as understood through the lens of single-molecule fluorescence observations. Single-molecule Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) provides an extensive and versatile toolbox for quantifying the characteristics of conformational distributions and the dynamics of disordered proteins across many different solution conditions, both in vitro and in living cells.
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6
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Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles. Nat Methods 2022; 19:751-758. [PMID: 35637303 PMCID: PMC9184284 DOI: 10.1038/s41592-022-01491-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 04/12/2022] [Indexed: 12/18/2022]
Abstract
Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes. Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel.
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7
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Fontana M, Ivanovaitė Š, Lindhoud S, van der Wijk E, Mathwig K, Berg WVD, Weijers D, Hohlbein J. Probing DNA - Transcription Factor Interactions Using Single-Molecule Fluorescence Detection in Nanofluidic Devices. Adv Biol (Weinh) 2022; 6:e2100953. [PMID: 34472724 DOI: 10.1002/adbi.202100953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/16/2021] [Indexed: 01/27/2023]
Abstract
Single-molecule fluorescence detection offers powerful ways to study biomolecules and their complex interactions. Here, nanofluidic devices and camera-based, single-molecule Förster resonance energy transfer (smFRET) detection are combined to study the interactions between plant transcription factors of the auxin response factor (ARF) family and DNA oligonucleotides that contain target DNA response elements. In particular, it is shown that the binding of the unlabeled ARF DNA binding domain (ARF-DBD) to donor and acceptor labeled DNA oligonucleotides can be detected by changes in the FRET efficiency and changes in the diffusion coefficient of the DNA. In addition, this data on fluorescently labeled ARF-DBDs suggest that, at nanomolar concentrations, ARF-DBDs are exclusively present as monomers. In general, the fluidic framework of freely diffusing molecules minimizes potential surface-induced artifacts, enables high-throughput measurements, and proved to be instrumental in shedding more light on the interactions between ARF-DBDs monomers and between ARF-DBDs and their DNA response element.
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Affiliation(s)
- Mattia Fontana
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Laboratory of Biochemistry, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Šarunė Ivanovaitė
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Elmar van der Wijk
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Laboratory of Biochemistry, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Klaus Mathwig
- Groningen Research Institute of Pharmacy, Pharmaceutical Analysis, University of Groningen, P.O. Box 196, 9700 AD, Groningen, The Netherlands.,Stichting Imec Nederland within OnePlanet Research Center, Bronland 10, Wageningen, 6708 WH, The Netherlands
| | - Willy van den Berg
- Laboratory of Biochemistry, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biochemistry, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Microspectroscopy Research Facility, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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8
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Alston JJ, Soranno A, Holehouse AS. Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins. Methods 2021; 193:116-135. [PMID: 33831596 PMCID: PMC8713295 DOI: 10.1016/j.ymeth.2021.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022] Open
Abstract
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
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9
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Wilson H, Wang Q. ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling. Nat Methods 2021; 18:816-820. [PMID: 34127856 DOI: 10.1038/s41592-021-01173-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/04/2021] [Indexed: 02/03/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has become a versatile and widespread method to probe nanoscale conformation and dynamics. However, current experimental modalities often resort to molecule immobilization for long observation times and do not always approach the resolution limit of FRET-based nanoscale metrology. Here we present ABEL-FRET, an immobilization-free platform for smFRET measurements with ultrahigh resolving power in FRET efficiency. Importantly, single-molecule diffusivity is used to provide additional size and shape information for hydrodynamic profiling of individual molecules, which, together with the concurrently measured intramolecular conformation through FRET, enables a holistic and dynamic view of biomolecules and their complexes.
