1
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Sethi S, Wijesinghe KM, Dhakal S. Single-Molecule FRET-Based Multiplexed Detection. Methods Mol Biol 2024; 2744:183-195. [PMID: 38683319 DOI: 10.1007/978-1-0716-3581-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Single-molecule multiplexed detection is a high-promise toolkit for the expanding field of biosensing and molecular diagnostics. Among many single-molecule techniques available today for biomarker sensing including fluorescence, force, electrochemical, spectroscopic, barcoding, and other techniques, fluorescence-based approaches are arguably the most widely used methods due to their high sensitivity, selectivity, and readily available fluorophore-labeling schemes for a wide variety of biomolecules. However, multiplexed imaging using fluorescence techniques has proven to be challenging due to the sophisticated labeling schemes often requiring multiple FRET (fluorescence resonance energy transfer) pairs and/or excitation sources, which lead to overlapping signals and complicate data analysis. Here, we describe a single-molecule FRET method that enables multiplexed analysis while still using only one FRET pair, and thus the described approach is a significant step forward from conventional FRET methods.
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Affiliation(s)
- Srishty Sethi
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
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2
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Durham RJ, Jayaraman V. Single-Molecule FRET Analyses of NMDA Receptors. Methods Mol Biol 2024; 2799:225-242. [PMID: 38727910 PMCID: PMC11164542 DOI: 10.1007/978-1-0716-3830-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) enables the real-time observation of conformational changes in a single protein molecule of interest. These observations are achieved by attaching fluorophores to proteins of interest in a site-specific manner and investigating the FRET between the fluorophores. Here we describe the method wherein the FRET is studied by adhering the protein molecules to a slide using affinity-based interactions and measuring the fluorophores' fluorescence intensity from a single molecule over time. The resulting information can be used to derive distance values for a point-to-point measurement within a protein or to calculate kinetic transition rates between various conformational states of a protein. Comparing these parameters between different conditions such as the presence of protein binding partners, application of ligands, or changes in the primary sequence of the protein can provide insights into protein structural changes as well as kinetics of these changes (if in the millisecond to second timescale) that underlie functional effects. Here we describe the procedure for conducting analyses of NMDA receptor conformational changes using the above methodology and provide a discussion of various considerations that affect the design, execution, and interpretation of similar smFRET studies.
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Affiliation(s)
- Ryan J Durham
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, USA.
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3
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van den Wildenberg SMJL, Prevo B, Peterman EJG. A Brief Introduction to Single-Molecule Fluorescence Methods. Methods Mol Biol 2024; 2694:111-132. [PMID: 37824002 DOI: 10.1007/978-1-0716-3377-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
One of the most popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster resonance energy transfer and orientation measurements with fluorescence polarization.
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Affiliation(s)
- Siet M J L van den Wildenberg
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Université Clermont Auvergne, CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, Clermont-Ferrand, France
| | - Bram Prevo
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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4
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Rashi, Kaur V, Devi A, Bain D, Sen T, Patra A. Probing the Fluorescence Intermittency of Bimetallic Nanoclusters using Single-Molecule Fluorescence Spectroscopy. J Phys Chem Lett 2023; 14:10166-10172. [PMID: 37925663 DOI: 10.1021/acs.jpclett.3c02823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Single-molecule spectroscopy (SMS) is a unique and competent technique to study molecule dynamics and sense biomolecules precisely. The design of an ultrahigh-stability single fluorophore probe with excellent photostability and long-lived dark transient states for single-molecule fluorescence microscopy is challenging. Here, we found that the photostability of bimetallic AuAg28 nanoclusters is better than monometallic Ag29 nanoclusters. The photon antibunching experiments unveiled exceptional brightness and remarkable photostability with high survival times of up to 218 s with minimal blinking. AuAg28 NCs exhibited longer "on" times and shorter "off" times as compared to Ag29 NCs. The statistical analysis was performed on at least 100 molecules that showed single-step photobleaching and almost a 5-fold enhancement in intensity on Au doping in Ag29 NCs. The distinctive and tunable photophysics of metal NCs can offer huge potential in pushing single-molecule dynamic measurements to be carried out biologically.
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Affiliation(s)
- Rashi
- Institute of Nano Science and Technology, Sector-81, Knowledge City, SAS Nagar, Mohali 140306, India
| | - Vishaldeep Kaur
- Institute of Nano Science and Technology, Sector-81, Knowledge City, SAS Nagar, Mohali 140306, India
| | - Aarti Devi
- Institute of Nano Science and Technology, Sector-81, Knowledge City, SAS Nagar, Mohali 140306, India
| | - Dipankar Bain
- Institute of Nano Science and Technology, Sector-81, Knowledge City, SAS Nagar, Mohali 140306, India
| | - Tapasi Sen
- Institute of Nano Science and Technology, Sector-81, Knowledge City, SAS Nagar, Mohali 140306, India
| | - Amitava Patra
- Institute of Nano Science and Technology, Sector-81, Knowledge City, SAS Nagar, Mohali 140306, India
- School of Materials Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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5
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Kümmerlin M, Mazumder A, Kapanidis AN. Bleaching-resistant, Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding. Chemphyschem 2023; 24:e202300175. [PMID: 37043705 PMCID: PMC10946581 DOI: 10.1002/cphc.202300175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/16/2023] [Indexed: 04/14/2023]
Abstract
Photobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions. Using two orthogonal sequences, we show that our method is adaptable to Förster Resonance Energy Transfer (FRET) and that can be used to study the conformational dynamics of dynamic structures, such as DNA Holliday junctions, for extended periods. By adjusting the temporal resolution and observation span, our approach enables capturing the conformational dynamics of proteins and nucleic acids over a wide range of timescales.
