151
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DeHaven AC, Norden IS, Hoskins AA. Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:683-701. [PMID: 27198613 PMCID: PMC4990488 DOI: 10.1002/wrna.1358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/20/2016] [Accepted: 04/04/2016] [Indexed: 11/06/2022]
Abstract
The process of removing intronic sequences from a precursor to messenger RNA (pre-mRNA) to yield a mature mRNA transcript via splicing is an integral step in eukaryotic gene expression. Splicing is carried out by a cellular nanomachine called the spliceosome that is composed of RNA components and dozens of proteins. Despite decades of study, many fundamentals of spliceosome function have remained elusive. Recent developments in single-molecule fluorescence microscopy have afforded new tools to better probe the spliceosome and the complex, dynamic process of splicing by direct observation of single molecules. These cutting-edge technologies enable investigators to monitor the dynamics of specific splicing components, whole spliceosomes, and even cotranscriptional splicing within living cells. WIREs RNA 2016, 7:683-701. doi: 10.1002/wrna.1358 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alexander C. DeHaven
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Ian S. Norden
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Aaron A. Hoskins
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
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152
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Ingargiola A, Lerner E, Chung S, Weiss S, Michalet X. FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET. PLoS One 2016; 11:e0160716. [PMID: 27532626 PMCID: PMC4988647 DOI: 10.1371/journal.pone.0160716] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/22/2016] [Indexed: 12/04/2022] Open
Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community.
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Affiliation(s)
- Antonino Ingargiola
- Dept. Chemistry and Biochemistry, Univ. of California Los Angeles, Los Angeles, CA, United States of America
- * E-mail:
| | - Eitan Lerner
- Dept. Chemistry and Biochemistry, Univ. of California Los Angeles, Los Angeles, CA, United States of America
| | - SangYoon Chung
- Dept. Chemistry and Biochemistry, Univ. of California Los Angeles, Los Angeles, CA, United States of America
| | - Shimon Weiss
- Dept. Chemistry and Biochemistry, Univ. of California Los Angeles, Los Angeles, CA, United States of America
| | - Xavier Michalet
- Dept. Chemistry and Biochemistry, Univ. of California Los Angeles, Los Angeles, CA, United States of America
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153
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Farooq S, Hohlbein J. Camera-based single-molecule FRET detection with improved time resolution. Phys Chem Chem Phys 2016; 17:27862-72. [PMID: 26439729 DOI: 10.1039/c5cp04137f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The achievable time resolution of camera-based single-molecule detection is often limited by the frame rate of the camera. Especially in experiments utilizing single-molecule Förster resonance energy transfer (smFRET) to probe conformational dynamics of biomolecules, increasing the frame rate by either pixel-binning or cropping the field of view decreases the number of molecules that can be monitored simultaneously. Here, we present a generalised excitation scheme termed stroboscopic alternating-laser excitation (sALEX) that significantly improves the time resolution without sacrificing highly parallelised detection in total internal reflection fluorescence (TIRF) microscopy. In addition, we adapt a technique known from diffusion-based confocal microscopy to analyse the complex shape of FRET efficiency histograms. We apply both sALEX and dynamic probability distribution analysis (dPDA) to resolve conformational dynamics of interconverting DNA hairpins in the millisecond time range.
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Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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154
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Pozzi N, Bystranowska D, Zuo X, Di Cera E. Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy. J Biol Chem 2016; 291:18107-16. [PMID: 27435675 DOI: 10.1074/jbc.m116.738310] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 01/29/2023] Open
Abstract
The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr(93) in kringle-1 onto Trp(547) in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. The open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.
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Affiliation(s)
- Nicola Pozzi
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
| | - Dominika Bystranowska
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
| | - Xiaobing Zuo
- the X-Ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
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155
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Lerner E, Ploetz E, Hohlbein J, Cordes T, Weiss S. A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET). J Phys Chem B 2016; 120:6401-10. [PMID: 27184889 PMCID: PMC4939467 DOI: 10.1021/acs.jpcb.6b03692] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Single-molecule,
protein-induced fluorescence enhancement (PIFE)
serves as a molecular ruler at molecular distances inaccessible to
other spectroscopic rulers such as Förster-type resonance energy
transfer (FRET) or photoinduced electron transfer. In order to provide
two simultaneous measurements of two distances on different molecular
length scales for the analysis of macromolecular complexes, we and
others recently combined measurements of PIFE and FRET (PIFE-FRET)
on the single molecule level. PIFE relies on steric hindrance of the
fluorophore Cy3, which is covalently attached to a biomolecule of
interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate.
In this work, we provide a theoretical framework that accounts for
relevant photophysical and kinetic parameters of PIFE-FRET, show how
this framework allows the extraction of the fold-decrease in isomerization
mobility from experimental data, and show how these results provide
information on changes in the accessible volume of Cy3. The utility
of this model is then demonstrated for experimental results on PIFE-FRET
measurement of different protein–DNA interactions. The proposed
model and extracted parameters could serve as a benchmark to allow
quantitative comparison of PIFE effects in different biological systems.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Evelyn Ploetz
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research , Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.,Microspectroscopy Centre, Wageningen University and Research , Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
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156
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Plochowietz A, El-Sagheer AH, Brown T, Kapanidis AN. Stable end-sealed DNA as robust nano-rulers for in vivo single-molecule fluorescence. Chem Sci 2016; 7:4418-4422. [PMID: 30155088 PMCID: PMC6014160 DOI: 10.1039/c6sc00639f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/21/2016] [Indexed: 11/24/2022] Open
Abstract
Protected DNA standards with chemically linked ends were synthesized as robust in vivo nano-rulers for smFRET studies.