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Affiliation(s)
- Hugh Wilson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Quan Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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10
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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11
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Dienerowitz M, Howard JAL, Quinn SD, Dienerowitz F, Leake MC. Single-molecule FRET dynamics of molecular motors in an ABEL trap. Methods 2021; 193:96-106. [PMID: 33571667 DOI: 10.1016/j.ymeth.2021.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Single-molecule Förster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key challenge of such FRET investigations is to observe a molecule in action for long enough without restricting its natural function. The Anti-Brownian ELectrokinetic Trap (ABEL trap) sets out to combine smFRET with molecular confinement to enable observation times of up to several seconds while removing any requirement of tethered surface attachment of the molecule in question. In addition, the ABEL trap's inherent ability to selectively capture FRET active molecules accelerates the data acquisition process. In this work we exemplify the capabilities of the ABEL trap in performing extended timescale smFRET measurements on the molecular motor Rep, which is crucial for removing protein blocks ahead of the advancing DNA replication machinery and for restarting stalled DNA replication. We are able to monitor single Rep molecules up to 6 seconds with sub-millisecond time resolution capturing multiple conformational switching events during the observation time. Here we provide a step-by-step guide for the rational design, construction and implementation of the ABEL trap for smFRET detection of Rep in vitro. We include details of how to model the electric potential at the trap site and use Hidden Markov analysis of the smFRET trajectories.
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Affiliation(s)
- Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2 - 4, 07743 Jena, Germany.
| | - Jamieson A L Howard
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven D Quinn
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Mark C Leake
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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12
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Celetti G, Paci G, Caria J, VanDelinder V, Bachand G, Lemke EA. The liquid state of FG-nucleoporins mimics permeability barrier properties of nuclear pore complexes. J Cell Biol 2020; 219:e201907157. [PMID: 31723007 PMCID: PMC7039189 DOI: 10.1083/jcb.201907157] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/21/2019] [Accepted: 10/09/2019] [Indexed: 01/31/2023] Open
Abstract
Nuclear pore complexes (NPCs) regulate all cargo traffic across the nuclear envelope. The transport conduit of NPCs is highly enriched in disordered phenylalanine/glycine-rich nucleoporins (FG-Nups), which form a permeability barrier of still elusive and highly debated molecular structure. Here we present a microfluidic device that triggered liquid-to-liquid phase separation of FG-Nups, which yielded droplets that showed typical properties of a liquid state. On the microfluidic chip, droplets were perfused with different transport-competent or -incompetent cargo complexes, and then the permeability barrier properties of the droplets were optically interrogated. We show that the liquid state mimics permeability barrier properties of the physiological nuclear transport pathway in intact NPCs in cells: that is, inert cargoes ranging from small proteins to large capsids were excluded from liquid FG-Nup droplets, but functional import complexes underwent facilitated import into droplets. Collectively, these data provide an experimental model of how NPCs can facilitate fast passage of cargoes across an order of magnitude in cargo size.
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Affiliation(s)
- Giorgia Celetti
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Giulia Paci
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joana Caria
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Virginia VanDelinder
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM
| | - George Bachand
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM
| | - Edward A. Lemke
- Biocentre, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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13
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Gilboa B, Jing B, Cui TJ, Sow M, Plochowietz A, Mazumder A, Kapanidis AN. Confinement-Free Wide-Field Ratiometric Tracking of Single Fluorescent Molecules. Biophys J 2019; 117:2141-2153. [PMID: 31711608 PMCID: PMC6895709 DOI: 10.1016/j.bpj.2019.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/25/2019] [Accepted: 10/21/2019] [Indexed: 11/24/2022] Open
Abstract
Single-molecule fluorescence has been highly instrumental in elucidating interactions and dynamics of biological molecules in the past two decades. Single-molecule fluorescence experiments usually rely on one of two detection geometries, either confocal point-detection or wide-field area detection, typically in a total internal reflection fluorescence (TIRF) format. However, each of these techniques suffers from fundamental drawbacks that limit their application. In this work, we present a new technique, solution wide-field imaging (SWiFi) of diffusing molecules, as an alternative to the existing methods. SWiFi is a simple extension to existing objective-type TIRF microscopes that allows wide-field observations of fast-diffusing molecules down to single fluorophores without the need of tethering the molecules to the surface. We demonstrate that SWiFi enables high-throughput ratiometric measurements with several thousands of individual data points per minute on double-stranded DNA standard (dsDNA) samples containing Förster resonance energy transfer pairs. We further display the capabilities of SWiFi by reporting on mobility and ratiometric characterization of fluorescent nanodiamonds, DNA Holliday junctions, and protein-DNA interactions. The ability of SWiFi for high-throughput, ratiometric measurements of fast-diffusing species renders it a valuable tool for the single-molecule research community by bridging between confocal and TIRF detection geometries in a simple and efficient way.
