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Werner S, Ebenhan J, Haupt C, Bacia K. A Quantitative and Reliable Calibration Standard for Dual-Color Fluorescence Cross-Correlation Spectroscopy. Chemphyschem 2018; 19:3436-3444. [PMID: 30489002 DOI: 10.1002/cphc.201800576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/29/2018] [Indexed: 11/06/2022]
Abstract
Dual-color Fluorescence Cross-Correlation Spectroscopy (dcFCCS) allows binding analysis of biomolecules. Combining cross- and autocorrelation amplitudes yields binding degrees and concentrations of bound and unbound species. However, non-ideal detection volume overlap reduces the cross-correlation, causing overestimation of the Kd . The overlap quality factor that relates measured and true cross-correlation amplitudes has been difficult to determine, because neither a perfect 1 : 1 labeled sample nor perfectly overlapping volumes are readily accomplished. Here, we describe how a stochastically labeled sample can be used for quantitative calibration. Lipid vesicles doped with green and red fluorescent dyes yield highly reproducible relative cross-correlations and allow determination of the setup-dependent overlap quality factor. This reliable, affordable and quick-to-prepare calibration standard expedites any quantitative co-localization or binding analysis by dcFCCS.
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Affiliation(s)
- Stefan Werner
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Jan Ebenhan
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Caroline Haupt
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Kirsten Bacia
- Institute of Chemistry, ZIK HALOmem and Charles-Tanford-Protein Center, University of Halle, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
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2
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Kaliszewski MJ, Shi X, Hou Y, Lingerak R, Kim S, Mallory P, Smith AW. Quantifying membrane protein oligomerization with fluorescence cross-correlation spectroscopy. Methods 2018; 140-141:40-51. [PMID: 29448037 DOI: 10.1016/j.ymeth.2018.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/17/2017] [Accepted: 02/07/2018] [Indexed: 01/27/2023] Open
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is an advanced fluorescence technique that can quantify protein-protein interactions in vivo. Due to the dynamic, heterogeneous nature of the membrane, special considerations must be made to interpret FCCS data accurately. In this study, we describe a method to quantify the oligomerization of membrane proteins tagged with two commonly used fluorescent probes, mCherry (mCH) and enhanced green (eGFP) fluorescent proteins. A mathematical model is described that relates the relative cross-correlation value (fc) to the degree of oligomerization. This treatment accounts for mismatch in the confocal volumes, combinatoric effects of using two fluorescent probes, and the presence of non-fluorescent probes. Using this model, we calculate a ladder of fc values which can be used to determine the oligomer state of membrane proteins from live-cell experimental data. Additionally, a probabilistic mathematical simulation is described to resolve the affinity of different dimeric and oligomeric protein controls.
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Affiliation(s)
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Yixuan Hou
- Food Animal Health Research Program, Ohio Agriculture Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA
| | - Ryan Lingerak
- Department of Biology, University of Akron, Akron, OH 44325, USA
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Paul Mallory
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA.
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3
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Abstract
Dual-color cross-correlation spectroscopy is a special kind of fluctuation analysis which selectively probes the formation or deletion of linkages between two different fluorescently labeled molecules at extremely low concentrations. Two-photon excitation can, under certain circumstances, significantly simplify this method if different probe molecules with distinct emission properties are accessible by a common IR excitation wavelength.
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Affiliation(s)
- P Schwille
- Experimental Biophysics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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4
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Sahoo H, Schwille P. FRET and FCS--friends or foes? Chemphyschem 2011; 12:532-41. [PMID: 21308943 DOI: 10.1002/cphc.201000776] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 01/07/2011] [Indexed: 11/05/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) are both scientific concepts that are frequently discussed in the context of single-molecule fluorescence techniques. In contrast to FCS, FRET is strictly not a technique but a photophysical phenomenon, which can be employed in combination with any method that probes fluorescence intensity or lifetime. Thus, the combination of FCS with FRET is possible and—although these concepts are quite often treated as alternative approaches, particularly for the analysis of biological systems—also quite attractive. However, under certain circumstances, for example, for applications of fluorescence cross-correlation spectroscopy, FRET effects can cause significant complications for quantitative data analysis, and careful calibration has to be carried out to avoid FRET-induced artifacts. This can be most elegantly done if alternating excitation schemes such as PIE (pulsed interleaved excitation) are employed. In this minireview, we discuss the potential and the caveats of FCS combined with FRET and give a short record on successful and promising applications.
