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Bonačić-Koutecký V, Kulesza A, Gell L, Mitrić R, Antoine R, Bertorelle F, Hamouda R, Rayane D, Broyer M, Tabarin T, Dugourd P. Silver cluster-biomolecule hybrids: from basics towards sensors. Phys Chem Chem Phys 2012; 14:9282-90. [PMID: 22414868 DOI: 10.1039/c2cp00050d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We focus on the functional role of small silver clusters in model hybrid systems involving peptides in the context of a new generation of nanostructured materials for biosensing. The optical properties of hybrids in the gas phase and at support will be addressed with the aim to bridge fundamental and application aspects. We show that extension and enhancement of absorption of peptides can be achieved by small silver clusters due to the interaction of intense intracluster excitations with the π-π* excitations of chromophoric aminoacids. Moreover, we demonstrate that the binding of a peptide to a supported silver cluster can be detected by the optical fingerprint. This illustrates that supported silver clusters can serve as building blocks for biosensing materials. Moreover, the clusters can be used simultaneously to immobilize biomolecules and to increase the sensitivity of detection, thus replacing the standard use of organic dyes and providing label-free detection. Complementary to that, we show that protected silver clusters containing a cluster core and a shell liganded by thiolates exhibit absorption properties with intense transitions in the visible regime which are also suitable for biosensing applications.
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Affiliation(s)
- Vlasta Bonačić-Koutecký
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
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52
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Kulesza A, Mitrić R, Bonačić-Koutecký V. Theoretical study of structural and optical properties of noble metal cluster–dipeptide hybrids at defect centers of MgO. Phys Chem Chem Phys 2012; 14:9330-5. [DOI: 10.1039/c2cp23500e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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53
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Schuler B, Müller-Späth S, Soranno A, Nettels D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol Biol 2012; 896:21-45. [PMID: 22821515 DOI: 10.1007/978-1-4614-3704-8_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a large degree of conformational heterogeneity. In such cases, classical experimental methods often yield only mean values, averaged over the entire ensemble of molecules. The microscopic distributions of conformations, trajectories, or sequences of events often remain unknown, and with them the underlying molecular mechanisms. Signal averaging can be avoided by observing individual molecules. A particularly versatile method is highly sensitive fluorescence detection. In combination with Förster resonance energy transfer (FRET), distances and conformational dynamics can be investigated in single molecules. This chapter introduces the practical aspects of applying confocal single-molecule FRET experiments to the study of IDPs.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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54
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Observation of protein folding/unfolding dynamics of ubiquitin trapped in agarose gel by single-molecule FRET. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:189-98. [DOI: 10.1007/s00249-011-0772-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/13/2011] [Accepted: 10/24/2011] [Indexed: 11/27/2022]
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55
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Kwak M, Herrmann A. Nucleic acid amphiphiles: synthesis and self-assembled nanostructures. Chem Soc Rev 2011; 40:5745-55. [PMID: 21858338 DOI: 10.1039/c1cs15138j] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review provides an overview of a relatively new class of bio-conjugates, DNA amphiphiles, which consist of oligonucleotides covalently bonded to synthetic hydrophobic units. The reader will find the basic principles for the structural design and preparation methods of the materials. Moreover, the self-assembly into superstructures of higher order will be highlighted. Finally, some potential applications will be described.
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Affiliation(s)
- Minseok Kwak
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
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56
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Kulesza A, Mitrić R, Bonačić-Koutecký V. Unique optical properties of silver cluster-biochromophore hybrids: Comparison with copper and gold. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2010.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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57
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Abstract
The atomic force microscope (AFM) is a high-resolution scanning-probe instrument which has become an important tool for cellular and molecular biophysics in recent years, but lacks the time resolution and functional specificities offered by fluorescence microscopic techniques. The advantages of both methods may be exploited by combining and synchronizing them. In this paper, the biological applications of AFM, fluorescence, and their combinations are briefly reviewed, and the assembly and utilization of a spatially and temporally synchronized AFM and total internal reflection fluorescence microscope are described. The application of the method is demonstrated on a fluorescently labeled cell culture.
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Affiliation(s)
- Miklós S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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58
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van den Wildenberg SMJL, Prevo B, Peterman EJG. A brief introduction to single-molecule fluorescence methods. Methods Mol Biol 2011; 783:81-99. [PMID: 21909884 DOI: 10.1007/978-1-61779-282-3_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which is the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches are addressed, we first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.
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59
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Choi J, Kim S, Tachikawa T, Fujitsuka M, Majima T. Unfolding dynamics of cytochrome c revealed by single-molecule and ensemble-averaged spectroscopy. Phys Chem Chem Phys 2011; 13:5651-8. [DOI: 10.1039/c0cp02689a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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60
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Göhler A, André S, Kaltner H, Sauer M, Gabius HJ, Doose S. Hydrodynamic properties of human adhesion/growth-regulatory galectins studied by fluorescence correlation spectroscopy. Biophys J 2010; 98:3044-53. [PMID: 20550917 DOI: 10.1016/j.bpj.2010.03.040] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 03/09/2010] [Accepted: 03/17/2010] [Indexed: 11/30/2022] Open
Abstract
Fluorescence correlation spectroscopy is applied on homologous human lectins (i.e., adhesion/growth-regulatory galectins) to detect influence of ligand binding and presence of the linker peptide in tandem-repeat-type proteins on hydrodynamic properties. Among five tested proteins, lactose binding increased the diffusion constant only in the cases of homodimeric galectin-1 and the linkerless variant of tandem-repeat-type galectin-4. To our knowledge, the close structural similarity among galectins does not translate into identical response to ligand binding. Kinetic measurements show association and dissociation rate constants in the order of 1 to 10(3) M(-1) s(-1) and 10(-4) s(-1), respectively. Presence of the linker peptide in tandem-repeat-type protein leads to anomalous scaling with molecular mass. These results provide what we believe to be new insights into lectin responses to glycan binding, detectable so far only by small angle neutron scattering, and the structural relevance of the linker peptide. Methodologically, fluorescence correlation spectroscopy is shown to be a rather simple technical tool to characterize hydrodynamic properties of these proteins at a high level of sensitivity.