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Affiliation(s)
- Barak Gilboa
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Bo Jing
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Tao J Cui
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Maabur Sow
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Abhishek Mazumder
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom.
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14
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Chen YI, Chang YJ, Nguyen TD, Liu C, Phillion S, Kuo YA, Vu HT, Liu A, Liu YL, Hong S, Ren P, Yankeelov TE, Yeh HC. Measuring DNA Hybridization Kinetics in Live Cells Using a Time-Resolved 3D Single-Molecule Tracking Method. J Am Chem Soc 2019; 141:15747-15750. [PMID: 31509386 DOI: 10.1021/jacs.9b08036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-molecule detection enables direct characterization of annealing/melting kinetics of nucleic acids without the need for synchronization of molecular states, but the current experiments are not carried out in a native cellular context. Here we describe an integrated 3D single-molecule tracking and lifetime measurement method that can follow individual DNA molecules diffusing inside a mammalian cell and observe multiple annealing and melting events on the same molecules. By comparing the hybridization kinetics of the same DNA strand in vitro, we found the association constants can be 13- to 163-fold higher in the molecular crowding cellular environment.
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Affiliation(s)
- Yuan-I Chen
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Yin-Jui Chang
- Department of Mechanical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Trung Duc Nguyen
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Cong Liu
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Stephanie Phillion
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Yu-An Kuo
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Huong T Vu
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Angela Liu
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Yen-Liang Liu
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Soonwoo Hong
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Pengyu Ren
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Thomas E Yankeelov
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States.,Oden Institute for Computational Engineering and Sciences, University of Texas at Austin , Austin , Texas 78712 , United States.,Department of Diagnostic Medicine , University of Texas at Austin , Austin , Texas 78712 , United States.,Department of Oncology , University of Texas at Austin , Austin , Texas 78712 , United States.,Livestrong Cancer Institutes, University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States.,Texas Materials Institute, University of Texas at Austin , Austin , Texas 78712 , United States
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15
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Bespalova MI, Mahanta S, Krishnan M. Single-molecule trapping and measurement in solution. Curr Opin Chem Biol 2019; 51:113-121. [DOI: 10.1016/j.cbpa.2019.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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16
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Grant J, O’Kane PT, Kimmel BR, Mrksich M. Using Microfluidics and Imaging SAMDI-MS To Characterize Reaction Kinetics. ACS CENTRAL SCIENCE 2019; 5:486-493. [PMID: 30937376 PMCID: PMC6439460 DOI: 10.1021/acscentsci.8b00867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Microfluidic platforms have enabled the simplification of biochemical assays with a significant reduction in the use of reagents, yet the current methods available for analyzing reaction products can limit applications of these approaches. This paper demonstrates a simple microfluidic device that incorporates a functionalized self-assembled monolayer to measure the rate constant for a chemical reaction. The device mixes the reactants and allows them to selectively immobilize to the monolayer at the base of a microfluidic channel in a time-dependent manner as they flow down the channel. Imaging self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (iSAMDI-MS) is used to acquire a quantitative image representing the time-resolved progress of the reaction as it flowed through the channel. Knowledge of the surface immobilization chemistry and the fluid front characteristics allows for the determination of the chemical reaction rate constant. This approach widens the applicability of microfluidics for chemical reaction monitoring and establishes a label-free method for studying processes that occur within a dispersive regime.
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Affiliation(s)
- Jennifer Grant
- Department
of Chemistry, Department of Chemical & Biological Engineering,
and Department of
Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Patrick T. O’Kane
- Department
of Chemistry, Department of Chemical & Biological Engineering,
and Department of
Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Blaise R. Kimmel
- Department
of Chemistry, Department of Chemical & Biological Engineering,
and Department of
Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department
of Chemistry, Department of Chemical & Biological Engineering,
and Department of
Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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17
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Fontana M, Fijen C, Lemay SG, Mathwig K, Hohlbein J. High-throughput, non-equilibrium studies of single biomolecules using glass-made nanofluidic devices. LAB ON A CHIP 2018; 19:79-86. [PMID: 30468446 DOI: 10.1039/c8lc01175c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Single-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. However, probing biomolecular interactions and reactions with high throughput and time resolution remains challenging, often requiring surface-immobilized entities. Here, we introduce glass-made nanofluidic devices for the high-throughput detection of freely-diffusing single biomolecules by camera-based fluorescence microscopy. Nanochannels of 200 nm height and a width of several micrometers confine the movement of biomolecules. Using pressure-driven flow through an array of parallel nanochannels and by tracking the movement of fluorescently labelled DNA oligonucleotides, we observe conformational changes with high throughput. In a device geometry featuring a T-shaped junction of nanochannels, we drive steady-state non-equilibrium conditions by continuously mixing reactants and triggering chemical reactions. We use the device to probe the conformational equilibrium of a DNA hairpin as well as to continuously observe DNA synthesis in real time. Our platform offers a straightforward and robust method for studying reaction kinetics at the single-molecule level.