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Affiliation(s)
- Mirjam Kümmerlin
- Department of PhysicsUniversity of OxfordOxfordOX1 3PUUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordDorothy Crowfoot Hodgkin BuildingOxfordOX1 3QUUK
| | - Abhishek Mazumder
- Department of PhysicsUniversity of OxfordOxfordOX1 3PUUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordDorothy Crowfoot Hodgkin BuildingOxfordOX1 3QUUK
- Structural Biology and Bioinformatics DivisionCSIR-Indian Institute of Chemical Biology4, Raja S. C. Mullick RoadKolkata700 032India
| | - Achillefs N. Kapanidis
- Department of PhysicsUniversity of OxfordOxfordOX1 3PUUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordDorothy Crowfoot Hodgkin BuildingOxfordOX1 3QUUK
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6
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Limanskaya OY, Limanskii OP. Intramolecular Interactions in the Fluorophore–Quencher System in Linear and Hairpin Probes for Real-Time PCR. CYTOL GENET+ 2023. [DOI: 10.3103/s009545272302007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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7
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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8
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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9
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Artyukh RI, Fatkhullin BF, Kachalova GS, Antipova VN, Perevyazova TA, Yunusova AK. Structural analysis of cysteine-free Nt.BspD6 nicking endonuclease and its functional features. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140756. [PMID: 35026466 DOI: 10.1016/j.bbapap.2022.140756] [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: 10/13/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Nicking endonuclease Nt.BspD6I (Nt.BspD6I) is the large subunit of the heterodimeric restriction endonuclease R.BspD6I. It recognizes the short specific DNA sequence 5´'- GAGTC and cleaves only the top strand in dsDNA at a distance of four nucleotides downstream the recognition site toward the 3´'-terminus. A mechanism of interaction of this protein with DNA is still unknown. Here we report the crystal structure of Cysteine-free Nt.BspD6I, with four cysteine residues (11, 160, 508, 578) substituted by serine, which was determined with a resolution of 1.93 Å. A comparative structural analysis showed that the substitution of cysteine residues induced marked conformational changes in the N-terminal recognition and the C-terminal cleavage domains. As a result of this changes were formed three new hydrogen bonds and the electrostatic field in these regions changed compared with wild type Nt.BspD6I. The substitution of cysteine residues did not alter the nicking function of Cysteine-free Nt.BspD6I but caused change in the activity of Cysteine-free heterodimeric restriction endonuclease R.BspD6I due to a change in the interaction between its large and small subunits. The results obtained contribute to the identification of factors influencing the interactions of subunits in the heterodimeric restriction enzyme R.BspD6I.
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Affiliation(s)
- Rimma I Artyukh
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
| | - Bulat F Fatkhullin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Galina S Kachalova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Valeriya N Antipova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Tatyana A Perevyazova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Alfiya K Yunusova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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10
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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11
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Zosel F, Holla A, Schuler B. Labeling of Proteins for Single-Molecule Fluorescence Spectroscopy. Methods Mol Biol 2022; 2376:207-233. [PMID: 34845612 DOI: 10.1007/978-1-0716-1716-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-molecule fluorescence spectroscopy has become an important technique for studying the conformational dynamics and folding of proteins. A key step for performing such experiments is the availability of high-quality samples. This chapter describes a simple and widely applicable strategy for preparing proteins that are site-specifically labeled with a donor and an acceptor dye for single-molecule Förster resonance energy transfer (FRET) experiments. The method is based on introducing two cysteine residues that are labeled with maleimide-functionalized fluorophores, combined with high-resolution chromatography. We discuss how to optimize site-specific labeling even in the absence of orthogonal coupling chemistry and present purification strategies that are suitable for samples ranging from intrinsically disordered proteins to large folded proteins. We also discuss common problems in protein labeling, how to avoid them, and how to stringently control sample quality.
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Affiliation(s)
- Franziska Zosel
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Novo Nordisk A/S, Måløv, Denmark
| | - Andrea Holla
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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12
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Stawicki CM, Rinker TE, Burns M, Tonapi SS, Galimidi RP, Anumala D, Robinson JK, Klein JS, Mallick P. Modular fluorescent nanoparticle DNA probes for detection of peptides and proteins. Sci Rep 2021; 11:19921. [PMID: 34620912 PMCID: PMC8497506 DOI: 10.1038/s41598-021-99084-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
Fluorescently labeled antibody and aptamer probes are used in biological studies to characterize binding interactions, measure concentrations of analytes, and sort cells. Fluorescent nanoparticle labels offer an excellent alternative to standard fluorescent labeling strategies due to their enhanced brightness, stability and multivalency; however, challenges in functionalization and characterization have impeded their use. This work introduces a straightforward approach for preparation of fluorescent nanoparticle probes using commercially available reagents and common laboratory equipment. Fluorescent polystyrene nanoparticles, Thermo Fisher Scientific FluoSpheres, were used in these proof-of-principle studies. Particle passivation was achieved by covalent attachment of amine-PEG-azide to carboxylated particles, neutralizing the surface charge from - 43 to - 15 mV. A conjugation-annealing handle and DNA aptamer probe were attached to the azide-PEG nanoparticle surface either through reaction of pre-annealed handle and probe or through a stepwise reaction of the nanoparticles with the handle followed by aptamer annealing. Nanoparticles functionalized with DNA aptamers targeting histidine tags and VEGF protein had high affinity (EC50s ranging from 3 to 12 nM) and specificity, and were more stable than conventional labels. This protocol for preparation of nanoparticle probes relies solely on commercially available reagents and common equipment, breaking down the barriers to use nanoparticles in biological experiments.
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Affiliation(s)
| | - Torri E Rinker
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA.
| | - Markus Burns
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Sonal S Tonapi
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Rachel P Galimidi
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Deepthi Anumala
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Julia K Robinson
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Joshua S Klein
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Parag Mallick
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
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13
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Sobhy MA, Tehseen M, Takahashi M, Bralić A, De Biasio A, Hamdan SM. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Comput Struct Biotechnol J 2021; 19:4456-4471. [PMID: 34471492 PMCID: PMC8385120 DOI: 10.1016/j.csbj.2021.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an important component of the intricate molecular machinery for DNA replication and repair. FEN1 is a structure-specific 5' nuclease that cleaves nascent single-stranded 5' flaps during the maturation of Okazaki fragments. Here, we review our research primarily applying single-molecule fluorescence to resolve important mechanistic aspects of human FEN1 enzymatic reaction. The methodology presented in this review is aimed as a guide for tackling other biomolecular enzymatic reactions by fluorescence enhancement, quenching, and FRET and their combinations. Using these methods, we followed in real-time the structures of the substrate and product and 5' flap cleavage during catalysis. We illustrate that FEN1 actively bends the substrate to verify its features and continues to mold it to induce a protein disorder-to-order transitioning that controls active site assembly. This mechanism suppresses off-target cleavage of non-cognate substrates and promotes their dissociation with an accuracy that was underestimated from bulk assays. We determined that product release in FEN1 after the 5' flap release occurs in two steps; a brief binding to the bent nicked-product followed by longer binding to the unbent nicked-product before dissociation. Based on our cryo-electron microscopy structure of the human lagging strand replicase bound to FEN1, we propose how this two-step product release mechanism may regulate the final steps during the maturation of Okazaki fragments.