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Affiliation(s)
- Harekrushna Sahoo
- Department of Biophysics, Biotechnologisches Zentrum, Technische Universität Dresden, Tatzberg 47-49, Dresden 01307, Germany
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5
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Mitsuhashi M, Sakata H, Kinjo M, Yazawa M, Takahashi M. Dynamic assembly properties of nonmuscle myosin II isoforms revealed by combination of fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy. J Biochem 2010; 149:253-63. [PMID: 21106542 DOI: 10.1093/jb/mvq134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Myosin II molecules assemble into filaments through their C-terminal rod region, and are responsible for several cellular motile activities. Three isoforms of nonmuscle myosin II (IIA, IIB and IIC) are expressed in mammalian cells. However, little is known regarding the isoform composition in filaments. To obtain new insight into the assembly properties of myosin II isoforms, especially regarding the isoform composition in filaments, we performed a combination analysis of fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS), which enables us to acquire information on both the interaction and the size of each molecule simultaneously. Using C-terminal rod fragments of IIA and IIB (ARF296 and BRF305) labelled with different fluorescent probes, we demonstrated that hetero-assemblies were formed from a mixture of ARF296 and BRF305, and that dynamic exchange of rod fragments occurred between preformed homo-assemblies of each isoform in an isoform-independent manner. We also showed that Mts1 (S100A4) specifically stripped ARF296 away from the hetero-assemblies, and consequently, homo-assemblies of BRF305 were formed. These results suggest that IIA and IIB can form hetero-filaments in an isoform-independent manner, and that a factor like Mts1 can remove one isoform from the hetero-filament, resulting in a formation of homo-filaments consisting of another isoform.
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Affiliation(s)
- Mariko Mitsuhashi
- Division of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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6
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Melnykov AV, Hall KB. Revival of high-order fluorescence correlation analysis: generalized theory and biochemical applications. J Phys Chem B 2010; 113:15629-38. [PMID: 19877707 DOI: 10.1021/jp906539k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analysis of high-order correlations in fluorescence fluctuation spectroscopy was developed in the late 1980s but since then has been replaced by alternative brightness analysis methods. However, high-order correlation has important advantages in many experiments. We present a new cumulant-based formalism of high-order correlation that greatly simplifies data analysis. The new formalism is used to derive general expressions for variance of high-order correlations that show good agreement with experiment in a model system of fluorescently labeled DNA oligomers. A simulation of binary systems in which both diffusion time and brightness are varied illustrates clearly that high-order analysis has better sensitivity to brightness than fluorescence correlation spectroscopy (FCS). These results have implications for analysis of isomerization reactions and dual-beam FCS with flow. We also demonstrate that high-order correlations can detect photobleaching in the observation volume. The application of this formalism to many FCS-based experiments allows more accurate analysis in addition to describing more molecular parameters.
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Affiliation(s)
- Artem V Melnykov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Box 8231, St. Louis, Missouri 63110, USA
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7
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Hwang LC, Wohland T. Recent Advances in Fluorescence Cross-correlation Spectroscopy. Cell Biochem Biophys 2007; 49:1-13. [PMID: 17873335 DOI: 10.1007/s12013-007-0042-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 11/30/1999] [Accepted: 05/21/2007] [Indexed: 12/14/2022]
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is a method that measures the temporal fluorescence fluctuations coming from two differently labeled molecules diffusing through a small sample volume. Cross-correlation analysis of the fluorescence signals from separate detection channels extracts information of the dynamics of the dual-labeled molecules. FCCS has become an essential tool for the characterization of diffusion coefficients, binding constants, kinetic rates of binding, and determining molecular interactions in solutions and cells. By cross-correlating between two focal spots, flow properties could also be measured. Recent developments in FCCS have been targeted at using different experimental schemes to improve on the sensitivity and address their limitations such as cross-talk and alignment issues. This review presents an overview of the different excitation and detection methodologies used in FCCS and their biological applications. This is followed by a description of the fluorescent probes currently available for the different methods. This will introduce biological readers to FCCS and its related techniques and provide a starting point to selecting which experimental scheme is suitable for their type of biological study.