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Affiliation(s)
- Antonia Göhler
- Applied Laser Physics and Laser Spectroscopy, Bielefeld University, Bielefeld, Germany
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61
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Hohlbein J, Gryte K, Heilemann M, Kapanidis AN. Surfing on a new wave of single-molecule fluorescence methods. Phys Biol 2010; 7:031001. [DOI: 10.1088/1478-3975/7/3/031001] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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62
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Lee AJ, Ensign AA, Krauss TD, Bren KL. Zinc porphyrin as a donor for FRET in Zn(II)cytochrome c. J Am Chem Soc 2010; 132:1752-3. [PMID: 20102193 DOI: 10.1021/ja909106p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate that Zn(II) porphyrin in Zn(II)cytochrome c (Zn cyt c) is a fluorescence resonance energy transfer (FRET) donor to an Alexa660 dye acceptor. The energy transfer efficiency is dependent on the distance between the two fluorophores as shown through protein denaturation studies of five Zn cyt c variants labeled with Alexa660 in different positions. The relative quantum yield, excitation and emission energies, and labeling efficiencies of this donor-acceptor pair allow for a method of analysis based on sensitized emission of the acceptor. These studies show that Zn(II) porphyrin is an effective energy donor for measurement of molecular-scale distances by FRET.
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Affiliation(s)
- Andrea J Lee
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
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63
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Sugawa M, Nishikawa S, Iwane AH, Biju V, Yanagida T. Single-molecule FRET imaging for enzymatic reactions at high ligand concentrations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:346-350. [PMID: 20033931 DOI: 10.1002/smll.200901827] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Mitsuhiro Sugawa
- Graduate School of Frontier Biosciences, Osaka University 7F Nanobiology Building, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
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64
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Chakraborty A, Wang D, Ebright YW, Ebright RH. Azide-specific labeling of biomolecules by Staudinger-Bertozzi ligation phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy. Methods Enzymol 2010; 472:19-30. [PMID: 20580957 DOI: 10.1016/s0076-6879(10)72018-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe the synthesis of phosphine derivatives of three fluorescent probes that have a brightness and photostability suitable for single-molecule fluorescence spectroscopy and microscopy: Alexa488, Cy3B, and Alexa647. In addition, we describe procedures for use of these reagents in azide-specific, bioorthogonal labeling through Staudinger-Bertozzi ligation, as well as procedures for the quantitation of labeling specificity and labeling efficiency. The reagents and procedures of this report enable chemoselective, site-selective labeling of azide-containing biomolecules for single-molecule fluorescence spectroscopy and microscopy.
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Affiliation(s)
- Anirban Chakraborty
- Department of Chemistry and Chemical Biology, Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
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65
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Abstract
Single-molecule methods have given researchers the ability to investigate the structural dynamics of biomolecules at unprecedented resolution and sensitivity. One of the preferred methods of studying single biomolecules is single-molecule fluorescence resonance energy transfer (smFRET). The popularity of smFRET stems from its ability to report on dynamic, either intra- or intermolecular interactions in real-time. For example, smFRET has been successfully used to characterize the role of dynamics in functional RNAs and their protein complexes, including ribozymes, the ribosome, and more recently the spliceosome. Being able to reliably extract quantitative kinetic and conformational parameters from smFRET experiments is crucial for the interpretation of their results. The need for efficient, unbiased analysis routines becomes more evident as the systems studied become more complex. In this chapter, we focus on the practical utility of statistical algorithms, particularly hidden Markov models, to aid in the objective quantification of complex smFRET trajectories with three or more discrete states, and to extract kinetic information from the trajectories. Additionally, we present a method for systematically eliminating transitions associated with uncorrelated fluorophore behavior that may occur due to dye anisotropy and quenching effects. We also highlight the importance of data condensation through the use of various transition density plots to fully understand the underlying conformational dynamics and kinetic behavior of the biological macromolecule of interest under varying conditions. Finally, the application of these techniques to studies of pre-mRNA conformational changes during eukaryotic splicing is discussed.
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Affiliation(s)
- Mario Blanco
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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66
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Helm M, Kobitski AY, Nienhaus GU. Single-molecule Förster resonance energy transfer studies of RNA structure, dynamics and function. Biophys Rev 2009; 1:161. [PMID: 28510027 PMCID: PMC5418384 DOI: 10.1007/s12551-009-0018-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 10/09/2009] [Indexed: 11/24/2022] Open
Abstract
Single-molecule fluorescence microscopy experiments on RNA molecules brought to light the highly complex dynamics of key biological processes, including RNA folding, catalysis of ribozymes, ligand sensing of riboswitches and aptamers, and protein synthesis in the ribosome. By using highly advanced biophysical spectroscopy techniques in combination with sophisticated biochemical synthesis approaches, molecular dynamics of individual RNA molecules can be observed in real time and under physiological conditions in unprecedented detail that cannot be achieved with bulk experiments. Here, we review recent advances in RNA folding and functional studies of RNA and RNA-protein complexes addressed by using single-molecule Förster (fluorescence) resonance energy transfer (smFRET) technique.
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Affiliation(s)
- Mark Helm
- Institute of Pharmacy, University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany.