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Affiliation(s)
- Mattia Fontana
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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18
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Direct Single-Molecule Observation of Sequential DNA Bending Transitions by the Sox2 HMG Box. Int J Mol Sci 2018; 19:ijms19123865. [PMID: 30518054 PMCID: PMC6321608 DOI: 10.3390/ijms19123865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/07/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
Sox2 is a pioneer transcription factor that initiates cell fate reprogramming through locus-specific differential regulation. Mechanistically, it was assumed that Sox2 achieves its regulatory diversity via heterodimerization with partner transcription factors. Here, utilizing single-molecule fluorescence spectroscopy, we show that Sox2 alone can modulate DNA structural landscape in a dosage-dependent manner. We propose that such stoichiometric tuning of regulatory DNAs is crucial to the diverse biological functions of Sox2, and represents a generic mechanism of conferring functional plasticity and multiplicity to transcription factors.
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19
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Juniper MPN, Weiss M, Platzman I, Spatz JP, Surrey T. Spherical network contraction forms microtubule asters in confinement. SOFT MATTER 2018; 14:901-909. [PMID: 29364311 DOI: 10.1039/c7sm01718a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Microtubules and motor proteins form active filament networks that are critical for a variety of functions in living cells. Network topology and dynamics are the result of a self-organisation process that takes place within the boundaries of the cell. Previous biochemical in vitro studies with biomimetic systems consisting of purified motors and microtubules have demonstrated that confinement has an important effect on the outcome of the self-organisation process. However, the pathway of motor/microtubule self-organisation under confinement and its effects on network morphology are still poorly understood. Here, we have investigated how minus-end directed microtubule cross-linking kinesins organise microtubules inside polymer-stabilised microfluidic droplets of well-controlled size. We find that confinement can impose a novel pathway of microtubule aster formation proceeding via the constriction of an initially spherical motor/microtubule network. This mechanism illustrates the close relationship between confinement, network contraction, and aster formation. The spherical constriction pathway robustly produces single, well-centred asters with remarkable reproducibility across thousands of droplets. These results show that the additional constraint of well-defined confinement can improve the robustness of active network self-organisation, providing insight into the design principles of self-organising active networks in micro-scale confinement.
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Affiliation(s)
| | - Marian Weiss
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Germany and Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Ilia Platzman
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Germany and Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Joachim P Spatz
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Germany and Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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20
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Voith von Voithenberg L, Lamb DC. Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics. Bioessays 2018; 40. [DOI: 10.1002/bies.201700078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 12/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Lena Voith von Voithenberg
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
- BIOSS Centre for Signalling Studies; Schänzlestr. 18 79104 Freiburg Germany
| | - Don C. Lamb
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
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21
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Hamadani KM, Howe J, Jensen MK, Wu P, Cate JHD, Marqusee S. An in vitro tag-and-modify protein sample generation method for single-molecule fluorescence resonance energy transfer. J Biol Chem 2017; 292:15636-15648. [PMID: 28754692 DOI: 10.1074/jbc.m117.791723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/25/2017] [Indexed: 11/06/2022] Open
Abstract
Biomolecular systems exhibit many dynamic and biologically relevant properties, such as conformational fluctuations, multistep catalysis, transient interactions, folding, and allosteric structural transitions. These properties are challenging to detect and engineer using standard ensemble-based techniques. To address this drawback, single-molecule methods offer a way to access conformational distributions, transient states, and asynchronous dynamics inaccessible to these standard techniques. Fluorescence-based single-molecule approaches are parallelizable and compatible with multiplexed detection; to date, however, they have remained limited to serial screens of small protein libraries. This stems from the current absence of methods for generating either individual dual-labeled protein samples at high throughputs or protein libraries compatible with multiplexed screening platforms. Here, we demonstrate that by combining purified and reconstituted in vitro translation, quantitative unnatural amino acid incorporation via AUG codon reassignment, and copper-catalyzed azide-alkyne cycloaddition, we can overcome these challenges for target proteins that are, or can be, methionine-depleted. We present an in vitro parallelizable approach that does not require laborious target-specific purification to generate dual-labeled proteins and ribosome-nascent chain libraries suitable for single-molecule FRET-based conformational phenotyping. We demonstrate the power of this approach by tracking the effects of mutations, C-terminal extensions, and ribosomal tethering on the structure and stability of three protein model systems: barnase, spectrin, and T4 lysozyme. Importantly, dual-labeled ribosome-nascent chain libraries enable single-molecule co-localization of genotypes with phenotypes, are well suited for multiplexed single-molecule screening of protein libraries, and should enable the in vitro directed evolution of proteins with designer single-molecule conformational phenotypes of interest.