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Affiliation(s)
- Ling Chin Hwang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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8
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Zwilling D, Cypionka A, Pohl WH, Fasshauer D, Walla PJ, Wahl MC, Jahn R. Early endosomal SNAREs form a structurally conserved SNARE complex and fuse liposomes with multiple topologies. EMBO J 2006; 26:9-18. [PMID: 17159904 PMCID: PMC1782365 DOI: 10.1038/sj.emboj.7601467] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 11/06/2006] [Indexed: 02/05/2023] Open
Abstract
SNARE proteins mediate membrane fusion in eukaryotic cells. They contain conserved SNARE motifs that are usually located adjacent to a C-terminal transmembrane domain. SNARE motifs spontaneously assemble into four helix bundles, with each helix belonging to a different subfamily. Liposomes containing SNAREs spontaneously fuse with each other, but it is debated how the SNAREs are distributed between the membranes. Here, we report that the SNAREs mediating homotypic fusion of early endosomes fuse liposomes in five out of seven possible combinations, in contrast to previously studied SNAREs involved in heterotypic fusion events. The crystal structure of the early endosomal SNARE complex resembles that of the neuronal and late endosomal complexes, but differs in surface side-chain interactions. We conclude that homotypic fusion reactions may proceed with multiple SNARE topologies, suggesting that the conserved SNARE structure allows for flexibility in the initial interactions needed for fusion.
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Affiliation(s)
- Daniel Zwilling
- Department of Neurobiology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Anna Cypionka
- AG Label-Free Biomolecular Analysis and Single-Molecule Detection, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Wiebke H Pohl
- AG Label-Free Biomolecular Analysis and Single-Molecule Detection, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Fasshauer
- Department of Neurobiology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Peter J Walla
- AG Label-Free Biomolecular Analysis and Single-Molecule Detection, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Biophysical Chemistry, Institute for Physical and Theoretical Chemistry, Technical University of Braunschweig, Braunschweig, Germany
| | - Markus C Wahl
- X-ray Crystallography Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Tel.: +49 551 201 1635; Fax: +49 551 201 1639; E-mail:
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9
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Hwang LC, Wohland T. Single wavelength excitation fluorescence cross-correlation spectroscopy with spectrally similar fluorophores: resolution for binding studies. J Chem Phys 2006; 122:114708. [PMID: 15836244 DOI: 10.1063/1.1862614] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It was shown recently that fluorescence cross-correlation spectroscopy (FCCS) can be performed using a single laser wavelength for excitation (SW-FCCS) [L. C. Hwang and T. Wohland, Chem. Phys. Chem 5, 549 (2004).]. This method simplifies the FCCS setup since it does not require the simultaneous alignment of two lasers to the same focal spot. But up to now the method was shown to work only with dyes possessing large Stokes' shifts, and thus was limited to the use of quantum dots and tandem dyes. In this work we show that standard organic dyes with overlapping emission spectra, for instance fluorescein and tetramethylrhodamine, can be used as fluorescent pairs in SW-FCCS. As a biological model system for ligand-receptor interactions we studied the binding of biotin to streptavidin. To investigate the applicability of SW-FCCS for binding studies we adapt the existing FCCS theory for SW-FCCS and calculate limits for the measurement of dissociation constants in dependence on sample concentration, sample purity, and spectral cross talk between the different detection channels.