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
| | - Andrei Yu Kobitski
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128, Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128, Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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67
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Doose S, Neuweiler H, Sauer M. Fluorescence quenching by photoinduced electron transfer: a reporter for conformational dynamics of macromolecules. Chemphyschem 2009; 10:1389-98. [PMID: 19475638 DOI: 10.1002/cphc.200900238] [Citation(s) in RCA: 373] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Photoinduced electron transfer (PET) between organic fluorophores and suitable electron donating moieties, for example, the amino acid tryptophan or the nucleobase guanine, can quench fluorescence upon van der Waals contact and thus report on molecular contact. PET-quenching has been used as reporter for monitoring conformational dynamics in polypeptides, proteins, and oligonucleotides. Whereas dynamic quenching transiently influences quantum yield and fluorescence lifetime of the fluorophore, static quenching in pi-stacked complexes efficiently suppresses fluorescence emission over time scales longer than the fluorescence lifetime. Static quenching therefore provides sufficient contrast to be observed at the single-molecule level. Here, we review complex formation and static quenching of different fluorophores by various molecular compounds, discuss applications as reporter system for macromolecular dynamics, and give illustrating examples.
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Affiliation(s)
- Sören Doose
- Applied Laser Physics and Laser Spectroscopy, Bielefeld University, Universitätsstr. 25, 33619 Bielefeld, Germany
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68
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Moran-Mirabal JM, Corgie SC, Bolewski JC, Smith HM, Cipriany BR, Craighead HG, Walker LP. Labeling and Purification of Cellulose-Binding Proteins for High Resolution Fluorescence Applications. Anal Chem 2009; 81:7981-7. [DOI: 10.1021/ac901183b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jose M. Moran-Mirabal
- Department of Biological and Environmental Engineering and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14850
| | - Stephane C. Corgie
- Department of Biological and Environmental Engineering and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14850
| | - Jacob C. Bolewski
- Department of Biological and Environmental Engineering and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14850
| | - Hanna M. Smith
- Department of Biological and Environmental Engineering and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14850
| | - Benjamin R. Cipriany
- Department of Biological and Environmental Engineering and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14850
| | - Harold G. Craighead
- Department of Biological and Environmental Engineering and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14850
| | - Larry P. Walker
- Department of Biological and Environmental Engineering and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14850
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69
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Yang JY, Yang WY. Site-Specific Two-Color Protein Labeling for FRET Studies Using Split Inteins. J Am Chem Soc 2009; 131:11644-5. [DOI: 10.1021/ja9030215] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jin-Yi Yang
- Institute of Biological Chemistry, Academia Sinica and Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wei Yuan Yang
- Institute of Biological Chemistry, Academia Sinica and Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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70
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Fox CB, Wayment JR, Myers GA, Endicott SK, Harris JM. Single-Molecule Fluorescence Imaging of Peptide Binding to Supported Lipid Bilayers. Anal Chem 2009; 81:5130-8. [DOI: 10.1021/ac9007682] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher B. Fox
- Department of Bioengineering, University of Utah, 50 South Central Campus Drive, Salt Lake City, Utah 84112-9202, Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, and HSC Core Research Facilities, University of Utah, 50 North Medical Drive, Salt Lake City, Utah 84132
| | - Joshua R. Wayment
- Department of Bioengineering, University of Utah, 50 South Central Campus Drive, Salt Lake City, Utah 84112-9202, Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, and HSC Core Research Facilities, University of Utah, 50 North Medical Drive, Salt Lake City, Utah 84132
| | - Grant A. Myers
- Department of Bioengineering, University of Utah, 50 South Central Campus Drive, Salt Lake City, Utah 84112-9202, Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, and HSC Core Research Facilities, University of Utah, 50 North Medical Drive, Salt Lake City, Utah 84132
| | - Scott K. Endicott
- Department of Bioengineering, University of Utah, 50 South Central Campus Drive, Salt Lake City, Utah 84112-9202, Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, and HSC Core Research Facilities, University of Utah, 50 North Medical Drive, Salt Lake City, Utah 84132
| | - Joel M. Harris
- Department of Bioengineering, University of Utah, 50 South Central Campus Drive, Salt Lake City, Utah 84112-9202, Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, and HSC Core Research Facilities, University of Utah, 50 North Medical Drive, Salt Lake City, Utah 84132
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71
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Abstract
The structural and dynamic details of protein folding are still widely unexplored due to the enormous level of heterogeneity intrinsic to this process. The unfolded polypeptide chain can assume a vast number of possible conformations, and many complex pathways lead from the ensemble of unfolded conformations to the ensemble of native conformations in an overall funnel-shaped energy landscape. Classical experimental methods involve measurements on bulk samples and usually yield only average values characteristic of the entire molecular ensemble under study. The observation of individual molecules avoids this averaging and allows, in principle, microscopic distributions of conformations and folding trajectories to be revealed. Fluorescence-based techniques are arguably the most versatile single-molecule methods at present, and Förster resonance energy transfer (FRET) between two dye molecules specifically attached to the protein of interest provides a means of studying the inter-dye distance and, thereby, the conformation of folding polypeptide chains in real time. This chapter focuses on practical aspects and different experimental realizations for protein folding investigations by using single-molecule fluorescence.
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72
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Blouin S, Craggs TD, Lafontaine DA, Penedo JC. Functional studies of DNA-protein interactions using FRET techniques. Methods Mol Biol 2009; 543:475-502. [PMID: 19378182 DOI: 10.1007/978-1-60327-015-1_28] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-DNA interactions underpin life and play key roles in all cellular processes and functions including DNA transcription, packaging, replication, and repair. Identifying and examining the nature of these interactions is therefore a crucial prerequisite to understand the molecular basis of how these fundamental processes take place. The application of fluorescence techniques and in particular fluorescence resonance energy transfer (FRET) to provide structural and kinetic information has experienced a stunning growth during the past decade. This has been mostly promoted by new advances in the preparation of dye-labeled nucleic acids and proteins and in optical sensitivity, where its implementation at the level of individual molecules has opened a new biophysical frontier. Nowadays, the application of FRET-based techniques to the analysis of protein-DNA interactions spans from the classical steady-state and time-resolved methods averaging over large ensembles to the analysis of distances, conformational changes, and enzymatic reactions in individual Protein-DNA complexes. This chapter introduces the practical aspects of applying these methods for the study of Protein-DNA interactions.