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Affiliation(s)
- Mohamed A Sobhy
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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14
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Fairlamb MS, Whitaker AM, Bain FE, Spies M, Freudenthal BD. Construction of a Three-Color Prism-Based TIRF Microscope to Study the Interactions and Dynamics of Macromolecules. BIOLOGY 2021; 10:biology10070571. [PMID: 34201434 PMCID: PMC8301196 DOI: 10.3390/biology10070571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/05/2023]
Abstract
Simple Summary Prism-based single-molecule total internal reflection fluorescence (prismTIRF) microscopes are excellent tools for studying macromolecular dynamics and interactions. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope using commercially available components with the hope of assisting those who aim to implement TIRF imaging techniques in their laboratory. Abstract Single-molecule total internal reflection fluorescence (TIRF) microscopy allows for the real-time visualization of macromolecular dynamics and complex assembly. Prism-based TIRF microscopes (prismTIRF) are relatively simple to operate and can be easily modulated to fit the needs of a wide variety of experimental applications. While building a prismTIRF microscope without expert assistance can pose a significant challenge, the components needed to build a prismTIRF microscope are relatively affordable and, with some guidance, the assembly can be completed by a determined novice. Here, we provide an easy-to-follow guide for the design, assembly, and operation of a three-color prismTIRF microscope which can be utilized for the study of macromolecular complexes, including the multi-component protein–DNA complexes responsible for DNA repair, replication, and transcription. Our hope is that this article can assist laboratories that aspire to implement single-molecule TIRF techniques, and consequently expand the application of this technology.
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Affiliation(s)
- Max S. Fairlamb
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Amy M. Whitaker
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
| | - Fletcher E. Bain
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; (F.E.B.); (M.S.)
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.S.F.); (A.M.W.)
- Correspondence:
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15
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Hou W, Ma D, He X, Han W, Ma J, Wang H, Xu C, Xie R, Fan Q, Ye F, Hu S, Li M, Lu Y. Subnanometer-Precision Measurements of Transmembrane Motions of Biomolecules in Plasma Membranes Using Quenchers in Extracellular Environment. NANO LETTERS 2021; 21:485-491. [PMID: 33280386 DOI: 10.1021/acs.nanolett.0c03941] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Characterization of biomolecular dynamics at cellular membranes lags far behind that in solutions because of challenges to measure transmembrane trafficking with subnanometer precision. Herein, by introducing nonfluorescent quenchers into extracellular environment of live cells, we adopted Förster resonance energy transfer from one donor to multiple quenchers to measure positional changes of biomolecules in plasma membranes. We demonstrated the method by monitoring flip-flops of individual lipids and by capturing transient states of the host defense peptide LL-37 in plasma membranes. The method was also applied to investigate the interaction of the necroptosis-associated protein MLKL with plasma membranes, showing a few distinct depths of MLKL insertion. Our method is especially powerful to quantitate the dynamics of proteins at the cytosolic leaflets of plasma membranes which are usually not accessible by conventional techniques. The method will find wide applications in the systematic analysis of fundamental cellular processes at plasma membranes.
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Affiliation(s)
- Wenqing Hou
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongfei Ma
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Xiaolong He
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Weijing Han
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Hao Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ruipei Xie
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qihui Fan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuxin Hu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Abrosimova LA, Samsonova AR, Perevyazova TA, Yunusova AK, Artyukh RI, Romanova EA, Zheleznaya LA, Oretskaya TS, Kubareva EA. The Role of Cysteine Residues in the Interaction of Nicking Endonuclease BspD6I with DNA. Mol Biol 2020. [DOI: 10.1134/s0026893320040020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Johansen JS, Kavaliauskas D, Pfeil SH, Blaise M, Cooperman BS, Goldman YE, Thirup SS, Knudsen CR. E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form. Nucleic Acids Res 2019; 46:8641-8650. [PMID: 30107565 PMCID: PMC6144822 DOI: 10.1093/nar/gky697] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 08/07/2018] [Indexed: 11/12/2022] Open
Abstract
According to the traditional view, GTPases act as molecular switches, which cycle between distinct ‘on’ and ‘off’ conformations bound to GTP and GDP, respectively. Translation elongation factor EF-Tu is a GTPase essential for prokaryotic protein synthesis. In its GTP-bound form, EF-Tu delivers aminoacylated tRNAs to the ribosome as a ternary complex. GTP hydrolysis is thought to cause the release of EF-Tu from aminoacyl-tRNA and the ribosome due to a dramatic conformational change following Pi release. Here, the crystal structure of Escherichia coli EF-Tu in complex with a non-hydrolysable GTP analogue (GDPNP) has been determined. Remarkably, the overall conformation of EF-Tu·GDPNP displays the classical, open GDP-bound conformation. This is in accordance with an emerging view that the identity of the bound guanine nucleotide is not ‘locking’ the GTPase in a fixed conformation. Using a single-molecule approach, the conformational dynamics of various ligand-bound forms of EF-Tu were probed in solution by fluorescence resonance energy transfer. The results suggest that EF-Tu, free in solution, may sample a wider set of conformations than the structurally well-defined GTP- and GDP-forms known from previous X-ray crystallographic studies. Only upon binding, as a ternary complex, to the mRNA-programmed ribosome, is the well-known, closed GTP-bound conformation, observed.
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Affiliation(s)
- Jesper S Johansen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Darius Kavaliauskas
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Shawn H Pfeil
- Department of Physics, West Chester University, West Chester, PA 19383, USA
| | - Mickaël Blaise
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yale E Goldman
- Pennsylvania Muscle Institute, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Søren S Thirup
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Charlotte R Knudsen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
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18
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Cai B, Yu L, Sharum SR, Zhang K, Diao J. Single-vesicle measurement of protein-induced membrane tethering. Colloids Surf B Biointerfaces 2019; 177:267-273. [PMID: 30769228 DOI: 10.1016/j.colsurfb.2019.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 12/30/2022]
Abstract
Functions of the proteins involved in membrane tethering, a crucial step in membrane trafficking, remain elusive due to the lack of effective tools to investigate protein-lipid interaction. To address this challenge, we introduce a method to study protein-induced membrane tethering via in vitro reconstitution of lipid vesicles, including detailed steps from the preparation of the PEGylated slides to the imaging of single vesicles. Furthermore, we demonstrate the measurement of protein-vesicle interaction in tethered vesicle pairs using two representative proteins, the cytoplasmic domain of synaptotagmin-1 (C2AB) and α-synuclein. Results from Förster (fluorescence) resonance energy transfer (FRET) reveal that membrane tethering is distinguished from membrane fusion. Single-vesicle measurement also allows for assessment of dose-dependent effects of proteins and ions on membrane tethering. We envision that the continuous development of advanced techniques in the single-vesicle measurement will enable the investigation of complex protein-membrane interactions in live cells or tissues.