Single-molecule fluorescence and Förster resonance energy transfer (smFRET) are important tools for studying molecular heterogeneity, cellular organization, and protein structure in living cells. However, in vivo smFRET studies are still very challenging, and a standardized approach for robust in vivo smFRET measurements is still missing. Here, we synthesized protected DNAs with chemically linked ends as robust in vivo nano-rulers. We efficiently internalized doubly-labeled end-sealed DNA standards into live bacteria using electroporation and obtained stable and long-lasting smFRET signatures. Single-molecule fluorescence signals could be extended to ∼1 min by studying multi-fluorophore DNA standards. The high stability of protected DNA standards offers a general approach to evaluate single-molecule fluorescence and FRET signals, autofluorescence background, and fluorophore density, and hence, quality check the workflow for studying single-molecule trajectories and conformational dynamics of biomolecules in vivo.
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Affiliation(s)
- A Plochowietz
- Department of Physics , University of Oxford , Clarendon Laboratory , Parks Road , Oxford , OX1 3PU , UK . ;
| | - A H El-Sagheer
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK.,Chemistry Branch , Department of Chemistry , Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - T Brown
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK
| | - A N Kapanidis
- Department of Physics , University of Oxford , Clarendon Laboratory , Parks Road , Oxford , OX1 3PU , UK . ;
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157
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Characterizing 3D RNA structure by single molecule FRET. Methods 2016; 103:57-67. [PMID: 26853327 DOI: 10.1016/j.ymeth.2016.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/26/2022] Open
Abstract
The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model.
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158
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Pozzi N, Chen Z, Di Cera E. How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J Biol Chem 2016; 291:6071-82. [PMID: 26763231 DOI: 10.1074/jbc.m115.700401] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 01/11/2023] Open
Abstract
A flexible linker (Lnk2) composed of 26 amino acids connects kringle-1 to kringle-2 in the coagulation factor prothrombin. Recent studies point to Lnk2 as a key determinant of the structure and function of this zymogen. Using a combination of mutagenesis, structural biology, and single molecule spectroscopy, we show how Lnk2 influences activation and conformational plasticity of prothrombin. Scrambling the sequence of Lnk2 is inconsequential on activation, and so is extension by as many as 22 residues. On the other hand, below a critical length of 15 residues, the rate of prothrombin activation increases (10-fold) in the absence of cofactor Va and decreases (3-fold) in the presence of cofactor. Furthermore, activation by prothrombinase takes place without preference along the prethrombin-2 (cleavage at Arg(271) first) or meizothrombin (cleavage at Arg(320) first) pathways. Notably, these transitions in the rate and pathway of activation require the presence of phospholipids, pointing to an important physiological role for Lnk2 when prothrombin is anchored to the membrane. Two new crystal structures of prothrombin lacking 22 (ProTΔ146-167) or 14 (ProTΔ154-167) residues of Lnk2 document striking conformational rearrangements of domains located across this linker. FRET measurements of freely diffusing single molecules prove that these structural transitions are genuine properties of the zymogen in solution. These findings support a molecular model of prothrombin activation where Lnk2 presents the sites of cleavage at Arg(271) and Arg(320) to factor Xa in different orientations by pivoting the C-terminal kringle-2/protease domain pair on the N-terminal Gla domain/kringle-1 pair anchored to the membrane.
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Affiliation(s)
- Nicola Pozzi
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Zhiwei Chen
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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159
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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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160
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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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161
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Ju MS, Na JH, Yu YG, Kim JY, Jeong C, Jung ST. Structural consequences of aglycosylated IgG Fc variants evolved for FcγRI binding. Mol Immunol 2015; 67:350-6. [DOI: 10.1016/j.molimm.2015.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/04/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
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162
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Hildebrandt LL, Preus S, Birkedal V. Quantitative single molecule FRET efficiencies using TIRF microscopy. Faraday Discuss 2015; 184:131-42. [PMID: 26416760 DOI: 10.1039/c5fd00100e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Förster resonance energy transfer (FRET) microscopy at the single molecule level has the potential to yield information on intra and intermolecular distances within the 2-10 nm range of molecules or molecular complexes that undergo frequent conformation changes. A pre-requirement for obtaining accurate distance information is to determine quantitative instrument independent FRET efficiency values. Here, we applied and evaluated a procedure to determine quantitative FRET efficiencies directly from individual fluorescence time traces of surface immobilized DNA molecules without the need for external calibrants. To probe the robustness of the approach over a wide range of FRET efficiencies we used a set of doubly labelled double stranded DNA samples, where the acceptor position was varied systematically. Interestingly, we found that fluorescence contributions arising from direct acceptor excitation following donor excitation are intrinsically taken into account in these conditions as other correction factors can compensate for inaccurate values of these parameters. We give here guidelines, that can be used through tools within the iSMS software (), for determining quantitative FRET and assess uncertainties linked with the procedure. Our results provide insights into the experimental parameters governing quantitative FRET determination, which is essential for obtaining accurate structural information from a wide range of biomolecules.
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Affiliation(s)
- Lasse L Hildebrandt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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163
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Kim HS, Im HN, An DR, Yoon JY, Jang JY, Mobashery S, Hesek D, Lee M, Yoo J, Cui M, Choi S, Kim C, Lee NK, Kim SJ, Kim JY, Bang G, Han BW, Lee BI, Yoon HJ, Suh SW. The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of L,D-Carboxypeptidase. J Biol Chem 2015; 290:25103-17. [PMID: 26306031 PMCID: PMC4599014 DOI: 10.1074/jbc.m115.658781] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori causes gastrointestinal diseases, including gastric cancer. Its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. In H. pylori, Csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. Csd6 is also involved in deglycosylation of the flagellar protein FlaA. To better understand its function, biochemical, biophysical, and structural characterizations were carried out. We show that Csd6 has a three-domain architecture and exists as a dimer in solution. The N-terminal domain plays a key role in dimerization. The middle catalytic domain resembles those of l,d-transpeptidases, but its pocket-shaped active site is uniquely defined by the four loops I to IV, among which loops I and III show the most distinct variations from the known l,d-transpeptidases. Mass analyses confirm that Csd6 functions only as an l,d-carboxypeptidase and not as an l,d-transpeptidase. The d-Ala-complexed structure suggests possible binding modes of both the substrate and product to the catalytic domain. The C-terminal nuclear transport factor 2-like domain possesses a deep pocket for possible binding of pseudaminic acid, and in silico docking supports its role in deglycosylation of flagellin. On the basis of these findings, it is proposed that H. pylori Csd6 and its homologs constitute a new family of l,d-carboxypeptidase. This work provides insights into the function of Csd6 in regulating the helical cell shape and motility of H. pylori.