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Affiliation(s)
- Simon Blouin
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boul. Université, Sherbrooke, QC, Canada, J1K 2R1
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73
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Probing complexes with single fluorophores: factors contributing to dispersion of FRET in DNA/RNA duplexes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:395-405. [DOI: 10.1007/s00249-008-0383-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 10/23/2008] [Accepted: 10/23/2008] [Indexed: 10/21/2022]
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74
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Giaume D, Poggi M, Casanova D, Mialon G, Lahlil K, Alexandrou A, Gacoin T, Boilot JP. Organic functionalization of luminescent oxide nanoparticles toward their application as biological probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:11018-11026. [PMID: 18771302 DOI: 10.1021/la8015468] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Luminescent inorganic nanoparticles are now widely studied for their applications as biological probes for in vitro or in vivo experiments. The functionalization of the particles is a key step toward these applications, since it determines the control of the coupling between the particles and the biological species of interest. This paper is devoted to the case of rare earth doped oxide nanoparticles and their functionalization through their surface encapsulation with a functional polysiloxane shell. The first step of the process is the adsorption of silicate ions that will act as a primary layer for the further surface polymerization of the silane, either aminopropyltriethoxysilane (APTES) or glycidoxypropyltrimethoxysilane (GPTMS). The amino- or epoxy- functions born by the silane allow the versatile coupling of the particles with bio-organic species following the chemistry that is commonly used in biochips. Special attention is paid to the careful characterization of each step of the functionalization process, especially concerning the average number of organic functions that are available for the final coupling of the particles with proteins. The surface density of amino or epoxy functions was found to be 0.4 and 1.9 functions per square nanometer for GPTMS and APTES silanized particles, respectively. An example of application of the amino-functionalized particles is given for the coupling with alpha-bungarotoxins. The average number (up to 8) and the distribution of the number of proteins per particle are given, showing the potentialities of the functionalization process for the labeling of biological species.
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Affiliation(s)
- Domitille Giaume
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Route de Saclay, 91128 Palaiseau, France
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75
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Zinc porphyrin: a fluorescent acceptor in studies of Zn-cytochrome c unfolding by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 2008; 105:10779-84. [PMID: 18669660 DOI: 10.1073/pnas.0802737105] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FRET between the zinc porphyrin (ZnP) chromophore in zinc-substituted cytochrome c (Zn-cyt c) and an Alexa Fluor dye attached to specific surface sites was used to characterize Zn-cyt c unfolding. The use of ZnP as a fluorescent acceptor eliminates the need to doubly label the protein with exogenous dyes to perform FRET experiments in which both donor and acceptor fluorescence is monitored. The requirement for attachment of only one dye also minimizes perturbation to the protein. This sensitive technique allowed for the determination of distances between the label placed at six different sites and ZnP through a range of denaturant concentrations. Fitting of the data to a three-state model provides distances in the unfolding intermediate. The use of ZnP as a fluorescent acceptor of energy in FRET has a significant potential for application to a range of other systems including heme-binding proteins and proteins to which a covalently attached heme tag may be added.
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76
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Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is one of the most general and adaptable single-molecule techniques. Despite the explosive growth in the application of smFRET to answer biological questions in the last decade, the technique has been practiced mostly by biophysicists. We provide a practical guide to using smFRET, focusing on the study of immobilized molecules that allow measurements of single-molecule reaction trajectories from 1 ms to many minutes. We discuss issues a biologist must consider to conduct successful smFRET experiments, including experimental design, sample preparation, single-molecule detection and data analysis. We also describe how a smFRET-capable instrument can be built at a reasonable cost with off-the-shelf components and operated reliably using well-established protocols and freely available software.
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77
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Walter NG, Huang CY, Manzo AJ, Sobhy MA. Do-it-yourself guide: how to use the modern single-molecule toolkit. Nat Methods 2008; 5:475-89. [PMID: 18511916 PMCID: PMC2574008 DOI: 10.1038/nmeth.1215] [Citation(s) in RCA: 272] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Single-molecule microscopy has evolved into the ultimate-sensitivity toolkit to study systems from small molecules to living cells, with the prospect of revolutionizing the modern biosciences. Here we survey the current state of the art in single-molecule tools including fluorescence spectroscopy, tethered particle microscopy, optical and magnetic tweezers, and atomic force microscopy. We also provide guidelines for choosing the right approach from the available single-molecule toolkit for applications as diverse as structural biology, enzymology, nanotechnology and systems biology.
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Affiliation(s)
- Nils G Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA.
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78
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Kao MWP, Yang LL, Lin JCK, Lim TS, Fann W, Chen RPY. Strategy for efficient site-specific FRET-dye labeling of ubiquitin. Bioconjug Chem 2008; 19:1124-6. [PMID: 18507427 DOI: 10.1021/bc700480j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To study conformational changes within a single protein molecule, sp-FRET (single pair fluorescence resonance energy transfer) is an important technique to provide distance information. However, incorporating donor and acceptor dyes into the same protein molecule is not an easy task. Here, we report a strategy for the efficient double-labeling of a protein on a solid support. An ubiquitin mutant with two Cys mutations, one with high solvent accessibility and the other with low solvent accessibility, was constructed. The protein was bound to magnetic beads and reacted with the dyes. The first dye reacted with the side-chain of the Cys with the high solvent accessibility and the second with the other Cys under partially denaturing conditions. Using this method, we can easily label two dyes in a site-specific way on ubiquitin with a satisfied yield. The labeling sites for donor and acceptor dyes can be easily swapped.