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10
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Pohl WH, Hellmuth H, Hilbert M, Seibel J, Walla PJ. A Two-Photon Fluorescence-Correlation Study of Lectins Interacting with Carbohydrated 20 nm Beads. Chembiochem 2006; 7:268-74. [PMID: 16408309 DOI: 10.1002/cbic.200500246] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present results of a two-photon fluorescence-correlation study carried out with glycosylated and untreated 20 nm fluorescing spheres that interacted with the carbohydrate-binding proteins soybean agglutinin (SBA) and concanavalin A (Con A). The assay principle allows protein-carbohydrate binding interactions to be determined without protein labeling. This assay might serve as a simple model system for studying physical and chemical interactions between proteins and carbohydrates, for example, at cell or virus surfaces. In experiments with galactosylated 20 nm beads and SBA, several stages of protein-carbohydrate interactions could be clearly distinguished. Initially, only a few lectins bound to the nanospheres. At higher lectin concentrations polymerization occurred, and aggregates consisting of about 2.6 x 10(5) glycosylated nanospheres were formed. At very high lectin concentrations, the degree of polymerization dropped, and the size of single SBA-covered nanospheres increased to approximately 40 nm. When Con A was used instead of SBA, a significantly smaller degree of aggregation (4 x 10(4) spheres) was obtained. Treatment of unglycosylated 20 nm beads with SBA as a negative control sample resulted in a much lower unspecific aggregation (5 x 10(3) spheres). The assay principle can thus help to elucidate relative binding affinities.
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Affiliation(s)
- Wiebke H Pohl
- Max-Planck-Institute for Biophysical Chemistry, Department of Spectroscopy and Photochemical Kinetics, Am Fassberg 11, 37077 Göttingen, Germany
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11
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Hilbert M, Hippchen H, Wehling A, Walla PJ. Correlational Analysis of Proteins and Nonmetallic Nanoparticles in a Deep-Nulling Microscope. J Phys Chem B 2005; 109:18162-70. [PMID: 16853332 DOI: 10.1021/jp052204d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a method for label-free microscopic analysis of nonmetallic nanoparticles such as biopolymers or technical polymers diffusing freely in an aqueous environment. We demonstrate the principal feasibility of the approach with first measurements of 20-200 nm sized polystyrene spheres and of the approximately 10 nm protein complex Photosystem I (PS I) of Thermosynechococcus elongatus. The approach is based on the combination of a microscope setup with a deep-nulling interferometer for measuring minute refractive index changes or absorptions in the focal area of the microscope. It is possible to obtain transient nulls in a microscope setup on the order of 10(-5), corresponding to optical pathway differences of less than 0.6 nm and to stabilize the nulls to about 5.10(-4). With this level of stabilization it is possible to perform a fast (1 s) correlational analysis of aqueous solutions containing the protein complex PS I or 20 nm spheres and to detect in real time single diffusional transits of larger nanospheres through the focal area of the microscope. A modulated heating of the samples in the microscope focus is not necessary for detection. The interferometer correlation data correspond well to conventional two-photon excited fluorescence correlation (FCS) data measured in the same setup, providing evidence that the detection volumes are of a similar size (approximately 200 nm). We also conducted first nulling experiments using coherent near-field sources of about 30 nm diameter. Theoretical considerations indicate that this combination with nanometric near-field sources will even allow label-free single-protein analysis.
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Affiliation(s)
- Michael Hilbert
- Max-Planck-Institute for Biophysical Chemistry, Department 010, Spectroscopy and Photochemical Kinetics, Am Fassberg 11, D-37077 Göttingen, Germany
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12
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Skakun VV, Hink MA, Digris AV, Engel R, Novikov EG, Apanasovich VV, Visser AJWG. Global analysis of fluorescence fluctuation data. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 34:323-34. [PMID: 15711810 DOI: 10.1007/s00249-004-0453-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Revised: 11/30/2004] [Accepted: 11/30/2004] [Indexed: 11/30/2022]
Abstract
Over the last decade the number of applications of fluorescence correlation spectroscopy (FCS) has grown rapidly. Here we describe the development and application of a software package, FCS Data Processor, to analyse the acquired correlation curves. The algorithms combine strong analytical power with flexibility in use. It is possible to generate initial guesses, link and constrain fit parameters to improve the accuracy and speed of analysis. A global analysis approach, which is most effective in analysing autocorrelation curves determined from fluorescence fluctuations of complex biophysical systems, can also be implemented. The software contains a library of frequently used models that can be easily extended to include user-defined models. The use of the software is illustrated by analysis of different experimental fluorescence fluctuation data sets obtained with Rhodamine Green in aqueous solution and enhanced green fluorescent protein in vitro and in vivo.