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Affiliation(s)
- Hyoun Sook Kim
- From the Departments of Chemistry and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ha Na Im
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | - Doo Ri An
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | - Ji Young Yoon
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | | | - Shahriar Mobashery
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Dusan Hesek
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Mijoon Lee
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Jakyung Yoo
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Minghua Cui
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Sun Choi
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Cheolhee Kim
- the Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Nam Ki Lee
- the Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Soon-Jong Kim
- the Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Jin Young Kim
- the Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea, and
| | - Geul Bang
- the Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea, and
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Il Lee
- the Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Gyeonggi 410-769, Republic of Korea
| | | | - Se Won Suh
- From the Departments of Chemistry and Biophysics and Chemical Biology, College of Natural Sciences, and
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164
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Osad'ko IS. Dependence of FRET efficiency on distance in single donor-acceptor pairs. J Chem Phys 2015; 142:125102. [PMID: 25833609 DOI: 10.1063/1.4915279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Possibility to create single donor-acceptor (D-A) pairs by attaching dye molecules to various sites of DNA strands with control of the inter-dye distance R enables one to measure average Förster resonance energy transfer (FRET) efficiency E as a function of R. Triplet states of the dyes influence the dependence E(R) considerably. Two types of FRET efficiency are considered: E = EA and E = ED. The efficiency EA(R) = JA(R)/[JA(R) + JD(R)] depends on the donor and the acceptor average intensities JD(R) and JA(R) measured in D- and A-fluorescence, whereas the efficiency ED(R) = 1 - JD(R)/JD(∞) depends only on the intensity of D-fluorescence, so-called the donor quenching method. The shape of the functions ED (R) and EA (R) depends strongly on whether the dyes have blinking fluorescence. FRET efficiencies ED (R) and EA (R) undergo the influence of many experimental factors and therefore, differ considerably from pure FRET efficiencies ED (s) (R) and EA (s) (R). Pure FRET efficiencies ED,A (s) (R) are calculated with the help of rate equations for D-A pairs, whose molecules have triplet states. It is shown how the calculated efficiencies ED,A (s) (R) can be compared to FRET efficiencies measured with the help of the intensities ID,A(R) corrected by cross talk and background light.
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Affiliation(s)
- I S Osad'ko
- Institute for Spectroscopy, RAS, 142190 Moscow, Russia
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165
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Buning R, Kropff W, Martens K, van Noort J. spFRET reveals changes in nucleosome breathing by neighboring nucleosomes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064103. [PMID: 25564102 DOI: 10.1088/0953-8984/27/6/064103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chromatin, the structure in which DNA is compacted in eukaryotic cells, plays a key role in regulating DNA accessibility. FRET experiments on single nucleosomes, the basic units in chromatin, have revealed a dynamic nucleosome where spontaneous DNA unwrapping from the ends provides access to the nucleosomal DNA. Here we investigated how this DNA breathing is affected by extension of the linker DNA and by the presence of a neighboring nucleosome. We found that both electrostatic interactions between the entering and exiting linker DNA and nucleosome-nucleosome interactions increase unwrapping. Interactions between neighboring nucleosomes are more likely in dinucleosomes spaced by 55 bp of linker DNA than in dinucleosomes spaced by 50 bp of linker DNA. Such increased unwrapping may not only increase the accessibility of nucleosomal DNA in chromatin fibers, it may also be key to folding of nucleosomes into higher order structures.
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Affiliation(s)
- Ruth Buning
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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166
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Flynn DC, Bhagwat AR, Brenner MH, Núñez MF, Mork BE, Cai D, Swanson JA, Ogilvie JP. Pulse-shaping based two-photon FRET stoichiometry. OPTICS EXPRESS 2015; 23:3353-72. [PMID: 25836193 PMCID: PMC4394757 DOI: 10.1364/oe.23.003353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
Förster Resonance Energy Transfer (FRET) based measurements that calculate the stoichiometry of intermolecular interactions in living cells have recently been demonstrated, where the technique utilizes selective one-photon excitation of donor and acceptor fluorophores to isolate the pure FRET signal. Here, we present work towards extending this FRET stoichiometry method to employ two-photon excitation using a pulse-shaping methodology. In pulse-shaping, frequency-dependent phases are applied to a broadband femtosecond laser pulse to tailor the two-photon excitation conditions to preferentially excite donor and acceptor fluorophores. We have also generalized the existing stoichiometry theory to account for additional cross-talk terms that are non-vanishing under two-photon excitation conditions. Using the generalized theory we demonstrate two-photon FRET stoichiometry in live COS-7 cells expressing fluorescent proteins mAmetrine as the donor and tdTomato as the acceptor.
