101
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Grünwald D, Spottke B, Buschmann V, Kubitscheck U. Intranuclear binding kinetics and mobility of single native U1 snRNP particles in living cells. Mol Biol Cell 2006; 17:5017-27. [PMID: 16987963 PMCID: PMC1679670 DOI: 10.1091/mbc.e06-06-0559] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are splicing factors, which are diffusely distributed in the nucleoplasm and also concentrated in nuclear speckles. Fluorescently labeled, native U1 snRNPs were microinjected into the cytoplasm of living HeLa cells. After nuclear import single U1 snRNPs could be visualized and tracked at a spatial precision of 30 nm at a frame rate of 200 Hz employing a custom-built microscope with single-molecule sensitivity. The single-particle tracks revealed that most U1 snRNPs were bound to specific intranuclear sites, many of those presumably representing pre-mRNA splicing sites. The dissociation kinetics from these sites showed a multiexponential decay behavior on time scales ranging from milliseconds to seconds, reflecting the involvement of U1 snRNPs in numerous distinct interactions. The average dwell times for U1 snRNPs bound at sites within the nucleoplasm did not differ significantly from those in speckles, indicating that similar processes occur in both compartments. Mobile U1 snRNPs moved with diffusion constants in the range from 0.5 to 8 microm2/s. These values were consistent with uncomplexed U1 snRNPs diffusing at a viscosity of 5 cPoise and U1 snRNPs moving in a largely restricted manner, and U1 snRNPs contained in large supramolecular assemblies such as spliceosomes or supraspliceosomes.
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Affiliation(s)
- David Grünwald
- *Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany; and
| | - Beatrice Spottke
- *Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany; and
| | | | - Ulrich Kubitscheck
- *Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, D-53115 Bonn, Germany; and
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102
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Shav-Tal Y, Darzacq X, Singer RH. Gene expression within a dynamic nuclear landscape. EMBO J 2006; 25:3469-79. [PMID: 16900099 PMCID: PMC1538565 DOI: 10.1038/sj.emboj.7601226] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 06/07/2006] [Indexed: 01/01/2023] Open
Abstract
Molecular imaging in living cells or organisms now allows us to observe macromolecular assemblies with a time resolution sufficient to address cause-and-effect relationships on specific molecules. These emerging technologies have gained much interest from the scientific community since they have been able to reveal novel concepts in cell biology, thereby changing our vision of the cell. One main paradigm is that cells stochastically vary, thus implying that population analysis may be misleading. In fact, cells should be analyzed within time-resolved single-cell experiments rather than being compared to other cells within a population. Technological imaging developments as well as the stochastic events present in gene expression have been reviewed. Here, we discuss how the structural organization of the nucleus is revealed using noninvasive single-cell approaches, which ultimately lead to the resolution required for the analysis of highly controlled molecular processes taking place within live cells. We also describe the efforts being made towards physiological approaches within the context of living organisms.
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Affiliation(s)
- Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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103
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Etienne E, Lenne PF, Sturgis JN, Rigneault H. Confined diffusion in tubular structures analyzed by fluorescence correlation spectroscopy on a mirror. APPLIED OPTICS 2006; 45:4497-507. [PMID: 16778960 DOI: 10.1364/ao.45.004497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In fluorescence correlation spectroscopy (FCS) analysis it is generally assumed that molecular species diffuse freely in volumes much larger than the three-dimensional FCS observation volume. However, this standard assumption is not valid in many measurement conditions, particularly in tubular structures with diameters in the micrometer range, such as those found in living cells (organelles, dendrites) and microfluidic devices (capillaries, reaction chambers). As a result the measured autocorrelation functions (ACFs) deviate from those predicted for free diffusion, and this can shift the measured diffusion coefficient by as much as ~50% when the tube diameter is comparable with the axial extension of the FCS observation volume. We show that the range of validity of the FCS measurements can be drastically improved if the tubular structures are located in the close vicinity of a mirror on which FCS is performed. In this case a new fluctuation time in the ACF, arising from the diffusion of fluorescent probes in optical fringes, permits measurement of the real diffusion coefficient within the tubular structure without assumptions about either the confined geometry or the FCS observation volume geometry. We show that such a measurement can be done when the tubular structure contains at least one pair of dark and bright fringes resulting from interference between the incoming and the reflected excitation beams on the mirror surface. Measurement of the diffusion coefficient of the enhanced green fluorescent protein (EGFP) and IscS-EGFP in the cytoplasm of living Escherichia coli illustrates the capabilities of the technique.
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Affiliation(s)
- Emilien Etienne
- Institut Fresnel, Mosaic Group, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Paul Cézanne Aix-Marseille III, France.
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104
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Vergara A, Capuano F, Paduano L, Sartorio R. Lysozyme Mutual Diffusion in Solutions Crowded by Poly(ethylene glycol). Macromolecules 2006. [DOI: 10.1021/ma0605705] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alessandro Vergara
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
| | - Fabio Capuano
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
| | - Luigi Paduano
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
| | - Roberto Sartorio
- Department of Chemistry, University of Naples “Federico II”, Via Cinthia, Complesso Monte S. Angelo, 80126 Naples, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, 80134, Naples, Italy
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105
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McDonald D, Carrero G, Andrin C, de Vries G, Hendzel MJ. Nucleoplasmic beta-actin exists in a dynamic equilibrium between low-mobility polymeric species and rapidly diffusing populations. ACTA ACUST UNITED AC 2006; 172:541-52. [PMID: 16476775 PMCID: PMC2063674 DOI: 10.1083/jcb.200507101] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
β-Actin, once thought to be an exclusively cytoplasmic protein, is now known to have important functions within the nucleus. Nuclear β-actin associates with and functions in chromatin remodeling complexes, ribonucleic acid polymerase complexes, and at least some ribonucleoproteins. Proteins involved in regulating actin polymerization are also found in the interphase nucleus. We define the dynamic properties of nuclear actin molecules using fluorescence recovery after photobleaching. Our results indicate that actin and actin-containing complexes are reduced in their mobility through the nucleoplasm diffusing at ∼0.5 μm2 s−1. We also observed that ∼20% of the total nuclear actin pool has properties of polymeric actin that turns over rapidly. This pool could be detected in endogenous nuclear actin by using fluorescent polymeric actin binding proteins and was sensitive to drugs that alter actin polymerization. Our results validate previous reports of polymeric forms of nuclear actin observed in fixed specimens and reveal that these polymeric forms are very dynamic.