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Affiliation(s)
- Bin Cai
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; Research Center for Nano-Biomaterial, Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Luning Yu
- Department of Physics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Savanna R Sharum
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA.
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19
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Umrao S, S A, Jain V, Chakraborty B, Roy R. Smartphone-based kanamycin sensing with ratiometric FRET. RSC Adv 2019; 9:6143-6151. [PMID: 35517283 PMCID: PMC9060919 DOI: 10.1039/c8ra10035g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/12/2019] [Indexed: 11/21/2022] Open
Abstract
Smartphone-based fluorescence detection is a promising avenue for biosensing that can aid on-site analysis. However, quantitative detection with fluorescence in the field has been limited due to challenges with robust excitation and calibration requirements. Here, we show that ratiometric analysis with Förster resonance energy transfer (FRET) between dye pairs on DNA aptamers can enable rapid and sensitive kanamycin detection. Since our detection scheme relies on ligand binding-induced changes in the aptamer tertiary structure, it is limited only by the kinetics of ligand binding to the aptamer. Our FRET-based kanamycin binding aptamer (KBA) sensor displays two linear ranges of 0.05-5 nM (detection limit of 0.18 nM) and 50-900 nM of kanamycin. The aptamer displays high specificity even in the presence of the 'natural' background from milk. By immobilizing the aptamer in the flow cell, our KBA sensor design is also suitable for repeated kanamycin detection. Finally, we show that the ratiometric FRET-based analysis can be implemented on a cheap custom-built smartphone setup. This smartphone-based FRET aptamer scheme detects kanamycin in a linear range of 50-500 nM with a limit of detection (LOD) of 28 nM.
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Affiliation(s)
- Saurabh Umrao
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Anusha S
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Vasundhara Jain
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
- Center for Biosystems Science and Engineering, Indian Institute of Science Bangalore 560012 India
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20
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Moosa MM, Ferreon JC, Ferreon ACM. Single-Molecule FRET Detection of Early-Stage Conformations in α-Synuclein Aggregation. Methods Mol Biol 2019; 1948:221-233. [PMID: 30771181 DOI: 10.1007/978-1-4939-9124-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Misfolding and aggregation of α-synuclein are linked to many neurodegenerative disorders, including Parkinson's and Alzheimer's disease. Despite intense research efforts, detailed structural characterization of early conformational transitions that initiate and drive α-synuclein aggregation remains elusive often due to the low sensitivity and ensemble averaging of commonly used techniques. Single-molecule Förster resonance energy transfer (smFRET) provides unique advantages in detecting minor conformations that initiate protein pathologic aggregation. In this chapter, we describe an smFRET-based method for characterizing early conformational conversions that are responsible for α-synuclein self-assembly and aggregation.
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Affiliation(s)
- Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
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21
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22
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Wagner BD, Arnold AE, Gallant ST, Grinton CR, Locke JK, Mills ND, Snow CA, Uhlig TB, Vessey CN. The polarity sensitivity factor of some fluorescent probe molecules used for studying supramolecular systems and other heterogeneous environments. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fluorescence spectroscopy provides an excellent technique for investigating heterogeneous systems, due to its high sensitivity and the large effect of the local environment on molecular emission. In addition, the use of polarity-sensitive fluorescent probes as guests in supramolecular host–guest inclusion complexes can be exploited in fluorescent sensors. This paper identifies, tabulates, and quantifies a series of useful polarity-sensitive fluorescent probes, with a wide range of polarity-dependent fluorescence responses. The degree of polarity sensitivity is quantified using the polarity sensitivity factor (PSF), developed in our laboratory. In most cases, such polarity-sensitive probes show increased emission as the local polarity is decreased (PSF > 1); 10 such probes are described. However, less commonly, “reverse polarity dependence” can occur in which probe emission decreases with decreasing polarity (PSF < 1); four such probes are described. The mechanism for the observed polarity-induced fluorescence changes will also be discussed in selected representative cases. The purpose of this paper is to present details on a broad arsenal of polarity-sensitive fluorescence probes with varying properties, with potentially useful applications in the study of heterogeneous systems, including inclusion phenomena, and in practical applications such as fluorescent sensors, which will be useful to researchers studying supramolecular and other heterogeneous systems using fluorescence spectroscopy.
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Affiliation(s)
- Brian D. Wagner
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Amy E. Arnold
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Spencer T. Gallant
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Carmen R. Grinton
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Julia K. Locke
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Natasha D. Mills
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Carrie A. Snow
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Timara B. Uhlig
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
| | - Christen N. Vessey
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1E 1Z5, Canada
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23
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Site-selective installation of an electrophilic handle on proteins for bioconjugation. Bioorg Med Chem 2018; 26:3060-3064. [DOI: 10.1016/j.bmc.2018.02.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 02/02/2023]
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24
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Ma JB, Jia Q, Xu CH, Li JH, Huang XY, Ma DF, Li M, Xi XG, Lu Y. Asynchrony of Base-Pair Breaking and Nucleotide Releasing of Helicases in DNA Unwinding. J Phys Chem B 2018; 122:5790-5796. [PMID: 29733603 DOI: 10.1021/acs.jpcb.8b01470] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Helicases harness the energy of nucleotide triphosphate hydrolysis to unwind double-stranded DNA (dsDNA) in discrete steps. In spite of intensive studies, the mechanism of stepping is still poorly understood. Here, we applied single-molecule fluorescent resonant energy transfer to characterize the stepping of two nonring helicases, Escherichia coli RecQ ( E. coli RecQ) and Saccharomyces cerevisiae Pif1 (ScPif1). Our data showed that when forked dsDNA with free overhangs are used as substrates, both E. coli RecQ and ScPif1 unwind the dsDNA in nonuniform steps that distribute over broad ranges. When tension is exerted on the overhangs, the overall profile of the step-size distribution of ScPif1 is narrowed, whereas that of E. coli RecQ remains unchanged. Moreover, the measured step sizes of the both helicases concentrate on integral multiples of a half base pair. We propose a universal stepping mechanism, in which a helicase breaks one base pair at a time and sequesters the nascent nucleotides and then releases them after a random number of base-pair breaking events. The mechanism can interpret the observed unwinding patterns quantitatively and provides a general view of the helicase activity.