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Affiliation(s)
- Daniel C. Flynn
- Macromolecular Science and Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109
USA
| | - Amar R. Bhagwat
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
| | - Meredith H. Brenner
- Applied Physics Program, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
| | - Marcos F. Núñez
- Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109
USA
| | - Briana E. Mork
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
| | - Dawen Cai
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109
USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109
USA
| | - Joel A. Swanson
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109
USA
| | - Jennifer P. Ogilvie
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI 48109
USA
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167
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Wang BB, Wang Q, Jin YG, Ma MH, Cai ZX. Two-color quantum dots-based fluorescence resonance energy transfer for rapid and sensitive detection of Salmonella on eggshells. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2014.10.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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168
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Ait-Bara S, Clerté C, Margeat E. Single-molecule FRET characterization of RNA remodeling induced by an antitermination protein. Methods Mol Biol 2015; 1259:349-68. [PMID: 25579596 DOI: 10.1007/978-1-4939-2214-7_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) is a useful technique to probe conformational changes within bio-macromolecules. Here, we introduce how to perform smFRET measurements in solution to investigate RNA remodeling and RNA-protein interactions. In particular, we focus on how the close-to-open transition of an antiterminator hairpin is influenced by the binding of the antitermination protein and the competition by oligonucleotides.
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Affiliation(s)
- Soraya Ait-Bara
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090, Montpellier, France
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169
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Perez-Gonzalez DC, Penedo JC. Single-Molecule Strategies for DNA and RNA Diagnostics. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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170
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Beckers M, Drechsler F, Eilert T, Nagy J, Michaelis J. Quantitative structural information from single-molecule FRET. Faraday Discuss 2015; 184:117-29. [DOI: 10.1039/c5fd00110b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-molecule studies can be used to study biological processes directly and in real-time. In particular, the fluorescence energy transfer between reporter dye molecules attached to specific sites on macromolecular complexes can be used to infer distance information. When several measurements are combined, the information can be used to determine the position and conformation of certain domains with respect to the complex. However, data analysis schemes that include all experimental uncertainties are highly complex, and the outcome depends on assumptions about the state of the dye molecules. Here, we present a new analysis algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering termed Fast-NPS that can analyse large smFRET networks in a relatively short time and yields the position of the dye molecules together with their respective uncertainties. Moreover, we show what effects different assumptions about the dye molecules have on the outcome. We discuss the possibilities and pitfalls in structure determination based on smFRET using experimental data for an archaeal transcription pre-initiation complex, whose architecture has recently been unravelled by smFRET measurements.
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Affiliation(s)
- M. Beckers
- Biophysics Institute
- Ulm University
- 89081 Ulm
- Germany
| | - F. Drechsler
- Biophysics Institute
- Ulm University
- 89081 Ulm
- Germany
| | - T. Eilert
- Biophysics Institute
- Ulm University
- 89081 Ulm
- Germany
| | - J. Nagy
- Biophysics Institute
- Ulm University
- 89081 Ulm
- Germany
| | - J. Michaelis
- Biophysics Institute
- Ulm University
- 89081 Ulm
- Germany
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171
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Fricke F, Dietz MS, Heilemann M. Single-Molecule Methods to Study Membrane Receptor Oligomerization. Chemphyschem 2014; 16:713-21. [DOI: 10.1002/cphc.201402765] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 11/06/2022]
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172
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Gouridis G, Schuurman-Wolters GK, Ploetz E, Husada F, Vietrov R, de Boer M, Cordes T, Poolman B. Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ. Nat Struct Mol Biol 2014; 22:57-64. [DOI: 10.1038/nsmb.2929] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/06/2014] [Indexed: 11/09/2022]
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173
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Kang J, Jung J, Kim SK. Flexibility of single-stranded DNA measured by single-molecule FRET. Biophys Chem 2014; 195:49-52. [DOI: 10.1016/j.bpc.2014.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/16/2014] [Accepted: 08/16/2014] [Indexed: 10/24/2022]
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174
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Michalet X, Ingargiola A, Colyer RA, Scalia G, Weiss S, Maccagnani P, Gulinatti A, Rech I, Ghioni M. Silicon photon-counting avalanche diodes for single-molecule fluorescence spectroscopy. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2014; 20:38044201-380442020. [PMID: 25309114 PMCID: PMC4190971 DOI: 10.1109/jstqe.2014.2341568] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Solution-based single-molecule fluorescence spectroscopy is a powerful experimental tool with applications in cell biology, biochemistry and biophysics. The basic feature of this technique is to excite and collect light from a very small volume and work in a low concentration regime resulting in rare burst-like events corresponding to the transit of a single molecule. Detecting photon bursts is a challenging task: the small number of emitted photons in each burst calls for high detector sensitivity. Bursts are very brief, requiring detectors with fast response time and capable of sustaining high count rates. Finally, many bursts need to be accumulated to achieve proper statistical accuracy, resulting in long measurement time unless parallelization strategies are implemented to speed up data acquisition. In this paper we will show that silicon single-photon avalanche diodes (SPADs) best meet the needs of single-molecule detection. We will review the key SPAD parameters and highlight the issues to be addressed in their design, fabrication and operation. After surveying the state-of-the-art SPAD technologies, we will describe our recent progress towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. The potential of this approach is illustrated with single-molecule Förster resonance energy transfer measurements.
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Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90046,
USA
| | | | - Ryan A. Colyer
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90046,
USA
- Department of Science, Cabrini College, Radnor, PA 19087, USA
| | - Giuseppe Scalia
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90046,
USA
- Département de Physique, Université de Fribourg, 1700
Fribourg, Switzerland
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90046,
USA
| | - Piera Maccagnani
- Istituto per la Microelettronica e Microsistemi (IMM-CNR), Sezione di
Bologna, 40129 Bologna, Italy
| | - Angelo Gulinatti
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di
Milano, 20133 Milano, Italy
| | - Ivan Rech
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di
Milano, 20133 Milano, Italy
| | - Massimo Ghioni
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di
Milano, 20133 Milano, Italy
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175
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Gust A, Zander A, Gietl A, Holzmeister P, Schulz S, Lalkens B, Tinnefeld P, Grohmann D. A starting point for fluorescence-based single-molecule measurements in biomolecular research. Molecules 2014; 19:15824-65. [PMID: 25271426 PMCID: PMC6271140 DOI: 10.3390/molecules191015824] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.