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Affiliation(s)
- Victor V Skakun
- Department of Systems Analysis, Belarusian State University, Minsk 220050, Belarus
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13
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Camacho A, Korn K, Damond M, Cajot JF, Litborn E, Liao B, Thyberg P, Winter H, Honegger A, Gardellin P, Rigler R. Direct quantification of mRNA expression levels using single molecule detection. J Biotechnol 2004; 107:107-14. [PMID: 14711494 DOI: 10.1016/j.jbiotec.2003.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determination of the gene expression by direct quantification of mRNA is becoming increasingly important in basic, pharmaceutical and clinical research. We present a novel approach for gene quantification based on direct hybridization of gene-specific probes to target mRNA sequences in solution at temperatures ensuring absolute specificity of the probe-target complex. No enzymatic steps like reverse transcription or amplification by PCR are involved within the quantification process. In order to increase specificity as well as sensitivity, two probes emitting fluorescence light in different colors are used for our homogeneous assay using fluorescence cross-correlation. We relate to the single molecule sensitivity of excitation and detection in confocal cavities avoiding the amplification of the detected signal. The analysis of the expression level of high, medium and low abundant genes is described in two different cell lines, whereby the genes are quantified in absolute numbers.
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MESH Headings
- Calcium-Binding Proteins
- Calibration
- Chromatography, High Pressure Liquid
- Cytoskeletal Proteins/analysis
- DNA, Complementary/chemical synthesis
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Complementary/metabolism
- Fluorescent Dyes
- Gene Expression
- HL-60 Cells
- Humans
- K562 Cells
- Membrane Glycoproteins/analysis
- Nerve Tissue Proteins/analysis
- Phosphoglycerate Kinase/analysis
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Reproducibility of Results
- Rhodamines
- Sensitivity and Specificity
- Solutions
- Spectrometry, Fluorescence/methods
- Spectrophotometry, Ultraviolet
- Synaptotagmins
- Time Factors
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Affiliation(s)
- Agnès Camacho
- Gnothis SA, PSE-B, EPFL, CH-1015 Lausanne, Switzerland
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14
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Nolan RL, Cai H, Nolan JP, Goodwin PM. A Simple Quenching Method for Fluorescence Background Reduction and Its Application to the Direct, Quantitative Detection of Specific mRNA. Anal Chem 2003; 75:6236-43. [PMID: 14616007 DOI: 10.1021/ac034803r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New genome sequence information is rapidly increasing the number of nucleic acid (NA) targets of use for characterizing and treating diseases. Detection of these targets by fluorescence-based assays is often limited by fluorescence background from unincorporated or unbound probes that are present in large excess over the target. To solve this problem, energy transfer-based probes have been developed and used to reduce the fluorescence from unbound probes. Although these probes have revolutionized NA target detection, their use requires scrupulous attention to design constraints, extensive probe quality control, and individually optimized experimental conditions. Here, we describe a simpler background reduction approach using singly labeled quencher oligomers to suppress excess unbound probe fluorescence following probe-target hybridization. A second limitation of most fluorescence-based NA target detection and quantification assays is the requirement for enzymatic amplification of target or signal for sensitivity. Amplification steps make quantification of original target copy number problematic because of variations in amplification efficiencies between the sequence targets and the experimental conditions. To avoid amplification, we coupled our quenching approach to a two-color NA assay with correlated, two-color, single-molecule fluorescence detection. We demonstrate a >100-fold background reduction and detection of targets present at concentrations as low as 100 fM using the two-color assay. The application of this technique to the detection and quantification of specific mRNA sequences enabled us to estimate beta-actin copy numbers in cell-derived total RNA without an amplification step.