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Affiliation(s)
- Jian-Bing Ma
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chun-Hua Xu
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China
| | - Jing-Hua Li
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China
| | - Xing-Yuan Huang
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Dong-Fei Ma
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.,School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xu-Guang Xi
- College of Life Sciences , Northwest A&F University , Yangling 712100 , Shaanxi , China.,LBPA, ENS de Cachan , CNRS, Université Paris-Saclay , Cachan F-94235 , France
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China
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25
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Sengupta B, Acharyya A, Sen P. Elucidation of the local dynamics of domain-III of human serum albumin over the ps-μs time regime using a new fluorescent label. Phys Chem Chem Phys 2018; 18:28548-28555. [PMID: 27711622 DOI: 10.1039/c6cp05743h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ps-μs dynamics of domain-III of human serum albumin (HSA) has been investigated using a new fluorescent marker selectively labeled to the Tyr-411 residue. The location of the marker has been confirmed using Förster resonance energy transfer (FRET) study. Steady state, time-resolved and single molecular level fluorescence techniques have been employed to understand the dynamics within the domain-III of HSA. It is found that solvent reorganization dynamics in domain-III is 1.7 times faster than that in domain-I. The timescale of the local rotational dynamics of domain-III is found to be 2.3 times faster than that of domain-I. Fluorescence correlation spectroscopic experiments reveal that domain-III of HSA has more conformational flexibility than domain-I. Together, the results deliver useful details of the local environment around the domain-III of HSA, which have not been explored earlier, mainly because of a lack of a suitable fluorescent marker for domain-III. The newly synthesized probe serves well as a site specific fluorescent marker for HSA, and can be used for further investigation of the ligand binding properties and enzymatic activity of domain-III of HSA.
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Affiliation(s)
- Bhaswati Sengupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208 016, UP, India.
| | - Arusha Acharyya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208 016, UP, India.
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208 016, UP, India.
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26
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van den Wildenberg SMJL, Prevo B, Peterman EJG. A Brief Introduction to Single-Molecule Fluorescence Methods. Methods Mol Biol 2018; 1665:93-113. [PMID: 28940065 DOI: 10.1007/978-1-4939-7271-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.
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Affiliation(s)
- Siet M J L van den Wildenberg
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
- Équipe de Volcanologie, Observatoire de Physique de Globe, Clermant-Ferrand, France
| | - Bram Prevo
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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27
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Kim JM, Seong BL. Highly chromophoric Cy5-methionine for N-terminal fluorescent tagging of proteins in eukaryotic translation systems. Sci Rep 2017; 7:11642. [PMID: 28912467 PMCID: PMC5599622 DOI: 10.1038/s41598-017-12028-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022] Open
Abstract
Despite significant advances on fluorescent labeling of target proteins to study their structural dynamics and function, there has been need for labeling with high quantum yield ensuring high sensitivity and selectivity without sacrificing the biological function of the protein. Here as a technical advancement over non-canonical amino acid incorporation, we provided a conceptual design of the N-terminal fluorescent tagging of proteins. Cy5-labeled methionine (Cy5-Met) was chemically synthesized, and then the purified Cy5-Met was coupled with synthetic human initiator tRNA by methionine tRNA synthetase. Cy5-Met-initiator tRNA (Cy5-Met-tRNAi) was purified and transfected into HeLa cells with HIV-Tat plasmid, resulting in an efficient production of Cy5-labeled HIV-Tat protein. Based on the universal requirement in translational initiation, the approach provides co-translational incorporation of N-terminal probe to a repertoire of proteins in the eukaryote system. This methodology has potential utility in the single molecule analysis of human proteins in vitro and in vivo for addressing to their complex biological structural and functional dynamics.
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Affiliation(s)
- Jung Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea. .,Vaccine Translational Research Center, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea.
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Blouin S, Craggs TD, Lafontaine DA, Penedo JC. Functional Studies of DNA-Protein Interactions Using FRET Techniques. Methods Mol Biol 2016; 1334:115-41. [PMID: 26404147 DOI: 10.1007/978-1-4939-2877-4_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Protein-DNA interactions underpin life and play key roles in all cellular processes and functions including DNA transcription, packaging, replication, and repair. Identifying and examining the nature of these interactions is therefore a crucial prerequisite to understand the molecular basis of how these fundamental processes take place. The application of fluorescence techniques and in particular fluorescence resonance energy transfer (FRET) to provide structural and kinetic information has experienced a stunning growth during the past decade. This has been mostly promoted by new advances in the preparation of dye-labeled nucleic acids and proteins and in optical sensitivity, where its implementation at the level of individual molecules has opened a new biophysical frontier. Nowadays, the application of FRET-based techniques to the analysis of protein-DNA interactions spans from the classical steady-state and time-resolved methods averaging over large ensembles to the analysis of distances, conformational changes, and enzymatic reactions in individual protein-DNA complexes. This chapter introduces the practical aspects of applying these methods for the study of protein-DNA interactions.
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Affiliation(s)
- Simon Blouin
- Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Daniel A Lafontaine
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard de L'Université, Sherbrooke, QC, Canada, J1K 2R1.
| | - J Carlos Penedo
- School of Physics and Astronomy, University of St. Andrews, St. Andrews, UK
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29
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Lee S, Jang Y, Lee SJ, Hohng S. Single-Molecule Multicolor FRET Assay for Studying Structural Dynamics of Biomolecules. Methods Enzymol 2016; 581:461-486. [DOI: 10.1016/bs.mie.2016.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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30
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Pereira TM, Vitório F, Amaral RC, Zanoni KPS, Murakami Iha NY, Kümmerle AE. Microwave-assisted synthesis and photophysical studies of novel fluorescent N-acylhydrazone and semicarbazone-7-OH-coumarin dyes. NEW J CHEM 2016. [DOI: 10.1039/c6nj01532h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Emissive 7-OH-coumarins were synthesized by a microwave-assisted protocol and spectral changes were induced after conformational changes in low polarity media.