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Affiliation(s)
- Darin McDonald
- Department of Oncology and 2Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 1Z2
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106
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Shav-Tal Y. The living test-tube: imaging of real-time gene expression. SOFT MATTER 2006; 2:361-370. [PMID: 32680249 DOI: 10.1039/b600234j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cells are dynamic entities. Not only are some cells motile but there is constant motion of organelles, proteins, nucleic acids and other molecules within every living cell. These complex molecular pathways control the life cycle of a cell and all come down to the basic players of the gene expression pathway: DNA, RNA and protein. It is therefore imperative to study biological processes as they naturally occur-in living cells, and to unravel the biophysical rules that govern intracellular dynamics. Towards this end, genetically encoded fluorescent proteins have become one of the major tools available for the study of kinetic processes taking place in real-time. This review will focus on the technical developments available for the study of gene activity in living cells and will summarize the novel biological information extracted from these approaches.
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Affiliation(s)
- Yaron Shav-Tal
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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107
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Gorski SA, Dundr M, Misteli T. The road much traveled: trafficking in the cell nucleus. Curr Opin Cell Biol 2006; 18:284-90. [PMID: 16621498 DOI: 10.1016/j.ceb.2006.03.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 03/27/2006] [Indexed: 11/20/2022]
Abstract
Trafficking of RNA molecules and proteins within the cell nucleus is central to genome function. Recent work has revealed the nature of RNA and protein motion within the nucleus and across the nuclear membrane. These studies have given insight into how molecules find their destinations within the nucleus and have uncovered some of the structural properties of the nuclear microenvironment. Control of RNA and protein trafficking is now emerging as a physiological regulatory mechanism in gene expression and nuclear function.
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108
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Tadakuma H, Ishihama Y, Shibuya T, Tani T, Funatsu T. Imaging of single mRNA molecules moving within a living cell nucleus. Biochem Biophys Res Commun 2006; 344:772-9. [PMID: 16631111 DOI: 10.1016/j.bbrc.2006.03.202] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2006] [Accepted: 03/30/2006] [Indexed: 10/24/2022]
Abstract
In eukaryotic cells, pre-mRNAs are transcribed in the nucleus, processed by 5' capping, 3'-polyadenylation, and splicing, and exported to the cytoplasm for translation. To examine the nuclear mRNA transport mechanism, intron-deficient mRNAs of truncated beta-globin and EGFP were synthesized, fluorescently labeled in vitro, and injected into the nucleus of living Xenopus A6 cells. The trajectories of single mRNA molecules in the nucleus were visualized using video-rate confocal microscopy. Approximately half the mRNAs moved by Brownian motion in the nucleoplasm, except the nucleoli, with an apparent diffusion coefficient of 0.2microm(2)/s, about 1/150 of that in water. The slow diffusion could not be explained by simple diffusion obeying the Stokes-Einstein equation, suggesting interactions of the mRNAs with nuclear components. The remaining mRNAs were stationary with an average residence time of about 30s, comparable to the time required for mRNA diffusion from the site of synthesis to nuclear pores.
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Affiliation(s)
- Hisashi Tadakuma
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
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109
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Dirks RW, Tanke HJ. Advances in fluorescent tracking of nucleic acids in living cell. Biotechniques 2006; 40:489-96. [PMID: 16629396 DOI: 10.2144/000112121] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleic acids are typically detected in morphologically preserved fixed cells and tissues using in situ hybridization techniques. This review discusses a variety of established and more challenging fluorescence-based methods for the detection and tracking of DNA or RNA sequences in living cells. Over the past few years, various fluorescent in vivo labeling methods have been developed, and dedicated microscope and image analysis tools have been designed. These advances in technologies indicate that live-cell imaging of nucleic acids is likely to become a standard research tool for understanding genome organization and gene expression regulation in the near future. Recent live-cell imaging studies have already provided important insights into the dynamic behaviors of chromatin and RNAs in the cell.
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Affiliation(s)
- Roeland W Dirks
- Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL, Leiden, The Netherlands.
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110
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Winkler RG, Keller S, Rädler JO. Intramolecular dynamics of linear macromolecules by fluorescence correlation spectroscopy. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:041919. [PMID: 16711848 DOI: 10.1103/physreve.73.041919] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Revised: 12/22/2005] [Indexed: 05/09/2023]
Abstract
A theoretical description of the dynamics of DNA molecules and actin filaments in solution as measured experimentally by fluorescence correlation spectroscopy is provided and compared to recent experimental results. Particular attention is paid to the contribution of the intramolecular dynamics to the fluorescence correlation function. Using a semiflexible chain model, a theoretical expression is presented for the fluorescence correlation spectroscopy correlation function. The dependence of this function on various model parameters, such as chain length, persistence length, and fluorescence label density, is discussed. Our investigations show that the intramolecular dynamics provides a significant contribution or even dominates the correlation function as soon as the longest intramolecular relaxation time significantly exceeds the shortest experimentally accessible time. Correspondingly, the shape of the correlation function changes considerably. Approximate analytical expressions are provided, which are in qualitative agreement with the exact theoretical solutions as well as experimental results, for both DNA and actin filaments. Our approach is in agreement with the predictions of the Zimm model, in the limit of very flexible polymers, as well as the predictions of semiflexible polymer models with respect to the intramolecular dynamics in solution.