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Affiliation(s)
- Rhiannon L Nolan
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, New Mexico 87545, USA
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15
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Kohl T, Heinze KG, Kuhlemann R, Koltermann A, Schwille P. A protease assay for two-photon crosscorrelation and FRET analysis based solely on fluorescent proteins. Proc Natl Acad Sci U S A 2002; 99:12161-6. [PMID: 12209012 PMCID: PMC129415 DOI: 10.1073/pnas.192433499] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
GFP and the red fluorescent protein, DsRed, have been combined to design a protease assay that allows not only for fluorescence resonance energy transfer (FRET) studies but also for dual-color crosscorrelation analysis, a single-molecule-based method that selectively probes the concomitant movement of two distinct tags. The measurement principle is based on a spectrally resolved detection of single molecules diffusing in and out of a diffraction-limited laser focus. Double-labeled substrate molecules are separated into two single-labeled products by specific cleavage at a protease cleavage site between the two flanking tags, DsRed and GFP, thus disrupting joint fluctuations in the two detection channels and terminating FRET between the two labels. In contrast to enzyme assays based solely on FRET, this method of dual-color crosscorrelation is not limited to a certain range of distances between the fluorophores and is much more versatile with respect to possible substrate design. To simplify the measurement setup, two-photon excitation was used, allowing for simultaneous excitation of both tags with a single infrared laser wavelength. The general concept was experimentally verified with a GFP-peptide-DsRed construct containing the cleavage site for tobacco etch virus protease. Two-photon excitation in the infrared and the use of cloneable tags make this assay easily adaptable to intracellular applications. Moreover, the combination of FRET and crosscorrelation analysis in a single-molecule-based approach promises exciting perspectives for miniaturized high-throughput screening based on fluorescence spectroscopy.
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Affiliation(s)
- Tobias Kohl
- Experimental Biophysics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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16
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Medina MA, Schwille P. Fluorescence correlation spectroscopy for the detection and study of single molecules in biology. Bioessays 2002; 24:758-64. [PMID: 12210537 DOI: 10.1002/bies.10118] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The recent development of single molecule detection techniques has opened new horizons for the study of individual macromolecules under physiological conditions. Conformational subpopulations, internal dynamics and activity of single biomolecules, parameters that have so far been hidden in large ensemble averages, are now being unveiled. Herein, we review a particular attractive solution-based single molecule technique, fluorescence correlation spectroscopy (FCS). This time-averaging fluctuation analysis which is usually performed in Confocal setups combines maximum sensitivity with high statistical confidence. FCS has proven to be a very versatile and powerful tool for detection and temporal investigation of biomolecules at ultralow concentrations on surfaces, in solution, and in living cells. The introduction of dual-color cross-correlation and two-photon excitation in FCS experiments is currently increasing the number of promising applications of FCS to biological research.
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Affiliation(s)
- Miguel Angel Medina
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Málaga, Spain.
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17
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Abstract
Fluorescence correlation spectroscopy (FCS) can measure dynamics of fluorescent molecules in cells. FCS measures the fluctuations in the number of fluorescent molecules in a small volume illuminated by a thin beam of excitation light. These fluctuations are processed statistically to yield an autocorrelation function from which rates of diffusion, convection, chemical reaction, and other processes can be extracted. The advantages of this approach include the ability to measure the mobility of a very small number of molecules, even down to the single molecule level, over a wide range of rates in very small regions of a cell. In addition to rates of diffusion and convection, FCS also provides unique information about the local concentration, states of aggregation and molecular interaction using fluctuation amplitude and cross-correlation methods. Recent advances in technology have rendered these once difficult measurements accessible to routine use in cell biology and biochemistry. This review provides a summary of the FCS method and describes current areas in which the FCS approach is being extended beyond its original scope.
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Affiliation(s)
- E L Elson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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