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Affiliation(s)
- Thiago Moreira Pereira
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory)
- Departament of Chemistry
- Universidade Federal Rural do Rio de Janeiro
- Rio de Janeiro
- Brazil
| | - Felipe Vitório
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory)
- Departament of Chemistry
- Universidade Federal Rural do Rio de Janeiro
- Rio de Janeiro
- Brazil
| | - Ronaldo Costa Amaral
- Laboratory of Photochemistry and Energy Conversion
- Departamento de Química Fundamental
- Instituto de Química
- Universidade de São Paulo
- São Paulo – SP 05508-000
| | - Kassio Papi Silva Zanoni
- Laboratory of Photochemistry and Energy Conversion
- Departamento de Química Fundamental
- Instituto de Química
- Universidade de São Paulo
- São Paulo – SP 05508-000
| | - Neyde Yukie Murakami Iha
- Laboratory of Photochemistry and Energy Conversion
- Departamento de Química Fundamental
- Instituto de Química
- Universidade de São Paulo
- São Paulo – SP 05508-000
| | - Arthur Eugen Kümmerle
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory)
- Departament of Chemistry
- Universidade Federal Rural do Rio de Janeiro
- Rio de Janeiro
- Brazil
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31
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Kapanidis A, Majumdar D, Heilemann M, Nir E, Weiss S. Alternating Laser Excitation for Solution-Based Single-Molecule FRET. Cold Spring Harb Protoc 2015; 2015:979-987. [PMID: 26527772 DOI: 10.1101/pdb.top086405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) has been widely applied to the study of fluorescently labeled biomolecules on surfaces and in solution. Sorting single molecules based on fluorescent dye stoichiometry provides one with further layers of information and also enables "filtering" of unwanted molecules from the analysis. We accomplish this sorting by using alternating laser excitation (ALEX) in combination with smFRET measurements; here we describe the implementation of these methodologies for the study of biomolecules in solution.
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32
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Watching conformational dynamics of ABC transporters with single-molecule tools. Biochem Soc Trans 2015; 43:1041-7. [DOI: 10.1042/bst20150140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
ATP-binding cassette (ABC) transporters play crucial roles in cellular processes, such as nutrient uptake, drug resistance, cell-volume regulation and others. Despite their importance, all proposed molecular models for transport are based on indirect evidence, i.e. functional interpretation of static crystal structures and ensemble measurements of function and structure. Thus, classical biophysical and biochemical techniques do not readily visualize dynamic structural changes. We recently started to use single-molecule fluorescence techniques to study conformational states and changes of ABC transporters in vitro, in order to observe directly how the different steps during transport are coordinated. This review summarizes our scientific strategy and some of the key experimental advances that allowed the substrate-binding mechanism of prokaryotic ABC importers and the transport cycle to be explored. The conformational states and transitions of ABC-associated substrate-binding domains (SBDs) were visualized with single-molecule FRET, permitting a direct correlation of structural and kinetic information of SBDs. We also delineated the different steps of the transport cycle. Since information in such assays are restricted by proper labelling of proteins with fluorescent dyes, we present a simple approach to increase the amount of protein with FRET information based on non-specific interactions between a dye and the size-exclusion chromatography (SEC) column material used for final purification.
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33
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Sustarsic M, Kapanidis AN. Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells. Curr Opin Struct Biol 2015; 34:52-9. [DOI: 10.1016/j.sbi.2015.07.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 07/02/2015] [Indexed: 12/29/2022]
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35
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Fili N, Toseland CP. Fluorescence and labelling: how to choose and what to do. ACTA ACUST UNITED AC 2014; 105:1-24. [PMID: 25095988 DOI: 10.1007/978-3-0348-0856-9_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This chapter provides an overview of fluorescent labelling of different reactants related to the biochemistry of motor proteins. The fluorescent properties of different labels and the advantages and disadvantages of the labelling methods are discussed. This will allow for a careful selection of fluorescent proteins for different applications relating to motor proteins.
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Affiliation(s)
- Natalia Fili
- Department of Cellular Physiology, Ludwig-Maximilians-Universität München, Schillerstrasse. 44, 80336, Munich, Germany,
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36
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Prevo B, Peterman EJG. Förster resonance energy transfer and kinesin motor proteins. Chem Soc Rev 2014; 43:1144-55. [PMID: 24071719 DOI: 10.1039/c3cs60292c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Förster Resonance Energy Transfer (FRET) is the phenomenon of non-radiative transfer of electronic excitations from a donor fluorophore to an acceptor, mediated by electronic dipole-dipole coupling. The transfer rate and, as a consequence, efficiency depend non-linearly on the distance between the donor and the acceptor. FRET efficiency can thus be used as an effective and accurate reporter of distance between two fluorophores and changes thereof. Over the last 50 years or so, FRET has been used as a spectroscopic ruler to measure conformations and conformational changes of biomolecules. More recently, FRET has been combined with microscopy, ultimately allowing measurement of FRET between a single donor and a single acceptor pair. In this review, we will explain the physical foundations of FRET and how FRET can be applied to biomolecules. We will highlight the power of the different FRET approaches by focusing on its application to the motor protein kinesin, which undergoes several conformational changes driven by enzymatic action, that ultimately result in unidirectional motion along microtubule filaments, driving active transport in the cell. Single-molecule and ensemble FRET studies of different aspects of kinesin have provided numerous insights into the complex chemomechanical mechanism of this fascinating protein.
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Affiliation(s)
- Bram Prevo
- Department of Physics and Astronomy and LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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37
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Murr PJ, Rauscher MS, Tremmel A, Schardt M, Koch AW. Fluorescence imaging of viscous materials in the ultraviolet-visible wavelength range. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:085111. [PMID: 25173316 DOI: 10.1063/1.4892477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper presents an approach of an innovative measurement principle for the quality control of viscous materials during a manufacturing process based on fluorescence imaging. The main contribution to the state of the art provided by this measurement system is that three equal fluorescence images of a static or moving viscous object are available in different optical paths. The independent images are obtained by two beam splitters which are connected in series. Based on these images, it is possible to evaluate each image separately. In our case, three optical bandpass filters with different center wavelengths of 405 nm, 420 nm, and 440 nm were used to filter the separate fluorescence images. The developed system is useable for the detection of impurities in the micrometer range. Further, incorrect mixing ratios of particular components and wrong single components in the viscous materials can be detected with the setup. Moreover, it is possible to realize static and dynamic measurements. In this case the maximum speed of the objects was 0.2 m/s for the dynamic measurements. Advantages of this measurement setup are the universality due to the use of optical standard components, the small dimension and the opportunity to integrate it easily into ongoing processes. In addition, the measurement system works on a non-contact basis. Thus, the expense for maintenance is at a very low level compared to currently available measurement setups for the investigated application. Furthermore, the setup provides for the first time a simultaneous analysis of more than one component and the detection of impurities concerning their nature and size in a manufacturing process.