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Affiliation(s)
- Kambiz M Hamadani
- From the California Institute for Quantitative Biosciences and .,the Department of Chemistry and Biochemistry, California State University, San Marcos, California 92096, and
| | - Jesse Howe
- the Department of Chemistry and Biochemistry, California State University, San Marcos, California 92096, and
| | | | - Peng Wu
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Jamie H D Cate
- From the California Institute for Quantitative Biosciences and .,the Departments of Molecular and Cell Biology and.,Chemistry, University of California, Berkeley, California 94720
| | - Susan Marqusee
- From the California Institute for Quantitative Biosciences and .,the Departments of Molecular and Cell Biology and
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22
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Optimal Background Estimators in Single-Molecule FRET Microscopy. Biophys J 2017; 111:1278-1286. [PMID: 27653486 DOI: 10.1016/j.bpj.2016.07.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/21/2016] [Accepted: 07/26/2016] [Indexed: 11/23/2022] Open
Abstract
Single-molecule total internal reflection fluorescence (TIRF) microscopy constitutes an umbrella of powerful tools that facilitate direct observation of the biophysical properties, population heterogeneities, and interactions of single biomolecules without the need for ensemble synchronization. Due to the low signal/noise ratio in single-molecule TIRF microscopy experiments, it is important to determine the local background intensity, especially when the fluorescence intensity of the molecule is used quantitatively. Here we compare and evaluate the performance of different aperture-based background estimators used particularly in single-molecule Förster resonance energy transfer. We introduce the general concept of multiaperture signatures and use this technique to demonstrate how the choice of background can affect the measured fluorescence signal considerably. A new, to our knowledge, and simple background estimator is proposed, called the local statistical percentile (LSP). We show that the LSP background estimator performs as well as current background estimators at low molecular densities and significantly better in regions of high molecular densities. The LSP background estimator is thus suited for single-particle TIRF microscopy of dense biological samples in which the intensity itself is an observable of the technique.
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23
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Friedrich R, Block S, Alizadehheidari M, Heider S, Fritzsche J, Esbjörner EK, Westerlund F, Bally M. A nano flow cytometer for single lipid vesicle analysis. LAB ON A CHIP 2017; 17:830-841. [PMID: 28128381 DOI: 10.1039/c6lc01302c] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 μl sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.
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Affiliation(s)
- Remo Friedrich
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Stephan Block
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | | | - Susanne Heider
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Marta Bally
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Institut Curie, Centre de Recherche, CNRS, UMR168, Physico-Chimie Curie, Paris, France
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24
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Sasmal DK, Pulido LE, Kasal S, Huang J. Single-molecule fluorescence resonance energy transfer in molecular biology. NANOSCALE 2016; 8:19928-19944. [PMID: 27883140 PMCID: PMC5145784 DOI: 10.1039/c6nr06794h] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics. Finally, we discuss the main limitations of smFRET in molecular biology.