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Affiliation(s)
- Michael Wen-Pin Kao
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, R. O. C
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79
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Kim Y, Ho SO, Gassman NR, Korlann Y, Landorf EV, Collart FR, Weiss S. Efficient site-specific labeling of proteins via cysteines. Bioconjug Chem 2008; 19:786-91. [PMID: 18275130 DOI: 10.1021/bc7002499] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods for chemical modifications of proteins have been crucial for the advancement of proteomics. In particular, site-specific covalent labeling of proteins with fluorophores and other moieties has permitted the development of a multitude of assays for proteome analysis. A common approach for such a modification is solvent-accessible cysteine labeling using thiol-reactive dyes. Cysteine is very attractive for site-specific conjugation due to its relative rarity throughout the proteome and the ease of its introduction into a specific site along the protein's amino acid chain. This is achieved by site-directed mutagenesis, most often without perturbing the protein's function. Bottlenecks in this reaction, however, include the maintenance of reactive thiol groups without oxidation before the reaction, and the effective removal of unreacted molecules prior to fluorescence studies. Here, we describe an efficient, specific, and rapid procedure for cysteine labeling starting from well-reduced proteins in the solid state. The efficacy and specificity of the improved procedure are estimated using a variety of single-cysteine proteins and thiol-reactive dyes. Based on UV/vis absorbance spectra, coupling efficiencies are typically in the range 70-90%, and specificities are better than approximately 95%. The labeled proteins are evaluated using fluorescence assays, proving that the covalent modification does not alter their function. In addition to maleimide-based conjugation, this improved procedure may be used for other thiol-reactive conjugations such as haloacetyl, alkyl halide, and disulfide interchange derivatives. This facile and rapid procedure is well suited for high throughput proteome analysis.
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Affiliation(s)
- Younggyu Kim
- Department of Chemistry and Biochemistry, Department of Physiology, California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
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80
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Schuler B, Eaton WA. Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 2008; 18:16-26. [PMID: 18221865 DOI: 10.1016/j.sbi.2007.12.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 12/05/2007] [Accepted: 12/05/2007] [Indexed: 11/27/2022]
Abstract
A complete understanding of a protein-folding mechanism requires description of the distribution of microscopic pathways that connect the folded and unfolded states. This distribution can, in principle, be described by computer simulations and theoretical models of protein folding, but is hidden in conventional experiments on large ensembles of molecules because only average properties are measured. A long-term goal of single-molecule fluorescence studies is to time-resolve the structural events as individual molecules make transitions between folded and unfolded states. Although such studies are still in their infancy, the work till now shows great promise and has already produced novel and important information on current issues in protein folding that has been impossible or difficult to obtain from ensemble measurements.
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Affiliation(s)
- Benjamin Schuler
- Biochemisches Institut, Universität Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
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81
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Quantum Optics: Colloidal Fluorescent Semiconductor Nanocrystals (Quantum Dots) in Single-Molecule Detection and Imaging. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-3-540-73924-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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82
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Kim S, Huang B, Zare RN. Microfluidic separation and capture of analytes for single-molecule spectroscopy. LAB ON A CHIP 2007; 7:1663-1665. [PMID: 18030384 DOI: 10.1039/b713103h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A complex mixture of fluorescently labeled biological molecules is separated electrophoretically on a chip and the constituent molecules are confined in a sub-nanolitre microchamber, which allows analysis by various single-molecule techniques.
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Affiliation(s)
- Samuel Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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83
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Jung C, Müller BK, Lamb DC, Nolde F, Müllen K, Bräuchle C. A new photostable terrylene diimide dye for applications in single molecule studies and membrane labeling. J Am Chem Soc 2007; 128:5283-91. [PMID: 16608365 DOI: 10.1021/ja0588104] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new terrylene diimide-based dye (WS-TDI) that is soluble in water has been synthesized, and its photophysical properties are characterized. WS-TDI forms nonfluorescing H-aggregates in water that show absorption bands being blue-shifted with respect to those of the fluorescing monomeric form. The ratio of monomeric WS-TDI to aggregated WS-TDI was determined to be 1 in 14 400 from fluorescence correlation spectroscopy (FCS) measurements, suggesting the presence of a large amount of soluble, nonfluorescent aggregates in water. The presence of a surfactant such as Pluronic P123 or CTAB leads to the disruption of the aggregates due to the formation of monomers in micelles. This is accompanied by a strong increase in fluorescence. A single molecule study of WS-TDI in polymeric films of PVA and PMMA reveals excellent photostability with respect to photobleaching, far above the photostability of other common water-soluble dyes, such as oxazine-1, sulforhodamine-B, and a water-soluble perylenediimide derivative. Furthermore, labeling of a single protein such as avidin is demonstrated by FCS and single molecule photostability measurements. The high tendency of WS-TDI to form nonfluorescent aggregates in water in connection with its high affinity to lipophilic environments is used for the fluorescence labeling of lipid membranes and membrane containing compartments such as artificial liposomes or endosomes in living HeLa cells. The superior fluorescence imaging quality of WS-TDI in such applications is demonstrated in comparison to other well-known membrane staining dyes such as Alexa647 conjugated with dextran and FM 4-64 lipophilic styryl dye.