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Affiliation(s)
- Patrik J Murr
- Institute for Measurement Systems and Sensor Technology, Technische Universität München, Theresienstraße 90, 80333 München, Germany
| | - Markus S Rauscher
- Institute for Measurement Systems and Sensor Technology, Technische Universität München, Theresienstraße 90, 80333 München, Germany
| | - Anton Tremmel
- Institute for Measurement Systems and Sensor Technology, Technische Universität München, Theresienstraße 90, 80333 München, Germany
| | - Michael Schardt
- Institute for Measurement Systems and Sensor Technology, Technische Universität München, Theresienstraße 90, 80333 München, Germany
| | - Alexander W Koch
- Institute for Measurement Systems and Sensor Technology, Technische Universität München, Theresienstraße 90, 80333 München, Germany
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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39
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Alemán E, de Silva C, Patrick EM, Musier-Forsyth K, Rueda D. Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle. J Phys Chem Lett 2014; 5:777-781. [PMID: 24803990 PMCID: PMC3985717 DOI: 10.1021/jz4025832] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/06/2014] [Indexed: 05/25/2023]
Abstract
Fluorescent nucleotide analogues, such as 2-aminopurine (2AP) and pyrrolo-C (PyC), have been extensively used to study nucleic acid local conformational dynamics in bulk experiments. Here we present a proof-of-principle approach using 2AP and PyC fluorescence at the single-molecule level. Our data show that ssDNA, dsDNA, or RNA containing both 2AP and PyC can be monitored using single-molecule fluorescence and a click chemistry immobilization method. We demonstrate that this approach can be used to monitor DNA and RNA in real time. This is the first reported assay using fluorescent nucleotide analogs at the single-molecule level. We anticipate that single 2AP or PyC fluorescence will have numerous applications in studies of DNA and RNA, including protein-induced base-flipping dynamics in protein-nucleic acid complexes.
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Affiliation(s)
- Elvin
A. Alemán
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Chamaree de Silva
- Department
of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Eric M. Patrick
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Karin Musier-Forsyth
- Department
of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - David Rueda
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
- Department of Medicine, Section of
Virology and Single Molecule Imaging Group,
MRC Clinical Sciences Center, Imperial College, Du Cane Road, London W12 0NN, United
Kingdom
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40
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Biomolecular dynamics and binding studies in the living cell. Phys Life Rev 2014; 11:1-30. [DOI: 10.1016/j.plrev.2013.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022]
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41
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Grußmayer KS, Kurz A, Herten DP. Single-Molecule Studies on the Label Number Distribution of Fluorescent Markers. Chemphyschem 2014; 15:734-42. [DOI: 10.1002/cphc.201300840] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/14/2014] [Indexed: 01/17/2023]
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42
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Heller I, Sitters G, Broekmans OD, Biebricher AS, Wuite GJL, Peterman EJG. Mobility analysis of super-resolved proteins on optically stretched DNA: comparing imaging techniques and parameters. Chemphyschem 2014; 15:727-33. [PMID: 24470208 DOI: 10.1002/cphc.201300813] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 12/04/2013] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy in conjunction with optical tweezers is well suited to the study of protein mobility on DNA. Here, we evaluate the benefits and drawbacks of super-resolution and conventional imaging techniques for the analysis of one-dimensional (1D) protein diffusion as commonly observed for DNA-binding proteins. In particular, we demonstrate the visualization of DNA-bound proteins using wide-field, confocal, and stimulated emission depletion (STED) microscopy. We review the suitability of these techniques to conditions of high protein density, and quantify their performance in terms of spatial and temporal resolution. Tracking proteins on DNA forces one to make a choice between localization precision on the one hand, and the number and rate of localizations on the other, by altering imaging modality, excitation intensity, and acquisition rate. Using simulated diffusion data, we quantify the effect of these imaging conditions on the accuracy of 1D diffusion analysis. In addition, we consider the case of diffusion confined between local roadblocks, a case particularly relevant for proteins bound to DNA. Together these results provide guidelines that can assist in judiciously optimizing the experimental conditions required for the analysis of protein mobility on DNA and other 1D systems.
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Affiliation(s)
- Iddo Heller
- Department of Physics and Astronomy and LaserLab Amsterdam, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam (The Netherlands)
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43
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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Abstract
Single-molecule spectroscopy has developed into a widely used method for probing the structure, dynamics, and mechanisms of biomolecular systems, especially in combination with Förster resonance energy transfer (FRET). In this introductory tutorial, essential concepts and methods will be outlined, from the FRET process and the basic considerations for sample preparation and instrumentation to some key elements of data analysis and photon statistics. Different approaches for obtaining dynamic information over a wide range of timescales will be explained and illustrated with examples, including the quantitative analysis of FRET efficiency histograms, correlation spectroscopy, fluorescence trajectories, and microfluidic mixing.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057
Zurich, Switzerland
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45
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Chatterjee S, Sengupta K, Bhattacharyya S, Nandi A, Samanta S, Mittra K, Dey A. Photophysical and ligand binding studies of metalloporphyrins bearing hydrophilic distal superstructure. J PORPHYR PHTHALOCYA 2013. [DOI: 10.1142/s1088424613500119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
UV-vis absorption and emission studies on zinc and iron porphyrin complexes bearing H-bonding distal superstructures have been performed in two different organic solvents- tetrahydrofuran (THF) (coordinating) and dichloromethane (DCM) (non-coordinating). Quantum yields and lifetimes have been measured for these complexes which are in good agreement with the other reported metalloporphyrins. Binding affinities with anionic ligands such as N3- , CN- , S-2 , F- were monitored for these two complexes in aqueous media and the respective binding constant values were calculated. The Zn complex shows more selectivity towards cyanide while the Fe complex shows more selectivity towards azide.
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Affiliation(s)
- Sudipta Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kushal Sengupta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sohini Bhattacharyya
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Amrit Nandi
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Subhra Samanta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kaustuv Mittra
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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46
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Toseland CP. Fluorescent labeling and modification of proteins. J Chem Biol 2013; 6:85-95. [PMID: 24432126 PMCID: PMC3691395 DOI: 10.1007/s12154-013-0094-5] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/01/2013] [Indexed: 10/27/2022] Open
Abstract
This review provides an outline for fluorescent labeling of proteins. Fluorescent assays are very diverse providing the most sensitive and robust methods for observing biological processes. Here, different types of labels and methods of attachment are discussed in combination with their fluorescent properties. The advantages and disadvantages of these different methods are highlighted, allowing the careful selection for different applications, ranging from ensemble spectroscopy assays through to single-molecule measurements.