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Affiliation(s)
- Dibyendu K Sasmal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Laura E Pulido
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Shan Kasal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Jun Huang
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
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25
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Hohlbein J, Kapanidis AN. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET. Methods Enzymol 2016; 581:353-378. [PMID: 27793286 DOI: 10.1016/bs.mie.2016.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open and closed conformations of DNA polymerases, our smFRET assays utilizing doubly labeled variants of Escherichia coli DNA polymerase I were pivotal in identifying and characterizing a partially closed conformation as a primary checkpoint for nucleotide selection. Here, we provide a comprehensive overview of the methods we used for the conformational analysis of wild-type DNA polymerase and some of its low-fidelity derivatives; these methods include strategies for protein labeling and our procedures for solution-based single-molecule fluorescence data acquisition and data analysis. We also discuss alternative single-molecule fluorescence strategies for analyzing the conformations of DNA polymerases in vitro and in vivo.
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Affiliation(s)
- J Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, The Netherlands; Microspectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands.
| | - A N Kapanidis
- Clarendon Laboratory, University of Oxford, Oxford, United Kingdom.
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Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers. Sci Rep 2016; 6:33257. [PMID: 27641327 PMCID: PMC5027553 DOI: 10.1038/srep33257] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 01/24/2023] Open
Abstract
Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
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DeHaven AC, Norden IS, Hoskins AA. Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:683-701. [PMID: 27198613 PMCID: PMC4990488 DOI: 10.1002/wrna.1358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/20/2016] [Accepted: 04/04/2016] [Indexed: 11/06/2022]
Abstract
The process of removing intronic sequences from a precursor to messenger RNA (pre-mRNA) to yield a mature mRNA transcript via splicing is an integral step in eukaryotic gene expression. Splicing is carried out by a cellular nanomachine called the spliceosome that is composed of RNA components and dozens of proteins. Despite decades of study, many fundamentals of spliceosome function have remained elusive. Recent developments in single-molecule fluorescence microscopy have afforded new tools to better probe the spliceosome and the complex, dynamic process of splicing by direct observation of single molecules. These cutting-edge technologies enable investigators to monitor the dynamics of specific splicing components, whole spliceosomes, and even cotranscriptional splicing within living cells. WIREs RNA 2016, 7:683-701. doi: 10.1002/wrna.1358 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alexander C. DeHaven
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Ian S. Norden
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Aaron A. Hoskins
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
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28
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Farooq S, Hohlbein J. Camera-based single-molecule FRET detection with improved time resolution. Phys Chem Chem Phys 2016; 17:27862-72. [PMID: 26439729 DOI: 10.1039/c5cp04137f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The achievable time resolution of camera-based single-molecule detection is often limited by the frame rate of the camera. Especially in experiments utilizing single-molecule Förster resonance energy transfer (smFRET) to probe conformational dynamics of biomolecules, increasing the frame rate by either pixel-binning or cropping the field of view decreases the number of molecules that can be monitored simultaneously. Here, we present a generalised excitation scheme termed stroboscopic alternating-laser excitation (sALEX) that significantly improves the time resolution without sacrificing highly parallelised detection in total internal reflection fluorescence (TIRF) microscopy. In addition, we adapt a technique known from diffusion-based confocal microscopy to analyse the complex shape of FRET efficiency histograms. We apply both sALEX and dynamic probability distribution analysis (dPDA) to resolve conformational dynamics of interconverting DNA hairpins in the millisecond time range.
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Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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29
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Banterle N, Lemke EA. Nanoscale devices for linkerless long-term single-molecule observation. Curr Opin Biotechnol 2016; 39:105-112. [PMID: 26990172 PMCID: PMC7611743 DOI: 10.1016/j.copbio.2016.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 01/07/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) can offer favorably high signal-to-noise observation of biological mechanisms. TIRFM can be used routinely to observe even single fluorescent molecules for a long duration (several seconds) at millisecond time resolution. However, to keep the investigated sample in the evanescent field, chemical surface immobilization techniques typically need to be implemented. In this review, we describe some of the recently developed novel nanodevices that overcome this limitation enabling long-term observation of free single molecules and outline their biological applications. The working concept of many devices is compatible with high-throughput strategies, which will further help to establish unbiased single molecule observation as a routine tool in biology to study the molecular underpinnings of even the most complex biological mechanisms.