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Affiliation(s)
- R G Winkler
- Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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111
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Couté Y, Burgess JA, Diaz JJ, Chichester C, Lisacek F, Greco A, Sanchez JC. Deciphering the human nucleolar proteome. MASS SPECTROMETRY REVIEWS 2006; 25:215-34. [PMID: 16211575 DOI: 10.1002/mas.20067] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nucleoli are plurifunctional nuclear domains involved in the regulation of several major cellular processes such as ribosome biogenesis, the biogenesis of non-ribosomal ribonucleoprotein complexes, cell cycle, and cellular aging. Until recently, the protein content of nucleoli was poorly described. Several proteomic analyses have been undertaken to discover the molecular bases of the biological roles fulfilled by nucleoli. These studies have led to the identification of more than 700 proteins. Extensive bibliographic and bioinformatic analyses allowed the classification of the identified proteins into functional groups and suggested potential functions of 150 human proteins previously uncharacterized. The combination of improvements in mass spectrometry technologies, the characterization of protein complexes, and data mining will assist in furthering our understanding of the role of nucleoli in different physiological and pathological cell states.
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Affiliation(s)
- Yohann Couté
- Biomedical Proteomics Research Group, Département de Biologie Structurale et Bioinformatique, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 14, Switzerland.
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112
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Politz JCR, Tuft RA, Prasanth KV, Baudendistel N, Fogarty KE, Lifshitz LM, Langowski J, Spector DL, Pederson T. Rapid, diffusional shuttling of poly(A) RNA between nuclear speckles and the nucleoplasm. Mol Biol Cell 2006; 17:1239-49. [PMID: 16371503 PMCID: PMC1382313 DOI: 10.1091/mbc.e05-10-0952] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 12/02/2005] [Indexed: 12/28/2022] Open
Abstract
Speckles are nuclear bodies that contain pre-mRNA splicing factors and polyadenylated RNA. Because nuclear poly(A) RNA consists of both mRNA transcripts and nucleus-restricted RNAs, we tested whether poly(A) RNA in speckles is dynamic or rather an immobile, perhaps structural, component. Fluorescein-labeled oligo(dT) was introduced into HeLa cells stably expressing a red fluorescent protein chimera of the splicing factor SC35 and allowed to hybridize. Fluorescence correlation spectroscopy (FCS) showed that the mobility of the tagged poly(A) RNA was virtually identical in both speckles and at random nucleoplasmic sites. This same result was observed in photoactivation-tracking studies in which caged fluorescein-labeled oligo(dT) was used as hybridization probe, and the rate of movement away from either a speckle or nucleoplasmic site was monitored using digital imaging microscopy after photoactivation. Furthermore, the tagged poly(A) RNA was observed to rapidly distribute throughout the entire nucleoplasm and other speckles, regardless of whether the tracking observations were initiated in a speckle or the nucleoplasm. Finally, in both FCS and photoactivation-tracking studies, a temperature reduction from 37 to 22 degrees C had no discernible effect on the behavior of poly(A) RNA in either speckles or the nucleoplasm, strongly suggesting that its movement in and out of speckles does not require metabolic energy.
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Affiliation(s)
- Joan C Ritland Politz
- Department of Biochemistry, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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113
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Tsay JM, Doose S, Weiss S. Rotational and translational diffusion of peptide-coated CdSe/CdS/ZnS nanorods studied by fluorescence correlation spectroscopy. J Am Chem Soc 2006; 128:1639-47. [PMID: 16448137 PMCID: PMC2535805 DOI: 10.1021/ja056162i] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CdSe/CdS/ZnS nanorods (NRs) of three aspect ratios were coated with phytochelatin-related peptides and studied using fluorescence correlation spectroscopy (FCS). Theoretical predictions of the NRs' rotational diffusion contribution to the correlation curves were experimentally confirmed. We monitored rotational and translational diffusion of NRs and extracted hydrodynamic radii from the extracted diffusion constants. Translational and rotational diffusion constants (D(trans) and D(rot)) for NRs were in good agreement with Tirado and Garcia de la Torre's as well as with Broersma's theories when accounting for the ligand dimensions. NRs fall in the size range where rotational diffusion can be monitored with higher sensitivity than translational diffusion due to a steeper length dependence, D(rot) approximately L(-)(3) versus D(trans) approximately L(-)(1). By titrating peptide-coated NRs with bovine serum albumin, we monitored (nonspecific) binding through rotational diffusion and showed that D(rot) is an advantageous observable for monitoring binding. Monitoring rotational diffusion of bioconjugated NRs using FCS might prove to be useful for observing binding and conformational dynamics in biological systems.