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Affiliation(s)
- Christophe Jung
- Department für Chemie und Biochemie and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Butenandtstrasse 11, D-81377, München, Germany
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84
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Moerner WE. New directions in single-molecule imaging and analysis. Proc Natl Acad Sci U S A 2007; 104:12596-602. [PMID: 17664434 PMCID: PMC1937512 DOI: 10.1073/pnas.0610081104] [Citation(s) in RCA: 286] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Indexed: 01/05/2023] Open
Abstract
Optical imaging and analysis of single molecules continue to unfold as powerful ways to study the individual behavior of biological systems, unobscured by ensemble averaging. Current expansion of interest in this field is great, as evidenced by new meetings, journal special issues, and the large number of new investigators. Selected recent advances in biomolecular analysis are described, and two new research directions are summarized: superresolution imaging using single-molecule fluorescence and trapping of single molecules in solution by direct suppression of Brownian motion.
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Affiliation(s)
- W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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85
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Calloway NT, Choob M, Sanz A, Sheetz MP, Miller LW, Cornish VW. Optimized fluorescent trimethoprim derivatives for in vivo protein labeling. Chembiochem 2007; 8:767-74. [PMID: 17378009 DOI: 10.1002/cbic.200600414] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The combined technologies of optical microscopy and selective probes allow for real-time analysis of protein function in living cells. Synthetic chemistry offers a means to develop specific, protein-targeted probes that exhibit greater optical and chemical functionality than the widely used fluorescent proteins. Here we describe pharmacokinetically optimized, fluorescent trimethoprim (TMP) analogues that can be used to specifically label recombinant proteins fused to E. coli dihydrofolate reductase (eDHFR) in living, wild-type mammalian cells. These improved fluorescent tags exhibited high specificity and fast labeling kinetics, and they could be detected at a high signal-to-noise ratio by using fluorescence microscopy and fluorescence-activated cell sorting (FACS). We also show that fluorescent TMP-eDHFR complexes are complements to green fluorescent protein (GFP) for two-color protein labeling experiments in cells.
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Affiliation(s)
- Nathaniel T Calloway
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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86
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Nakkiran A, Thirumalai J, Jagannathan R. Luminescence blinking in Eu3+ doped yttrium oxysulfide (Y2O2S:Eu3+) quantum-dot ensembles: Photo-assisted relaxation of surface state(s). Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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87
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Nienhaus GU. Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis. Macromol Biosci 2007; 6:907-22. [PMID: 17099864 DOI: 10.1002/mabi.200600158] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteins are highly complex biopolymers, exhibiting a substantial degree of structural variability in their properly folded, native state. In the presence of denaturants, this heterogeneity is greatly enhanced, and fluctuations take place among vast numbers of folded and unfolded conformations via many different pathways. To better understand protein folding it is necessary to explore the structural and energetic properties of the folded and unfolded polypeptide chain, as well as the trajectories along which the chain navigates through its multi-dimensional conformational energy landscape. In recent years, single-molecule fluorescence spectroscopy has been established as a powerful tool in this research area, as it allows one to monitor the structure and dynamics of individual polypeptide chains in real time with atomic scale resolution using Förster resonance energy transfer (FRET). Consequently, time trajectories of folding transitions can be directly observed, including transient intermediates that may exist along these pathways. Here we illustrate the power of single-molecule fluorescence with our recent work on the structure and dynamics of the small enzyme RNase H in the presence of the chemical denaturant guanidinium chloride (GdmCl). For FRET analysis, a pair of fluorescent dyes was attached to the enzyme at specific locations. In order to observe conformational changes of individual protein molecules for up to several hundred seconds, the proteins were immobilized on nanostructured, polymer coated glass surfaces specially developed to have negligible interactions with folded and unfolded proteins. The single-molecule FRET analysis gave insight into structural changes of the unfolded polypeptide chain in response to varying the denaturant concentration, and the time traces revealed stepwise transitions in the FRET levels, reflecting conformational dynamics. Barriers in the free energy landscape of RNase H were estimated from the kinetics of the transitions.
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88
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Abstract
Single-molecule spectroscopy is an important new approach for studying the intrinsically heterogeneous process of protein folding. This Review illustrates how different single-molecule fluorescence techniques have improved our understanding of mechanistic aspects in protein folding, exemplified by a series of recent experiments on a small protein.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
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89
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Jeong S, Hollingsworth JA. Polymerization of nanocrystal quantum dot-tubulin bioconjugates. IEEE Trans Nanobioscience 2006; 5:239-45. [PMID: 17181022 DOI: 10.1109/tnb.2006.886561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nanocrystal quantum dot (NQD)-tubulin bioconjugates were prepared using a two-step crosslinking procedure. NQD-decorated microtubules were successfully polymerized directly from the NQD-tubulin conjugates to form nonaggregated, full-length (several micrometers) biopolymers. However, polymerization kinetics were slowed in comparison with unmodified tubulin and tubulin modified with small-molecule dyes or biotin. Association with the relatively large nanocrystals, therefore, interferes to some extent with tubulin's ability to polymerize. These results suggest that before NQDs are used extensively as fluorescent labels in studies of biomolecular activity, the impact of NQD bioconjugation must be well understood.
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Affiliation(s)
- Sohee Jeong
- Los Alamos National Laboratory Chemistry Division, Los Alamos, NM 87545, USA.
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90
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Abstract
Colloidal semiconductor quantum dots are promising for single-molecule biological imaging due to their outstanding brightness and photostability. As a proof of concept for single-molecule fluorescence resonance energy transfer (FRET) applications, we measured FRET between a single quantum dot and a single organic fluorophore Cy5. DNA Holliday junction dynamics measured with the quantum dot/Cy5 pair are identical to those obtained with the conventional Cy3/Cy5 pair, that is, conformational changes of individual molecules can be observed by using the quantum dot as the donor.