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Affiliation(s)
- Alexander Gust
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Adrian Zander
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Birka Lalkens
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany.
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176
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Hohlbein J, Craggs TD, Cordes T. Alternating-laser excitation: single-molecule FRET and beyond. Chem Soc Rev 2014; 43:1156-71. [PMID: 24037326 DOI: 10.1039/c3cs60233h] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems.
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Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands.
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177
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Banerjee PR, Deniz AA. Shedding light on protein folding landscapes by single-molecule fluorescence. Chem Soc Rev 2014; 43:1172-88. [PMID: 24336839 DOI: 10.1039/c3cs60311c] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-molecule (SM) fluorescence methods have been increasingly instrumental in our current understanding of a number of key aspects of protein folding and aggregation landscapes over the past decade. With the advantage of a model free approach and the power of probing multiple subpopulations and stochastic dynamics directly in a heterogeneous structural ensemble, SM methods have emerged as a principle technique for studying complex systems such as intrinsically disordered proteins (IDPs), globular proteins in the unfolded basin and during folding, and early steps of protein aggregation in amyloidogenesis. This review highlights the application of these methods in investigating the free energy landscapes, folding properties and dynamics of individual protein molecules and their complexes, with an emphasis on inherently flexible systems such as IDPs.
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Affiliation(s)
- Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
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178
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Crawford R, Torella JP, Aigrain L, Plochowietz A, Gryte K, Uphoff S, Kapanidis AN. Long-lived intracellular single-molecule fluorescence using electroporated molecules. Biophys J 2014; 105:2439-50. [PMID: 24314075 DOI: 10.1016/j.bpj.2013.09.057] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/12/2013] [Accepted: 09/06/2013] [Indexed: 11/28/2022] Open
Abstract
Studies of biomolecules in vivo are crucial to understand their function in a natural, biological context. One powerful approach involves fusing molecules of interest to fluorescent proteins to study their expression, localization, and action; however, the scope of such studies would be increased considerably by using organic fluorophores, which are smaller and more photostable than their fluorescent protein counterparts. Here, we describe a straightforward, versatile, and high-throughput method to internalize DNA fragments and proteins labeled with organic fluorophores into live Escherichia coli by employing electroporation. We studied the copy numbers, diffusion profiles, and structure of internalized molecules at the single-molecule level in vivo, and were able to extend single-molecule observation times by two orders of magnitude compared to green fluorescent protein, allowing continuous monitoring of molecular processes occurring from seconds to minutes. We also exploited the desirable properties of organic fluorophores to perform single-molecule Förster resonance energy transfer measurements in the cytoplasm of live bacteria, both for DNA and proteins. Finally, we demonstrate internalization of labeled proteins and DNA into yeast Saccharomyces cerevisiae, a model eukaryotic system. Our method should broaden the range of biological questions addressable in microbes by single-molecule fluorescence.
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Affiliation(s)
- Robert Crawford
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
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179
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Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics. Biophys J 2014; 106:220-31. [PMID: 24411254 DOI: 10.1016/j.bpj.2013.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/19/2013] [Accepted: 11/04/2013] [Indexed: 01/10/2023] Open
Abstract
Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10(-11) liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20-100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation.
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180
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Single-molecule FRET reveals a corkscrew RNA structure for the polymerase-bound influenza virus promoter. Proc Natl Acad Sci U S A 2014; 111:E3335-42. [PMID: 25071209 DOI: 10.1073/pnas.1406056111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The influenza virus is a major human and animal pathogen responsible for seasonal epidemics and occasional pandemics. The genome of the influenza A virus comprises eight segments of single-stranded, negative-sense RNA with highly conserved 5' and 3' termini. These termini interact to form a double-stranded promoter structure that is recognized and bound by the viral RNA-dependent RNA polymerase (RNAP); however, no 3D structural information for the influenza polymerase-bound promoter exists. Functional studies have led to the proposal of several 2D models for the secondary structure of the bound promoter, including a corkscrew model in which the 5' and 3' termini form short hairpins. We have taken advantage of an insect-cell system to prepare large amounts of active recombinant influenza virus RNAP, and used this to develop a highly sensitive single-molecule FRET assay to measure distances between fluorescent dyes located on the promoter and map its structure both with and without the polymerase bound. These advances enabled the direct analysis of the influenza promoter structure in complex with the viral RNAP, and provided 3D structural information that is in agreement with the corkscrew model for the influenza virus promoter RNA. Our data provide insights into the mechanisms of promoter binding by the influenza RNAP and have implications for the understanding of the regulatory mechanisms involved in the transcription of viral genes and replication of the viral RNA genome. In addition, the simplicity of this system should translate readily to the study of any virus polymerase-promoter interaction.
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181
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Gamari BD, Zhang D, Buckman RE, Milas P, Denker JS, Chen H, Li H, Goldner LS. Inexpensive electronics and software for photon statistics and correlation spectroscopy. AMERICAN JOURNAL OF PHYSICS 2014; 82:708-722. [PMID: 26924846 PMCID: PMC4768833 DOI: 10.1119/1.4869188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 03/10/2014] [Indexed: 06/05/2023]
Abstract
Single-molecule-sensitive microscopy and spectroscopy are transforming biophysics and materials science laboratories. Techniques such as fluorescence correlation spectroscopy (FCS) and single-molecule sensitive fluorescence resonance energy transfer (FRET) are now commonly available in research laboratories but are as yet infrequently available in teaching laboratories. We describe inexpensive electronics and open-source software that bridges this gap, making state-of-the-art research capabilities accessible to undergraduates interested in biophysics. We include a discussion of the intensity correlation function relevant to FCS and how it can be determined from photon arrival times. We demonstrate the system with a measurement of the hydrodynamic radius of a protein using FCS that is suitable for the undergraduate teaching laboratory. The FPGA-based electronics, which are easy to construct, are suitable for more advanced measurements as well, and several applications are described. As implemented, the system has 8 ns timing resolution, can control up to four laser sources, and can collect information from as many as four photon-counting detectors.