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Affiliation(s)
- Niccolò Banterle
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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30
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Varon Silva D. ECBS & ICBS 2015 Joint Meeting: Bringing Chemistry to Life. Chembiochem 2016; 17:447-52. [PMID: 26710339 DOI: 10.1002/cbic.201500684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 01/11/2023]
Abstract
The European Chemical Biology Society (ECBS) and the International Chemical Biology Society (ICBS) recently organized a joint meeting in Berlin. This meeting had more than 250 participants. Four keynote lectures were given by Timothy Mitchison, David Tirrell, Carolyn Bertozzi and Jason Chin; in addition there were 13 invited speakers, 20 selected oral talks and 30 talks selected from 90 posters. The meeting was divided into six topics: chemoproteomics, epigenetics, conjugates for target delivering, anti-infectives, molecular imaging and probing the structure, and function of post-translational modifications. The highlights of the meeting are presented in this report.
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Affiliation(s)
- Daniel Varon Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 01, 14476, Potsdam, Germany.
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31
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Friedrich SM, Zec HC, Wang TH. Analysis of single nucleic acid molecules in micro- and nano-fluidics. LAB ON A CHIP 2016; 16:790-811. [PMID: 26818700 PMCID: PMC4767527 DOI: 10.1039/c5lc01294e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.
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Affiliation(s)
- Sarah M Friedrich
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Helena C Zec
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA. and Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
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32
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Okamoto K, Sako Y. State transition analysis of spontaneous branch migration of the Holliday junction by photon-based single-molecule fluorescence resonance energy transfer. Biophys Chem 2016; 209:21-7. [DOI: 10.1016/j.bpc.2015.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/27/2015] [Accepted: 11/28/2015] [Indexed: 11/17/2022]
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Deniz AA. Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution. J Mol Biol 2015; 428:301-307. [PMID: 26707199 DOI: 10.1016/j.jmb.2015.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/16/2015] [Accepted: 12/16/2015] [Indexed: 01/12/2023]
Abstract
The structural features and dynamics of biological macromolecules underlie the molecular biology and correct functioning of cells. However, heterogeneity and other complexity of these molecules and their interactions often lead to loss of important information in traditional biophysical experiments. Single-molecule methods have dramatically altered the conceptual thinking and experimental tests available for such studies, leveraging their ability to avoid ensemble averaging. Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects.
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Affiliation(s)
- Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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34
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Ishitsuka Y, Azadfar N, Kobitski AY, Nienhaus K, Johnsson N, Nienhaus GU. Evaluation of Genetically Encoded Chemical Tags as Orthogonal Fluorophore Labeling Tools for Single-Molecule FRET Applications. J Phys Chem B 2015; 119:6611-9. [PMID: 25978145 DOI: 10.1021/acs.jpcb.5b03584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorescence resonance energy transfer (FRET) is a superb technique for measuring conformational changes of proteins on the single molecule level (smFRET) in real time. It requires introducing a donor and acceptor fluorophore pair at specific locations on the protein molecule of interest, which has often been a challenging task. By using two different self-labeling chemical tags, such as Halo-, TMP-, SNAP- and CLIP-tags, orthogonal labeling may be achieved rapidly and reliably. However, these comparatively large tags add extra distance and flexibility between the desired labeling location on the protein and the fluorophore position, which may affect the results. To systematically characterize chemical tags for smFRET measurement applications, we took the SNAP-tag/CLIP-tag combination as a model system and fused a flexible unstructured peptide, rigid polyproline peptides of various lengths, and the calcium sensor protein calmodulin between the tags. We could reliably identify length variations as small as four residues in the polyproline peptide. In the calmodulin system, the added length introduced by these tags was even beneficial for revealing subtle conformational changes upon variation of the buffer conditions. This approach opens up new possibilities for studying conformational dynamics, especially in large protein systems that are difficult to specifically conjugate with fluorophores.
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Affiliation(s)
- Yuji Ishitsuka
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Naghmeh Azadfar
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Andrei Yu Kobitski
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Karin Nienhaus
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Nils Johnsson
- §Institute of Molecular Genetics and Cell Biology, Ulm University, James Franck Ring N27, 89081 Ulm, Germany
| | - G Ulrich Nienhaus
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany.,∥Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,⊥Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
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35
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Kim JY, Kim C, Lee NK. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering. Nat Commun 2015; 6:6992. [PMID: 25908552 PMCID: PMC4421855 DOI: 10.1038/ncomms7992] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 03/23/2015] [Indexed: 01/15/2023] Open
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s–1 between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution. Single-molecule fluorescence resonance energy transfer is widely used to probe biomolecular dynamics, but is limited by its temporal resolution. Here, Kim et al. push the limit to submillisecond for the duration of tens of milliseconds by tethering target molecules to liposomes in buffer solutions.