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Affiliation(s)
- Sungchul Hohng
- Physics Department, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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91
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Michalet X, Weiss S, Jäger M. Single-molecule fluorescence studies of protein folding and conformational dynamics. Chem Rev 2006; 106:1785-813. [PMID: 16683755 PMCID: PMC2569857 DOI: 10.1021/cr0404343] [Citation(s) in RCA: 415] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xavier Michalet
- Department of Chemistry & Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095
| | - Marcus Jäger
- Department of Chemistry & Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095
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92
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Brau RR, Tarsa PB, Ferrer JM, Lee P, Lang MJ. Interlaced optical force-fluorescence measurements for single molecule biophysics. Biophys J 2006; 91:1069-77. [PMID: 16648165 PMCID: PMC1563781 DOI: 10.1529/biophysj.106.082602] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combining optical tweezers with single molecule fluorescence offers a powerful technique to study the biophysical properties of single proteins and molecules. However, such integration into a combined, coincident arrangement has been severely limited by the dramatic reduction in fluorescence longevity of common dyes under simultaneous exposure to trapping and fluorescence excitation beams. We present a novel approach to overcome this problem by alternately modulating the optical trap and excitation beams to prevent simultaneous exposure of the fluorescent dye. We demonstrate the dramatic reduction of trap-induced photobleaching effects on the common single molecule fluorescence dye Cy3, which is highly susceptible to this destructive pathway. The extension in characteristic fluorophore longevity, a 20-fold improvement when compared to simultaneous exposure to both beams, prolongs the fluorescence emission to several tens of seconds in a combined, coincident arrangement. Furthermore, we show that this scheme, interlaced optical force-fluorescence, does not compromise the trap stiffness or single molecule fluorescence sensitivity at sufficiently high modulation frequencies. Such improvement permits the simultaneous measurement of the mechanical state of a system with optical tweezers and the localization of molecular changes with single molecule fluorescence, as demonstrated by mechanically unzipping a 15-basepair DNA segment labeled with Cy3.
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Affiliation(s)
- Ricardo R Brau
- Department of Mechanical Engineering, Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, 02139, USA
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93
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Perroud TD, Bokoch MP, Zare RN. Cytochrome c conformations resolved by the photon counting histogram: watching the alkaline transition with single-molecule sensitivity. Proc Natl Acad Sci U S A 2005; 102:17570-5. [PMID: 16314563 PMCID: PMC1308922 DOI: 10.1073/pnas.0508975102] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We apply the photon counting histogram (PCH) model, a fluorescence technique with single-molecule sensitivity, to study pH-induced conformational changes of cytochrome c. PCH is able to distinguish different protein conformations based on the brightness of a fluorophore sensitive to its local environment. We label cytochrome c through its single free cysteine with tetramethylrhodamine-5-maleimide (TMR), a fluorophore with specific brightnesses that we associate with specific protein conformations. Ensemble measurements demonstrate two different fluorescence responses with increasing pH: (i) a decrease in fluorescence intensity caused by the alkaline transition of cytochrome c (pH 7.0-9.5), and (ii) an increase in intensity when the protein unfolds (pH 9.5-10.8). The magnitudes of these two responses depend strongly on the molar ratio of TMR used to label cytochrome c. Using PCH we determine that this effect arises from the proportion of a nonfunctional conformation in the sample, which can be differentiated from the functional conformation. We further determine the causes of each ensemble fluorescence response: (i) during the alkaline transition, the fluorophore enters a dark state and discrete conformations are observed, and (ii) as cytochrome c unfolds, the fluorophore incrementally brightens, but discrete conformations are no longer resolved. Moreover, we also show that functional TMR-cytochrome c undergoes a response of identical magnitude regardless of the proportion of nonfunctional protein in the sample. As expected for a technique with single-molecule sensitivity, we demonstrate that PCH can directly observe the most relevant conformation, unlike ensemble fluorometry.
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Affiliation(s)
- Thomas D Perroud
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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94
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Kapanidis AN, Laurence TA, Lee NK, Margeat E, Kong X, Weiss S. Alternating-laser excitation of single molecules. Acc Chem Res 2005; 38:523-33. [PMID: 16028886 DOI: 10.1021/ar0401348] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Single-molecule fluorescence spectroscopy addresses biological mechanisms and enables ultrasensitive diagnostics. We describe a new family of single-molecule fluorescence methods that uses alternating-laser excitation (ALEX) of diffusing or immobilized biomolecules to study their structure, interactions, and dynamics. This is accomplished using ratios that report on the distance between and the stoichiometry of fluorophores attached to the molecules of interest. The principle of alternation is compatible with several time scales, allowing monitoring of fast dynamics or simultaneous monitoring of a large number of individual molecules.
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Affiliation(s)
- Achillefs N Kapanidis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA.
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95
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Willets KA, Nishimura SY, Schuck PJ, Twieg RJ, Moerner WE. Nonlinear optical chromophores as nanoscale emitters for single-molecule spectroscopy. Acc Chem Res 2005; 38:549-56. [PMID: 16028889 DOI: 10.1021/ar0401294] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence imaging of single molecules at room temperature is a powerful technique for studying complex condensed phase systems and revealing structure and dynamics hidden by ensemble measurements. Successful single-molecule spectroscopic experiments rely upon strong emitters that can be detected at the level of individual copies above the relevant background signals. This Account discusses a class of nonlinear optical chromophores that not only are well-suited for single-molecule imaging but also offer additional beneficial properties such as a significant ground-state dipole moment, moderate hyperpolarizability, and sensitivity to local environment. An overview of the photophysical properties of several members of this class of molecules as well as a mechanism to help understand the environmental sensitivity is presented. Some preliminary applications of the chromophores as single-molecule reporters in cellular and polymer systems are discussed, along with detection of the emitters by two-photon fluorescence.