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Affiliation(s)
- Benjamin D. Gamari
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01002
| | - Dianwen Zhang
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01002
| | - Richard E. Buckman
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01002
| | - Peker Milas
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01002
| | - John S. Denker
- AT&T Laboratories Research (ret.), Florham Park NJ, 07932
| | - Hui Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, New York 12208
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, New York 12208 and Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, P.O. BOX 509, Albany, New York 12201-0509
| | - Lori S. Goldner
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01002
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182
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Statistical filtering in fluorescence microscopy and fluorescence correlation spectroscopy. Anal Bioanal Chem 2014; 406:4797-813. [DOI: 10.1007/s00216-014-7892-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 01/21/2023]
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183
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Hieb AR, Gansen A, Böhm V, Langowski J. The conformational state of the nucleosome entry-exit site modulates TATA box-specific TBP binding. Nucleic Acids Res 2014; 42:7561-76. [PMID: 24829456 PMCID: PMC4081063 DOI: 10.1093/nar/gku423] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is needed. Using bulk and single-molecule FRET, we find that TBP binds a minimal consensus TATA box as a two-state equilibrium process, showing no evidence for intermediate states. However, upon addition of flanking DNA sequence, we observe non-specific cooperative binding to multiple DNA sites that compete for TATA-box specificity. Thus, we conclude that TBP binding is defined by a branched pathway, wherein TBP initially binds with little sequence specificity and is thermodynamically positioned by its kinetic stability to the TATA box. Furthermore, we observed the real-time access of TBP binding to TATA box DNA located within the DNA entry–exit site of the nucleosome. From these data, we determined salt-dependent changes in the nucleosome conformation regulate TBP's access to the TATA box, where access is highly constrained under physiological conditions, but is alleviated by histone acetylation and TFIIA.
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Affiliation(s)
- Aaron R Hieb
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Alexander Gansen
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Vera Böhm
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
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184
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Hughes CD, Simons M, Mackenzie CE, Van Houten B, Kad NM. Single molecule techniques in DNA repair: a primer. DNA Repair (Amst) 2014; 20:2-13. [PMID: 24819596 DOI: 10.1016/j.dnarep.2014.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.
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Affiliation(s)
- Craig D Hughes
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Cassidy E Mackenzie
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil M Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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185
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Holmstrom ED, Nesbitt DJ. Single-molecule fluorescence resonance energy transfer studies of the human telomerase RNA pseudoknot: temperature-/urea-dependent folding kinetics and thermodynamics. J Phys Chem B 2014; 118:3853-63. [PMID: 24617561 PMCID: PMC4030807 DOI: 10.1021/jp501893c] [Citation(s) in RCA: 21] [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: 02/23/2014] [Indexed: 02/06/2023]
Abstract
The ribonucleoprotein telomerase is an RNA-dependent DNA polymerase that catalyzes the repetitive addition of a short, species-specific, DNA sequence to the ends of linear eukaryotic chromosomes. The single RNA component of telomerase contains both the template sequence for DNA synthesis and a functionally critical pseudoknot motif, which can also exist as a less stable hairpin. Here we use a minimal version of the human telomerase RNA pseudoknot to study this hairpin-pseudoknot structural equilibrium using temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) experiments. The urea dependence of these experiments aids in determination of the folding kinetics and thermodynamics. The wild-type pseudoknot behavior is compared and contrasted to a mutant pseudoknot sequence implicated in a genetic disorder-dyskeratosis congenita. These findings clearly identify that this 2nt noncomplementary mutation destabilizes the folding of the wild-type pseudoknot by substantially reducing the folding rate constant (≈ 400-fold) while only nominally increasing the unfolding rate constant (≈ 5-fold). Furthermore, the urea dependence of the equilibrium and rate constants is used to develop a free energy landscape for this unimolecular equilibrium and propose details about the structure of the transition state. Finally, the urea-dependent folding experiments provide valuable physical insights into the mechanism for destabilization of RNA pseudoknots by such chemical denaturants.
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Affiliation(s)
- Erik D. Holmstrom
- JILA, University of Colorado and National
Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - David J. Nesbitt
- JILA, University of Colorado and National
Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
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186
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Abstract
Förster resonance energy transfer (FRET) is a phenomenon used for bioimaging ranging from single molecules to in vivo scale. A large variety of organic dyes and fluorescent proteins are available for FRET probes. In this review, we introduce the representative pairs of FRET probes developed thus far. The efficiency of FRET is depending on the spectral overlap of donor emission and acceptor absorption, the orientation of donor and acceptor and their distance. For FRET-based indicators composed of fluorescent proteins, their orientation and dimeric property of donor and acceptor largely affect the FRET efficiency, indicating the effect for the performance of indicators. In addition, three major applications of FRET, including genetically encoded indicators, single-molecule FRET, and enhancement of chemiluminescent proteins, have been introduced and their functions have also been discussed.
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187
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Farooq S, Fijen C, Hohlbein J. Studying DNA-protein interactions with single-molecule Förster resonance energy transfer. PROTOPLASMA 2014; 251:317-32. [PMID: 24374460 DOI: 10.1007/s00709-013-0596-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has emerged as a powerful tool for elucidating biological structure and mechanisms on the molecular level. Here, we focus on applications of smFRET to study interactions between DNA and enzymes such as DNA and RNA polymerases. SmFRET, used as a nanoscopic ruler, allows for the detection and precise characterisation of dynamic and rarely occurring events, which are otherwise averaged out in ensemble-based experiments. In this review, we will highlight some recent developments that provide new means of studying complex biological systems either by combining smFRET with force-based techniques or by using data obtained from smFRET experiments as constrains for computer-aided modelling.