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Affiliation(s)
- James M. Tsay
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095
- California NanoSystems Institute, University of California at Los Angeles, Los Angeles, CA 90095
| | - Sören Doose
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095
- California NanoSystems Institute, University of California at Los Angeles, Los Angeles, CA 90095
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095
- Department of Physiology, University of California at Los Angeles, Los Angeles, CA 90095
- California NanoSystems Institute, University of California at Los Angeles, Los Angeles, CA 90095
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114
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Widengren J, Thyberg P. FCS cell surface measurements—Photophysical limitations and consequences on molecular ensembles with heterogenic mobilities. Cytometry A 2005; 68:101-12. [PMID: 16237686 DOI: 10.1002/cyto.a.20193] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Fluorescence Correlation Spectroscopy is a powerful method to analyze densities and diffusive behavior of molecules in membranes, but effects of photodegradation can easily be overlooked. METHOD Based on experimental photophysical parameters, calculations were performed to analyze the consequences of photobleaching in fluorescence correlation spectroscopy (FCS) cell surface experiments, covering a range of standard measurement conditions. RESULTS Cumulative effects of photobleaching can be prominent, although an absolute majority of the fluorescent molecules would pass the laser excitation beam without being photo-bleached. Given a distribution of molecules on a cell surface with different diffusive properties, the fraction of molecules that is actually analyzed depends strongly on the excitation intensities and measurement times, as well as on the size of the reservoir of freely diffusing molecules. Both the slower and the faster diffusing molecules can be disfavored. CONCLUSIONS Apart from quantifying photobleaching effects, the calculations suggest that the effects can be used to extract additional information, for instance about the size of the reservoirs of free diffusion. By certain choices of measurement conditions, it may be possible to more specifically analyze certain species within a population, based on their different diffusive properties, different areas of free diffusion, or different kinetics of possible transient binding.
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Affiliation(s)
- Jerker Widengren
- Department of Physics, Division of Experimental Biomolecular Physics, Royal Institute of Technology, Albanova University Center, 10691 Stockholm, Sweden.
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115
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Vargas DY, Raj A, Marras SAE, Kramer FR, Tyagi S. Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci U S A 2005; 102:17008-13. [PMID: 16284251 PMCID: PMC1287982 DOI: 10.1073/pnas.0505580102] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The mechanism of transport of mRNA-protein (mRNP) complexes from transcription sites to nuclear pores has been the subject of many studies. Using molecular beacons to track single mRNA molecules in living cells, we have characterized the diffusion of mRNP complexes in the nucleus. The mRNP complexes move freely by Brownian diffusion at a rate that assures their dispersion throughout the nucleus before they exit into the cytoplasm, even when the transcription site is located near the nuclear periphery. The diffusion of mRNP complexes is restricted to the extranucleolar, interchromatin spaces. When mRNP complexes wander into dense chromatin, they tend to become stalled. Although the movement of mRNP complexes occurs without the expenditure of metabolic energy, ATP is required for the complexes to resume their motion after they become stalled. This finding provides an explanation for a number of observations in which mRNA transport appeared to be an enzymatically facilitated process.
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Affiliation(s)
- Diana Y Vargas
- Department of Molecular Genetics, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
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116
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Dahl KN, Engler AJ, Pajerowski JD, Discher DE. Power-law rheology of isolated nuclei with deformation mapping of nuclear substructures. Biophys J 2005; 89:2855-64. [PMID: 16055543 PMCID: PMC1366783 DOI: 10.1529/biophysj.105.062554] [Citation(s) in RCA: 233] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Accepted: 07/19/2005] [Indexed: 01/21/2023] Open
Abstract
Force-induced changes in genome expression as well as remodeling of nuclear architecture in development and disease motivate a deeper understanding of nuclear mechanics. Chromatin and green fluorescent protein-lamin B dynamics were visualized in a micropipette aspiration of isolated nuclei, and both were shown to contribute to viscoelastic properties of the somatic cell nucleus. Reversible swelling by almost 200% in volume, with changes in salt, demonstrates the resilience and large dilational capacity of the nuclear envelope, nucleoli, and chromatin. Swelling also proves an effective way to separate the mechanical contributions of nuclear elements. In unswollen nuclei, chromatin is a primary force-bearing element, whereas swollen nuclei are an order of magnitude softer, with the lamina sustaining much of the load. In both cases, nuclear deformability increases with time, scaling as a power law-thus lacking any characteristic timescale-when nuclei are either aspirated or indented by atomic force microscopy. The nucleus is stiff and resists distortion at short times, but it softens and deforms more readily at longer times. Such results indicate an essentially infinite spectrum of timescales for structural reorganization, with implications for regulating genome expression kinetics.
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117
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Abstract
Understanding the different molecular mechanisms responsible for gene expression has been a central interest of molecular biologists for several decades. Transcription, the initial step of gene expression, consists of converting the genetic code into a dynamic messenger RNA that will specify a required cellular function following translocation to the cytoplasm and translation. We now possess an in-depth understanding of the mechanism and regulations of transcription. By contrast, an understanding of the dynamics of an individual gene's expression in real time is just beginning to emerge following recent technological developments.