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Affiliation(s)
- Katherine A Willets
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, Kent State University, Kent, Ohio 44242, USA
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96
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Allen MW, Urbauer RJB, Zaidi A, Williams TD, Urbauer JL, Johnson CK. Fluorescence labeling, purification, and immobilization of a double cysteine mutant calmodulin fusion protein for single-molecule experiments. Anal Biochem 2005; 325:273-84. [PMID: 14751262 DOI: 10.1016/j.ab.2003.10.045] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present a method of labeling and immobilizing a low-molecular-weight protein, calmodulin (CaM), by fusion to a larger protein, maltose binding protein (MBP), for single-molecule fluorescence experiments. Immobilization in an agarose gel matrix eliminates potential interactions of the protein and the fluorophore(s) with a glass surface and allows prolonged monitoring of protein dynamics. The small size of CaM hinders its immobilization in low-weight-percentage agarose gels; however, fusion of CaM to MBP via a flexible linker provides sufficient restriction of translational mobility in 1% agarose gels. Cysteine residues were engineered into MBP.CaM (MBP-T34C,T110C-CaM) and labeled with donor and acceptor fluorescent probes yielding a construct (MBP.CaM-DA) which can be used for single-molecule single-pair fluorescence resonance energy transfer (spFRET) experiments. Mass spectrometry was used to verify the mass of MBP.CaM-DA. Assays measuring the activity of CaM reveal minimal activity differences between wild-type CaM and MBP.CaM-DA. Single-molecule fluorescence images of the donor and acceptor dyes were fit to a two-dimensional Gaussian function to demonstrate colocalization of donor and acceptor dyes. FRET is demonstrated both in bulk fluorescence spectra and in fluorescence trajectories of single MBP.CaM-DA molecules. The extension of this method to other biomolecules is also proposed.
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Affiliation(s)
- Michael W Allen
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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97
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Tinnefeld P, Sauer M. Branching Out of Single‐Molecule Fluorescence Spectroscopy: Challenges for Chemistry and Influence on Biology. Angew Chem Int Ed Engl 2005; 44:2642-2671. [PMID: 15849689 DOI: 10.1002/anie.200300647] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the last decade emerging single-molecule fluorescence-spectroscopy tools have been developed and adapted to analyze individual molecules under various conditions. Single-molecule-sensitive optical techniques are now well established and help to increase our understanding of complex problems in different disciplines ranging from materials science to cell biology. Previous dreams, such as the monitoring of the motility and structural changes of single motor proteins in living cells or the detection of single-copy genes and the determination of their distance from polymerase molecules in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this Review we demonstrate that single-molecule fluorescence spectroscopy has become an independent discipline capable of solving problems in molecular biology. We outline the challenges and future prospects for optical single-molecule techniques which can be used in combination with smart labeling strategies to yield quantitative three-dimensional information about the dynamic organization of living cells.
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Affiliation(s)
- Philip Tinnefeld
- Applied Laserphysics und Laserspectroscopy, Faculty of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany, Fax: (+49) 521-106-2958
| | - Markus Sauer
- Applied Laserphysics und Laserspectroscopy, Faculty of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany, Fax: (+49) 521-106-2958
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98
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Tinnefeld P, Sauer M. Neue Wege in der Einzelmolekül-Fluoreszenzspektroskopie: Herausforderungen für die Chemie und Einfluss auf die Biologie. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200300647] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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99
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Abstract
Single-molecule imaging and manipulation techniques have evolved in the past decade from mere jaw-dropping attractions to essential laboratory tools. By applying single-molecule methods important insights otherwise unavailable have been obtained on various biomolecular systems. Constantly improving single-molecule imaging techniques keep expanding the scale of the explorable spatial detail, thereby providing possible solutions to getting around the debilitating diffraction limit present in physiological-condition structural investigations. In some areas, such as motor protein studies, single-molecule methods have become part of the routine and essential research toolkit. Entire research fields, such as single-molecule force spectroscopy, have been born. In the present review single-molecule visualization and manipulation methods are reviewed with a focus on proteins. Relevant signals and prominent applications are discussed along with experimental examples and recent important results. Finally, the perspectives of the single-molecule field are explored.
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Affiliation(s)
- Miklós S Z Kellermayer
- Department of Biophysics, Faculty of Medicine, University of Pécs, Szigeti út 12. Pécs H-7624, Hungary.
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100
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Lee NK, Kapanidis AN, Wang Y, Michalet X, Mukhopadhyay J, Ebright RH, Weiss S. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J 2005; 88:2939-53. [PMID: 15653725 PMCID: PMC1282518 DOI: 10.1529/biophysj.104.054114] [Citation(s) in RCA: 322] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Fluorescence resonance energy transfer (FRET) between a donor (D) and an acceptor (A) at the single-molecule level currently provides qualitative information about distance, and quantitative information about kinetics of distance changes. Here, we used the sorting ability of confocal microscopy equipped with alternating-laser excitation (ALEX) to measure accurate FRET efficiencies and distances from single molecules, using corrections that account for cross-talk terms that contaminate the FRET-induced signal, and for differences in the detection efficiency and quantum yield of the probes. ALEX yields accurate FRET independent of instrumental factors, such as excitation intensity or detector alignment. Using DNA fragments, we showed that ALEX-based distances agree well with predictions from a cylindrical model of DNA; ALEX-based distances fit better to theory than distances obtained at the ensemble level. Distance measurements within transcription complexes agreed well with ensemble-FRET measurements, and with structural models based on ensemble-FRET and x-ray crystallography. ALEX can benefit structural analysis of biomolecules, especially when such molecules are inaccessible to conventional structural methods due to heterogeneity or transient nature.
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Affiliation(s)
- Nam Ki Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
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