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Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands
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188
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Sharma A, Leach RN, Gell C, Zhang N, Burrows PC, Shepherd DA, Wigneshweraraj S, Smith DA, Zhang X, Buck M, Stockley PG, Tuma R. Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies. Nucleic Acids Res 2014; 42:5177-90. [PMID: 24553251 PMCID: PMC4005640 DOI: 10.1093/nar/gku146] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recognition of bacterial promoters is regulated by two distinct classes of sequence-specific sigma factors, σ70 or σ54, that differ both in their primary sequence and in the requirement of the latter for activation via enhancer-bound upstream activators. The σ54 version controls gene expression in response to stress, often mediating pathogenicity. Its activator proteins are members of the AAA+ superfamily and use adenosine triphosphate (ATP) hydrolysis to remodel initially auto-inhibited holoenzyme promoter complexes. We have mapped this remodeling using single-molecule fluorescence spectroscopy. Initial remodeling is nucleotide-independent and driven by binding both ssDNA during promoter melting and activator. However, DNA loading into the RNA polymerase active site depends on co-operative ATP hydrolysis by the activator. Although the coupled promoter recognition and melting steps may be conserved between σ70 and σ54, the domain movements of the latter have evolved to require an activator ATPase.
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Affiliation(s)
- Amit Sharma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Robert N. Leach
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Christopher Gell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Nan Zhang
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Patricia C. Burrows
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Dale A. Shepherd
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Sivaramesh Wigneshweraraj
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - David Alastair Smith
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Xiaodong Zhang
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Martin Buck
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- *To whom correspondence should be addressed. Tel: +44 1133 433092; Fax: +44 1133 437897;
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- Correspondence may also be addressed to Roman Tuma. Tel: +44 1133 433080; Fax: +44 1133 437897;
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189
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Hohlbein J, Aigrain L, Craggs TD, Bermek O, Potapova O, Shoolizadeh P, Grindley NDF, Joyce CM, Kapanidis AN. Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nat Commun 2014; 4:2131. [PMID: 23831915 PMCID: PMC3715850 DOI: 10.1038/ncomms3131] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 06/11/2013] [Indexed: 01/04/2023] Open
Abstract
The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides before phosphoryl transfer. Here, we combine single-molecule FRET with the use of DNA polymerase I and various fidelity mutants to highlight mechanisms by which active-site side chains influence the conformational transitions and free-energy landscape that underlie fidelity decisions in DNA synthesis. Ternary complexes of high fidelity derivatives with complementary dNTPs adopt mainly a fully closed conformation, whereas a conformation with a FRET value between those of open and closed is sparsely populated. This intermediate-FRET state, which we attribute to a partially closed conformation, is also predominant in ternary complexes with incorrect nucleotides and, strikingly, in most ternary complexes of low-fidelity derivatives for both correct and incorrect nucleotides. The mutator phenotype of the low-fidelity derivatives correlates well with reduced affinity for complementary dNTPs and highlights the partially closed conformation as a primary checkpoint for nucleotide selection. The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides. Here, by using an intramolecular single-molecule FRET assay, the authors establish and characterize the partially closed conformation as a crucial fidelity checkpoint.
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Affiliation(s)
- Johannes Hohlbein
- Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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190
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Karedla N, Chizhik AI, Gregor I, Chizhik AM, Schulz O, Enderlein J. Single-molecule metal-induced energy transfer (smMIET): resolving nanometer distances at the single-molecule level. Chemphyschem 2014; 15:705-11. [PMID: 24478241 DOI: 10.1002/cphc.201300760] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 12/07/2013] [Indexed: 11/08/2022]
Abstract
We present a new concept for measuring distance values of single molecules from a surface with nanometer accuracy using the energy transfer from the excited molecule to surface plasmons of a metal film. We measure the fluorescence lifetime of individual dye molecules deposited on a dielectric spacer as a function of a spacer thickness. By using our theoretical model, we convert the lifetime values into the axial distance of individual molecules. Similar to Förster resonance energy transfer (FRET), this allows emitters to be localized with nanometer accuracy, but in contrast to FRET the distance range at which efficient energy transfer takes place is an order of magnitude larger. Our technique can be potentially used as a tool for measuring intramolecular distances of biomolecules and complexes.
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Affiliation(s)
- Narain Karedla
- Georg-August-Universität, III. Institute of Physics-Biophysics, Friedrich-Hund-Platz 1, 37077 Göttingen (Germany), Fax: (+49) 551-39 7720
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191
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MFD-PIE and PIE-FI: Ways to Extract More Information with TCSPC. SPRINGER SERIES ON FLUORESCENCE 2014. [DOI: 10.1007/4243_2014_66] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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192
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Plochowietz A, Crawford R, Kapanidis AN. Characterization of organic fluorophores forin vivoFRET studies based on electroporated molecules. Phys Chem Chem Phys 2014; 16:12688-94. [DOI: 10.1039/c4cp00995a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We optimized electroporation conditions and characterized photostability and brightness of organic fluorophores for single-cell FRET studies in live bacteria.