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Affiliation(s)
- Xavier Darzacq
- Department of Anatomy, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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118
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Thews E, Gerken M, Eckert R, Zäpfel J, Tietz C, Wrachtrup J. Cross talk free fluorescence cross correlation spectroscopy in live cells. Biophys J 2005; 89:2069-76. [PMID: 15951373 PMCID: PMC1366709 DOI: 10.1529/biophysj.104.057919] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is now a widely used technique to measure small ensembles of labeled biomolecules with single molecule detection sensitivity (e.g., low endogenous concentrations). Fluorescence cross correlation spectroscopy (FCCS) is a derivative of this technique that detects the synchronous movement of two biomolecules with different fluorescence labels. Both methods can be applied to live cells and, therefore, can be used to address a variety of unsolved questions in cell biology. Applications of FCCS with autofluorescent proteins (AFPs) have been hampered so far by cross talk between the detector channels due to the large spectral overlap of the fluorophores. Here we present a new method that combines advantages of these techniques to analyze binding behavior of proteins in live cells. To achieve this, we have used dual color excitation of a common pair of AFPs, ECFP and EYFP, being discriminated in excitation rather than in emission. This is made possible by pulsed excitation and detection on a shorter timescale compared to the average residence time of particles in the FCS volume element. By this technique we were able to eliminate cross talk in the detector channels and obtain an undisturbed cross correlation signal. The setup was tested with ECFP/EYFP lysates as well as chimeras as negative and positive controls and demonstrated to work in live HeLa cells coexpressing the two fusion proteins ECFP-connexin and EYFP-connexin.
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Affiliation(s)
- Elmar Thews
- Institute of Physics and Department of Biophysics, Institute of Biology, University of Stuttgart, D-70550 Stuttgart, Germany
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119
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Cui ZQ, Zhang ZP, Zhang XE, Wen JK, Zhou YF, Xie WH. Visualizing the dynamic behavior of poliovirus plus-strand RNA in living host cells. Nucleic Acids Res 2005; 33:3245-52. [PMID: 15942027 PMCID: PMC1143693 DOI: 10.1093/nar/gki629] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Dynamic analysis of viral nucleic acids in host cells is important for understanding virus–host interaction. By labeling endogenous RNA with molecular beacon, we have realized the direct visualization of viral nucleic acids in living host cells and have studied the dynamic behavior of poliovirus plus-strand RNA. Poliovirus plus-strand RNA was observed to display different distribution patterns in living Vero cells at different post-infection time points. Real-time imaging suggested that the translocation of poliovirus plus-strand RNA is a characteristic rearrangement process requiring intact microtubule network of host cells. Confocal-FRAP measurements showed that 49.4 ± 3.2% of the poliovirus plus-strand RNA molecules diffused freely (with a D-value of 9.6 ± 1.6 × 10−10 cm2/s) within their distribution region, while the remaining (50.5 ± 2.9%) were almost immobile and moved very slowly only with change of the RNA distribution region. Under the electron microscope, it was found that virus-induced membrane rearrangement is microtubule-associated in poliovirus-infected Vero cells. These results reveal an entrapment and diffusion mechanism for the movement of poliovirus plus-strand RNA in living mammalian cells, and demonstrate that the mechanism is mainly associated with microtubules and virus-induced membrane structures.
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Affiliation(s)
- Zong-Qiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
- Graduate School, Chinese Academy SciencesBeijing 100039, China
| | - Zhi-Ping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Xian-En Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of SciencesBeijing 100101, China
- To whom correspondence should be addressed. Tel: + 86 10 58881508; Fax: +86 10 58881559;
| | - Ji-Kai Wen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Ya-Feng Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
| | - Wei-Hong Xie
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan 430071, China
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120
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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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121
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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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122
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Nomura Y, Kinjo M. Real-time monitoring of in vitro transcriptional RNA by using fluorescence correlation spectroscopy. Chembiochem 2005; 5:1701-3. [PMID: 15526332 DOI: 10.1002/cbic.200400046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yasutomo Nomura
- Department of Bio-System Engineering, Faculty of Engineering, Yamagata University, Yonezawa 992-8510, Japan.
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123
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Chen Y, Wei LN, Müller JD. Unraveling protein-protein interactions in living cells with fluorescence fluctuation brightness analysis. Biophys J 2005; 88:4366-77. [PMID: 15805168 PMCID: PMC1305664 DOI: 10.1529/biophysj.105.059170] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence correlation spectroscopy is a potentially powerful tool for measuring protein-protein interactions directly in single living cells. We previously reported on the detection of homodimer formation in cells using molecular brightness analysis. Here, we extend the technique to detect binding between different proteins. Proteins are labeled with the fluorescent markers YFP and CFP. We first determine the coexpression ratio of both proteins by measuring the intensity ratio with a dual-color setup. The effect of fluorescence resonance energy transfer on the intensity ratio is explicitly taken into account. The brightness of cells coexpressing both proteins is measured in a single-color setup. Selecting the laser wavelength of the two-photon light source allows us to either coexcite both proteins or to selectively excite YFP-labeled proteins. This approach enables us to distinguish between homodimer and heterodimer formation. We first present the theory and then demonstrate experimental feasibility using the ligand binding domains of retinoic acid receptor (RARLBD) and of retinoid X receptor (RXRLBD). Both proteins form heterodimers, and RXRLBD also forms homodimers in the presence of its agonist. We explore binding between these proteins in the presence and absence of RXR agonist. Our results demonstrate that brightness analysis offers a quantitative method for determining protein interactions in cells.
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Affiliation(s)
- Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, USA.
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124
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Maertens G, Vercammen J, Debyser Z, Engelborghs Y. Measuring protein‐protein interactions inside living cells using single color fluorescence correlation spectroscopy. Application to human immunodeficiency virus type 1 integrase and LEDGF/p75. FASEB J 2005; 19:1039-41. [PMID: 15788449 DOI: 10.1096/fj.04-3373fje] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recently we described the interaction of human immunodeficiency virus type 1 (HIV-1)1 integrase (IN) with a cellular protein, lens epithelium-derived growth factor/transcription co-activator p75 (LEDGF/p75). We now present the study of the diffusion behavior of the three independent domains of IN and LEDGF/p75 using fluorescence correlation microscopy (FCM). We show that diffusion in the cell of the different enhanced green fluorescent protein (EGFP) fusion proteins is described by two components with different fractions and that the average parameters in the nucleus are comparable with those in the cytoplasm. In addition, we demonstrate that specific interaction between EGFP-fused HIV-1 IN and LEDGF/p75 results in a shift in diffusion coefficient (D). The opposite shift was observed in an IN-deletion mutant that does not exhibit LEDGF/p75 binding or in a LEDGF/p75 knock-down experiment using siRNA. We thus demonstrate that protein-protein interactions can be studied in living cells, using single-color FCM (scFCM).