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Affiliation(s)
- Christopher P. Toseland
- Institut für Zelluläre Physiologie and Center for NanoScience (CeNS), Physiologisches Institut, Ludwig Maximilians Universität, Munich, 80336 Germany
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47
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Schäfer P, van de Linde S, Lehmann J, Sauer M, Doose S. Methylene Blue- and Thiol-Based Oxygen Depletion for Super-Resolution Imaging. Anal Chem 2013; 85:3393-400. [DOI: 10.1021/ac400035k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Philip Schäfer
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Sebastian van de Linde
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Julian Lehmann
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
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48
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Introduction of a unique tryptophan residue into various positions of Bacillus licheniformis DnaK. Int J Biol Macromol 2012; 52:231-43. [PMID: 23085489 DOI: 10.1016/j.ijbiomac.2012.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/08/2012] [Accepted: 10/10/2012] [Indexed: 11/22/2022]
Abstract
Site-directed mutagenesis together with biochemical and biophysical techniques were used to probe effects of single-tryptophan-incorporated mutations on a bacterial molecular chaperone, Bacillus licheniformis DnaK (BlDnaK). Specifically, five phenylalanine residues (Phe(120), Phe(174), Phe(186), Phe(378) and Phe(396)) of BlDnaK were individually replaced by single tryptophans, thus creating site-specific probes for the fluorescence analysis of the protein. The steady-state ATPase activity for BlDnaK, F120W, F174W, F186W, F378W, and F396W was determined to be 76.01, 52.82, 25.32, 53.31, 58.84, and 47.53 nmol Pi/min/mg, respectively. Complementation test revealed that the single mutation at codons 120, 186, and 378 of the dnaK gene still allowed an Escherichia coli dnaK756-Ts strain to grow at a stringent temperature of 44°C. Simultaneous addition of co-chaperones and NR-peptide did not synergistically stimulate the ATPase activity of F174W and F396W, and these two proteins were unable to assist the refolding of GdnHCl-denatured luciferase. The heat-induced denaturation of all variants could be fitted adequately to a three-state model, in agreement with the observation for the wild-type protein. By CD spectral analysis, GdnHCl-induced unfolding transition for BlDnaK was 1.51 M corresponding to ΔG(N-U) of 1.69 kcal/mol; however, the transitions for mutant proteins were 1.07-1.55 M equivalent to ΔG(N-U) of 0.94-2.93 kcal/mol. The emission maximum of single-tryptophan-incorporated variants was in the range of 333.2-335.8 nm. Acrylamide quenching analysis showed that the mutant proteins had a dynamic quenching constant of 3.0-4.2 M(-1). Taken together, these results suggest that the molecular properties of BlDnaK have been significantly changed upon the individual replacement of selected phenylalanine residues by tryptophan.
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Zadran S, Standley S, Wong K, Otiniano E, Amighi A, Baudry M. Fluorescence resonance energy transfer (FRET)-based biosensors: visualizing cellular dynamics and bioenergetics. Appl Microbiol Biotechnol 2012; 96:895-902. [PMID: 23053099 DOI: 10.1007/s00253-012-4449-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
Abstract
Förster (or fluorescence) resonance energy transfer (FRET) is a process involving the radiation-less transfer of energy from a "donor" fluorophore to an "acceptor" fluorophore. FRET technology enables the quantitative analysis of molecular dynamics in biophysics and in molecular biology, such as the monitoring of protein-protein interactions, protein-DNA interactions, and protein conformational changes. FRET-based biosensors have been utilized to monitor cellular dynamics not only in heterogeneous cellular populations, but also at the single-cell level in real time. Lately, applications of FRET-based biosensors range from basic biological to biomedical disciplines. Despite the diverse applications of FRET, FRET-based sensors still face many challenges. There is an increasing need for higher fluorescence resolution and improved specificity of FRET biosensors. Additionally, as more FRET-based technologies extend to medical diagnostics, the affordability of FRET reagents becomes a significant concern. Here, we will review current advances and limitations of FRET-based biosensor technology and discuss future FRET applications.
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Affiliation(s)
- Sohila Zadran
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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Tynan CJ, Clarke DT, Coles BC, Rolfe DJ, Martin-Fernandez ML, Webb SED. Multicolour single molecule imaging in cells with near infra-red dyes. PLoS One 2012; 7:e36265. [PMID: 22558412 PMCID: PMC3338497 DOI: 10.1371/journal.pone.0036265] [Citation(s) in RCA: 25] [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: 02/14/2012] [Accepted: 04/04/2012] [Indexed: 11/20/2022] Open
Abstract
Background The autofluorescence background of biological samples impedes the detection of single molecules when imaging. The most common method of reducing the background is to use evanescent field excitation, which is incompatible with imaging beyond the surface of biological samples. An alternative would be to use probes that can be excited in the near infra-red region of the spectrum, where autofluorescence is low. Such probes could also increase the number of labels that can be imaged in multicolour single molecule microscopes. Despite being widely used in ensemble imaging, there is a currently a shortage of information available for selecting appropriate commercial near infra-red dyes for single molecule work. It is therefore important to characterise available near infra-red dyes relevant to multicolour single molecule imaging. Methodology/Principal Findings A range of commercially available near infra-red dyes compatible with multi-colour imaging was screened to find the brightest and most photostable candidates. Image series of immobilised samples of the brightest dyes (Alexa 700, IRDye 700DX, Alexa 790 and IRDye 800CW) were analysed to obtain the mean intensity of single dye molecules, their photobleaching rates and long period blinking kinetics. Using the optimum dye pair, we have demonstrated for the first time widefield, multi-colour, near infra-red single molecule imaging using a supercontinuum light source in MCF-7 cells. Conclusions/Significance We have demonstrated that near infra-red dyes can be used to avoid autofluorescence background in samples where restricting the illumination volume of visible light fails or is inappropriate. We have also shown that supercontinuum sources are suited to single molecule multicolour imaging throughout the 470–1000 nm range. Our measurements of near infra-red dye properties will enable others to select optimal dyes for single molecule imaging.
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Affiliation(s)
- Christopher J. Tynan
- Central Laser Facility, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - David T. Clarke
- Central Laser Facility, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - Benjamin C. Coles
- Central Laser Facility, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - Daniel J. Rolfe
- Central Laser Facility, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - Marisa L. Martin-Fernandez
- Central Laser Facility, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - Stephen E. D. Webb
- Central Laser Facility, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
- * E-mail:
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