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Affiliation(s)
| | - R. Crawford
- Clarendon Laboratory
- Department of Physics
- Oxford, UK
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193
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The Power of Single-Molecule FRET Microscopy Applied to DNA Nanotechnology. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-38815-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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194
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Orevi T, Lerner E, Rahamim G, Amir D, Haas E. Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics. Methods Mol Biol 2014; 1076:113-169. [PMID: 24108626 DOI: 10.1007/978-1-62703-649-8_7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Most proteins are nanomachines that are selected to execute specific functions and therefore should have some degree of flexibility. The driving force that excites specific motions of domains and smaller chain elements is the thermal fluctuations of the solvent bath which are channeled to selected modes of motions by the structural constraints. Consequently characterization of the ensembles of conformers of proteins and their dynamics should be expressed in statistical terms, i.e., determination of probability distributions of the various conformers. This can be achieved by measurements of time-resolved dynamic non-radiative excitation energy transfer (trFRET) within ensembles of site specifically labeled protein molecules. Distributions of intramolecular segmental end-to-end distances and their fast fluctuations can be determined, and fast and slow conformational transitions within selected sections of the molecule can be monitored and analyzed. Both ensemble and single-molecule detection methods can be applied for data collection. In combination with synchronization methods, time-resolved FRET was also used for studies of fast conformational transitions, in particular the folding/unfolding transitions.
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Affiliation(s)
- Tomer Orevi
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
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195
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Zander A, Holzmeister P, Klose D, Tinnefeld P, Grohmann D. Single-molecule FRET supports the two-state model of Argonaute action. RNA Biol 2013; 11:45-56. [PMID: 24442234 DOI: 10.4161/rna.27446] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Argonaute can be found in all three domains of life and is the functional core of the eukaryotic RNA-silencing machinery. In order to shed light on the conformational changes that drive Argonaute action, we performed single-molecule FRET measurements employing a so far uncharacterized member of the Argonaute family, namely Argonaute from the archaeal organism Methanocaldococcus jannaschii (MjAgo). We show that MjAgo is a catalytically active Argonaute variant hydrolyzing exclusively DNA target strands out of a DNA/DNA hybrid. We studied the interplay between Argonaute and nucleic acids using fluorescent dyes covalently attached at different positions of the DNA guide as steric reporters. This allowed us to determine structurally confined parts of the protein scaffold and flexible regions of the DNA guide. Single-molecule FRET measurements demonstrate that the 3'end of the DNA guide is released from the PAZ domain upon target strand loading. This conformational change does not necessitate target strand cleavage but a fully complementary target strand. Thus, our data support the two state model for Argonaute action.
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Affiliation(s)
- Adrian Zander
- Physikalische und Theoretische Chemie - NanoBioSciences; Technische Universität Braunschweig; Hans-Sommer-Strasse 10; Braunschweig, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences; Technische Universität Braunschweig; Hans-Sommer-Strasse 10; Braunschweig, Germany
| | - Daniel Klose
- Department of Physics; University of Osnabrück; Barbarastrasse 7; Osnabrück, Germany
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences; Technische Universität Braunschweig; Hans-Sommer-Strasse 10; Braunschweig, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences; Technische Universität Braunschweig; Hans-Sommer-Strasse 10; Braunschweig, Germany
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196
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Single molecule FRET data analysis procedures for FRET efficiency determination: Probing the conformations of nucleic acid structures. Methods 2013; 64:36-42. [DOI: 10.1016/j.ymeth.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/23/2022] Open
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197
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Tsukanov R, Tomov TE, Masoud R, Drory H, Plavner N, Liber M, Nir E. Detailed Study of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by DNA Origami. J Phys Chem B 2013; 117:11932-42. [DOI: 10.1021/jp4059214] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Roman Tsukanov
- Department of Chemistry and
the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Toma E. Tomov
- Department of Chemistry and
the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Rula Masoud
- Department of Chemistry and
the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Hagai Drory
- Department of Chemistry and
the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Noa Plavner
- Department of Chemistry and
the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Miran Liber
- Department of Chemistry and
the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Eyal Nir
- Department of Chemistry and
the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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198
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Affiliation(s)
- Jens Michaelis
- Biophysics
Institute, Faculty of Natural Sciences, Ulm University, Albert-Einstein-Allee
11, 89081 Ulm, Germany
- Center
for Integrated Protein Science Munich (CIPSM), Department
of Chemistry and Biochemistry, Munich University, Butenandtstrasse 5-13, 81377 München, Germany
| | - Barbara Treutlein
- Department
of Bioengineering, Stanford University, James H. Clark Center, E-300, 318
Campus Drive, Stanford, California 94305-5432, United States
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199
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Mashaghi A, Kramer G, Lamb DC, Mayer MP, Tans SJ. Chaperone Action at the Single-Molecule Level. Chem Rev 2013; 114:660-76. [DOI: 10.1021/cr400326k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Alireza Mashaghi
- AMOLF Institute, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Günter Kramer
- Zentrum
für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Don C. Lamb
- Physical
Chemistry, Department of Chemistry, Munich Center for Integrated Protein
Science (CiPSM) and Center for Nanoscience, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Gerhard-Ertl-Building, 81377 Munich, Germany
| | - Matthias P. Mayer
- Zentrum
für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Sander J. Tans
- AMOLF Institute, Science Park
104, 1098 XG Amsterdam, The Netherlands
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200
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Wang Y, Xiao M, Li Y. Heterogeneity of single molecule FRET signals reveals multiple active ribosome subpopulations. Proteins 2013; 82:1-9. [PMID: 23609951 DOI: 10.1002/prot.24308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 11/06/2022]
Abstract
Single molecule methods have revealed that heterogeneity is common in biological systems. However, interpretations of the complex signals are challenging. By tracking the fluorescence resonance energy transfer (FRET) signals between the A-site tRNA and L27 protein in single ribosomes, we attempt to develop a qualitative method to subtract the inherent patterns of the heterogeneous single molecule FRET data. Seven ribosome subpopulations are identified using this method and spontaneous exchanges among these subpopulations are observed. All of the pretranslocation subpopulations are competent in real-time translocation, but via distinguished pathways. These observations suggest that the ribosome may function through multiple reaction pathways.
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Affiliation(s)
- Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas, 77214
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