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Affiliation(s)
- Goedele Maertens
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Leuven, Belgium
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125
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Sommerville J, Brumwell CL, Politz JCR, Pederson T. Signal recognition particle assembly in relation to the function of amplified nucleoli ofXenopusoocytes. J Cell Sci 2005; 118:1299-307. [PMID: 15741230 DOI: 10.1242/jcs.01726] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The signal recognition particle (SRP) is a ribonucleoprotein machine that controls the translation and intracellular sorting of membrane and secreted proteins. The SRP contains a core RNA subunit with which six proteins are assembled. Recent work in both yeast and mammalian cells has identified the nucleolus as a possible initial site of SRP assembly. In the present study, SRP RNA and protein components were identified in the extrachromosomal, amplified nucleoli of Xenopus laevis oocytes. Fluorescent SRP RNA microinjected into the oocyte nucleus became specifically localized in the nucleoli, and endogenous SRP RNA was also detected in oocyte nucleoli by RNA in situ hybridization. An initial step in the assembly of SRP involves the binding of the SRP19 protein to SRP RNA. When green fluorescent protein (GFP)-tagged SRP19 protein was injected into the oocyte cytoplasm it was imported into the nucleus and became concentrated in the amplified nucleoli. After visiting the amplified nucleoli, GFP-tagged SRP19 protein was detected in the cytoplasm in a ribonucleoprotein complex, having a sedimentation coefficient characteristic of the SRP. These results suggest that the amplified nucleoli of Xenopus oocytes produce maternal stores not only of ribosomes, the classical product of nucleoli, but also of SRP, presumably as a global developmental strategy for stockpiling translational machinery for early embryogenesis.
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Affiliation(s)
- John Sommerville
- Division of Cell and Molecular Biology, School of Biology, University of St Andrews, KY16 9TS, UK.
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126
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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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127
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Lucas B, Remaut K, Sanders NN, Braeckmans K, De Smedt SC, Demeester J. Towards a better understanding of the dissociation behavior of liposome-oligonucleotide complexes in the cytosol of cells. J Control Release 2005; 103:435-50. [PMID: 15763625 DOI: 10.1016/j.jconrel.2004.12.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 12/10/2004] [Accepted: 12/16/2004] [Indexed: 11/21/2022]
Abstract
To obtain real breakthroughs in antisense therapy, it is necessary to understand the cellular behavior of antisense delivery systems. Fluorescence fluctuation spectroscopy (FFS), which measures in time fluorescence fluctuations in the excitation volume of a microscope and which can thus be applied on a cellular scale, shows potential for this purpose. In this study dual color FFS was explored to characterize the complexation (association and dissociation) between Cy5-labeled oligonucleotides (Cy5-ONs) and FITC-labeled cationic liposomes (FITC-liposomes) in respectively buffer, cell lysate and the cytosol of Vero cells. In Hepes buffer the association of the Cy5-ONs to the FITC-liposomes could be clearly observed from the high peaks of Cy5- and FITC-fluorescence, which appeared simultaneously in the excitation volume. This was explained by the fact that in the complexed state many Cy5-ONs and FITC-liposomes are bound to each other and thus move together through the excitation volume thereby resulting in high fluorescence 'FITC/Cy5-peaks'. FFS measurements on FITC-liposome/Cy5-ONs complexes in cell lysate revealed that a minor part of the Cy5-ONs was released from the complexes. The major part of the Cy5-ONs remained in the complexes, which also seemed to aggregate in cell lysate. In agreement with the measurements in cell lysate, after microinjection of FITC-liposome/Cy5-ONs complexes in the cytosol of Vero cells a part of the Cy5-ONs was released (as Cy-ONs were detected by FFS in the nuclei) while the other part remained bound (as Cy5-peaks were frequently observed in the cytosol). As will be explained, the Cy5-peaks could be due both to Cy5-ONs clustered with cytosol components and Cy5-ONs still complexed to FITC-liposomes with quenched FITC-fluorescence.
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Affiliation(s)
- B Lucas
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
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128
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Bridger JM, Kalla C, Wodrich H, Weitz S, King JA, Khazaie K, Kräusslich HG, Lichter P. Nuclear RNAs confined to a reticular compartment between chromosome territories. Exp Cell Res 2005; 302:180-93. [PMID: 15561100 DOI: 10.1016/j.yexcr.2004.07.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Revised: 07/30/2004] [Indexed: 12/15/2022]
Abstract
RNA polymerase II transcripts are confined to nuclear compartments. A detailed analysis of the nuclear topology of RNA from individual genes was performed for transcripts from the marker gene coding for chloramphenicol acetyltransferase, expressed at a high level from the HTLV-1 LTR promoter. The construct was transfected into A293 cells where the RNA was organized as an extensive reticular network. We also studied the RNA distribution from combinations of neighboring HIV and bacterial resistance genes that co-integrated within the genome of COS-7 cells-revealing spherical or track-like accumulations of RNA that were extensively branched. There were many nuclei with distinct but overlapping RNA accumulations. Since the coding genes localized at the overlapping points, the RNAs are synthesized at a common region and diverge. The correlation between the frequency of the separation of the transcripts and the physical distance of the respective genes suggests a subcompartmentalization in the microenvironment of genes on the basis of geometric parameters. Thus, the more distant the genes are on the same chromosome, the more likely they are confined to separated subcompartments of an extensive reticular system. Co-delineation of the RNA transcripts with Cajal bodies and chromosome territories indicated the organization of nuclear RNA transcripts in a reticular interchromosome domain compartment.