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Affiliation(s)
- Jae-Yeol Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Nam Ki Lee
- 1] Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea [2] School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, Korea
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36
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Tran EJ, King MC, Corbett AH. Macromolecular transport between the nucleus and the cytoplasm: Advances in mechanism and emerging links to disease. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2784-2795. [PMID: 25116306 PMCID: PMC4161953 DOI: 10.1016/j.bbamcr.2014.08.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 01/08/2023]
Abstract
Transport of macromolecules between the cytoplasm and the nucleus is critical for the function of all eukaryotic cells. Large macromolecular channels termed nuclear pore complexes that span the nuclear envelope mediate the bidirectional transport of cargoes between the nucleus and cytoplasm. However, the influence of macromolecular trafficking extends past the nuclear pore complex to transcription and RNA processing within the nucleus and signaling pathways that reach into the cytoplasm and beyond. At the Mechanisms of Nuclear Transport biennial meeting held from October 18 to 23, 2013 in Woods Hole, MA, researchers in the field met to report on their recent findings. The work presented highlighted significant advances in understanding nucleocytoplasmic trafficking including how transport receptors and cargoes pass through the nuclear pore complex, the many signaling pathways that impinge on transport pathways, interplay between the nuclear envelope, nuclear pore complexes, and transport pathways, and numerous links between transport pathways and human disease. The goal of this review is to highlight newly emerging themes in nuclear transport and underscore the major questions that are likely to be the focus of future research in the field.
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Affiliation(s)
- Elizabeth J Tran
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907, USA.
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, 4117 Rollins Research Center, 1510 Clifton Road, NE, Atlanta, GA 30322, USA.
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37
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Gust A, Zander A, Gietl A, Holzmeister P, Schulz S, Lalkens B, Tinnefeld P, Grohmann D. A starting point for fluorescence-based single-molecule measurements in biomolecular research. Molecules 2014; 19:15824-65. [PMID: 25271426 PMCID: PMC6271140 DOI: 10.3390/molecules191015824] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.
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Affiliation(s)
- Alexander Gust
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Adrian Zander
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Birka Lalkens
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany.
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38
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Robison AD, Finkelstein IJ. High-throughput single-molecule studies of protein-DNA interactions. FEBS Lett 2014; 588:3539-46. [PMID: 24859086 DOI: 10.1016/j.febslet.2014.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/11/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Fluorescence and force-based single-molecule studies of protein-nucleic acid interactions continue to shed critical insights into many aspects of DNA and RNA processing. As single-molecule assays are inherently low-throughput, obtaining statistically relevant datasets remains a major challenge. Additionally, most fluorescence-based single-molecule particle-tracking assays are limited to observing fluorescent proteins that are in the low-nanomolar range, as spurious background signals predominate at higher fluorophore concentrations. These technical limitations have traditionally limited the types of questions that could be addressed via single-molecule methods. In this review, we describe new approaches for high-throughput and high-concentration single-molecule biochemical studies. We conclude with a discussion of outstanding challenges for the single-molecule biologist and how these challenges can be tackled to further approach the biochemical complexity of the cell.
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Affiliation(s)
- Aaron D Robison
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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39
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Single-molecule motions enable direct visualization of biomolecular interactions in solution. Nat Methods 2014; 11:555-8. [PMID: 24608179 DOI: 10.1038/nmeth.2882] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/25/2014] [Indexed: 11/08/2022]
Abstract
Biomolecular interactions are generally accompanied by modifications in size and charge of biomolecules at the nanometer scale. Here we describe a single-molecule method to sense these changes in real time based on statistical learning of diffusive and electric field-induced motion parameters of a trapped molecule in solution. We demonstrate the approach by resolving a monomer-trimer mixture along a protein dissociation pathway and visualizing the binding-unbinding kinetics of a single DNA molecule.
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