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Affiliation(s)
- Joanna M Bridger
- Abteilung Molekulare Genetik, Deutsches Krebsforschungszentrum, D-69120 Heidelberg, Germany
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129
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Tyagi S, Alsmadi O. Imaging native beta-actin mRNA in motile fibroblasts. Biophys J 2004; 87:4153-62. [PMID: 15377515 PMCID: PMC1304924 DOI: 10.1529/biophysj.104.045153] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Accepted: 08/27/2004] [Indexed: 11/18/2022] Open
Abstract
Nuclease-resistant, cytoplasmically resident molecular beacons were used to specifically label beta-actin mRNA in living and motile chicken embryonic fibroblasts. beta-actin mRNA signals were most abundant in active lamellipodia, which are protrusions that cells extend to adhere to surfaces. Time-lapse images show that the immediate sources of beta-actin mRNA for nascent lamellipodia are adjacent older protrusions. During the development of this method, we observed that conventional molecular beacons are rapidly sequestered in cell nuclei, leaving little time for them to find and bind to their cytoplasmic mRNA targets. By linking molecular beacons to a protein that tends to stay within the cytoplasm, nuclear sequestration was prevented, enabling cytoplasmic mRNAs to be detected and imaged. Probing beta-actin mRNA with these cytoplasmically resident molecular beacons did not affect the motility of the fibroblasts. Furthermore, mRNAs bound to these probes undergo translation within the cell. The use of cytoplasmically resident molecular beacons will enable further studies of the mechanism of beta-actin mRNA localization, and will be useful for understanding the dynamics of mRNA distribution in other living cells.
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Affiliation(s)
- Sanjay Tyagi
- Department of Molecular Genetics, Public Health Research Institute, Newark, New Jersey 07103, USA.
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130
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Abstract
Technical advances in the field of live-cell imaging have introduced the cell biologist to a new, dynamic, subcellular world. The static world of molecules in fixed cells has now been extended to the time dimension. This allows the visualization and quantification of gene expression and intracellular trafficking events of the studied molecules and the associated enzymatic processes in individual cells, in real time.
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Affiliation(s)
- Yaron Shav-Tal
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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131
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Molenaar C, Abdulle A, Gena A, Tanke HJ, Dirks RW. Poly(A)+ RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells. ACTA ACUST UNITED AC 2004; 165:191-202. [PMID: 15117966 PMCID: PMC2172041 DOI: 10.1083/jcb.200310139] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Many of the protein factors that play a role in nuclear export of mRNAs have been identified, but still little is known about how mRNAs are transported through the cell nucleus and which nuclear compartments are involved in mRNA transport. Using fluorescent 2'O-methyl oligoribonucleotide probes, we investigated the mobility of poly(A)+ RNA in the nucleoplasm and in nuclear speckles of U2OS cells. Quantitative analysis of diffusion using photobleaching techniques revealed that the majority of poly(A)+ RNA move throughout the nucleus, including in and out of speckles (also called SC-35 domains), which are enriched for splicing factors. Interestingly, in the presence of the transcription inhibitor 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole, the association of poly(A)+ RNA with speckles remained dynamic. Our results show that RNA movement is energy dependent and that the proportion of nuclear poly(A)+ RNA that resides in speckles is a dynamic population that transiently interacts with speckles independent of the transcriptional status of the cell. Rather than the poly(A)+ RNA within speckles serving a stable structural role, our findings support the suggestion of a more active role of these regions in nuclear RNA metabolism and/or transport.
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Affiliation(s)
- Chris Molenaar
- Dept. of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Netherlands
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132
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Elson EL. Quick tour of fluorescence correlation spectroscopy from its inception. JOURNAL OF BIOMEDICAL OPTICS 2004; 9:857-64. [PMID: 15447006 DOI: 10.1117/1.1779234] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) was originally developed in the early 1970s as a way to measure the kinetics of chemical reactions under zero perturbation conditions. At its inception, the measurement was difficult due to experimental limitations and was primarily used during the 1970s and 1980s to characterize diffusion. More recently, as a result of technological advances, FCS measurements have become easier and more versatile. In addition to measurements of diffusion both in solution and in cells, FCS is now also used to measure not only chemical reaction kinetics but also extents of molecular aggregation, the dynamics of photophysical processes, conformational fluctuations, molecular interactions in solution and in cells, and has even found application as a pharmaceutical screening method. From its inception to the present, the contributions of Webb and his coworkers have had a central and defining role in the development and applications of FCS.
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Affiliation(s)
- Elliot L Elson
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, Campus Box 8231, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA.
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133
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Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL, Singer RH. Dynamics of single mRNPs in nuclei of living cells. Science 2004; 304:1797-800. [PMID: 15205532 PMCID: PMC4765737 DOI: 10.1126/science.1099754] [Citation(s) in RCA: 365] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Understanding gene expression requires the ability to follow the fate of individual molecules. Here we use a cellular system for monitoring messenger RNA (mRNA)expression to characterize the movement in real time of single mRNA-protein complexes (mRNPs) in the nucleus of living mammalian cells. This mobility was not directed but was governed by simple diffusion. Some mRNPs were partially corralled throughout the nonhomogenous nuclear environment, but no accumulation at subnuclear domains was observed. Following energy deprivation, energy-independent motion of mRNPs was observed in a highly ATP-dependent nuclear environment; movements were constrained to chromatin-poor domains and excluded by newly formed chromatin barriers. This observation resolves a controversy, showing that the energetic requirements of nuclear mRNP trafficking are consistent with a diffusional model.
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Affiliation(s)
- Yaron Shav-Tal
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xavier Darzacq
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Shailesh M. Shenoy
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dahlene Fusco
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan M. Janicki
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - David L. Spector
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Robert H. Singer
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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134
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Tseng Y, Lee JSH, Kole TP, Jiang I, Wirtz D. Micro-organization and visco-elasticity of the interphase nucleus revealed by particle nanotracking. J Cell Sci 2004; 117:2159-67. [PMID: 15090601 DOI: 10.1242/jcs.01073] [Citation(s) in RCA: 210] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microstructure of the nucleus, one of the most studied but least understood cellular organelles, is the subject of much debate. Through the use of particle nanotracking, we detect and quantify the micro-organization as well as the viscoelastic properties of the intranuclear region in single, live, interphase somatic cells. We find that the intranuclear region is much stiffer than the cytoplasm; it is also more elastic than viscous, which reveals that the intranuclear region displays an unexpectedly strong solid-like behavior. The mean shear viscosity and elasticity of the intranuclear region of Swiss 3T3 fibroblasts are 520 Poise (P) and 180 dyn/cm2, respectively. These measurements determine a lower bound of the propulsive forces (3-15 picoNewton) required for nuclear organelles such as promyelocytic-leukemia bodies to undergo processive transport within the nucleus by overcoming friction forces set by the intranuclear viscosity. Dynamic analysis of the spontaneous movements of nanospheres embedded in the nucleus reveals the presence of putative transient nuclear microdomains of mean size 290±50 nm, which are mostly absent in the cytoplasm. The strong elastic character and micro-organization of the intranuclear region revealed by particle nanotracking analysis may help the nucleus to preserve its structural coherence. These studies also highlight the difference between the low interstitial nucleoplasmic viscosity, which controls the transport of nuclear proteins and molecules, and the much higher mesoscale viscosity, which affects the diffusion and directed transport of nuclear organelles and re-organization of interphase chromosomes.
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Affiliation(s)
- Yiider Tseng
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, 3400 N. Charles Street, MD 21218, USA
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135
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Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV, Ried T, Shav-Tal Y, Bertrand E, Singer RH, Spector DL. From silencing to gene expression: real-time analysis in single cells. Cell 2004; 116:683-98. [PMID: 15006351 PMCID: PMC4942132 DOI: 10.1016/s0092-8674(04)00171-0] [Citation(s) in RCA: 535] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 01/21/2004] [Accepted: 01/23/2004] [Indexed: 12/29/2022]
Abstract
We have developed an inducible system to visualize gene expression at the levels of DNA, RNA and protein in living cells. The system is composed of a 200 copy transgene array integrated into a euchromatic region of chromosome 1 in human U2OS cells. The condensed array is heterochromatic as it is associated with HP1, histone H3 methylated at lysine 9, and several histone methyltransferases. Upon transcriptional induction, HP1alpha is depleted from the locus and the histone variant H3.3 is deposited suggesting that histone exchange is a mechanism through which heterochromatin is transformed into a transcriptionally active state. RNA levels at the transcription site increase immediately after the induction of transcription and the rate of synthesis slows over time. Using this system, we are able to correlate changes in chromatin structure with the progression of transcriptional activation allowing us to obtain a real-time integrative view of gene expression.
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Affiliation(s)
- Susan M Janicki
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | | | - Simone E Salghetti
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - William P Tansey
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Ravi Sachidanandam
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | | | - Thomas Ried
- Genetics Branch, Center for Cancer Research/National Cancer Institute/NIH, 50 South Drive, Bethesda, MD 20892 USA
| | - Yaron Shav-Tal
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Edouard Bertrand
- Institut de Genetique Moleculaire de Montpellier-CNRS, 1919 Route de Mende, 34293 Montpellier, France
| | - Robert H Singer
- Departments of Anatomy and Structural Biology and Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - David L Spector
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
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136
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Bulseco DA, Wolf DE. Fluorescence correlation spectroscopy: molecular complexing in solution and in living cells. Methods Cell Biol 2004; 72:465-98. [PMID: 14719345 DOI: 10.1016/s0091-679x(03)72022-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
FCS is an important technique for biophysicists, biochemists, and cell biologists. FCS represents an example of how one can make use of the microscope and electronics to extract information beyond the resolution limit of classical optics. It can be used to study single-molecules both in solution and in living cells and can be used to monitor a wide variety of macromolecular interactions. When used as an in vitro technique, FCS measurements are easy to conduct and can be made on simplified instrumentation. When used in vivo on living cells, many additional factors must be considered when evaluating experimental data. Despite these concerns, FCS represents a new approach that has broad applicability for the determination of molecular stoichiometry both in vivo and in vitro for a variety of membrane and soluble receptor systems.
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Affiliation(s)
- Dylan A Bulseco
- Sensor Technologies, LLC, Shrewsbury, Massachusetts 01545, USA
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137
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Wang Z, Shah JV, Chen Z, Sun CH, Berns MW. Fluorescence correlation spectroscopy investigation of a GFP mutant-enhanced cyan fluorescent protein and its tubulin fusion in living cells with two-photon excitation. JOURNAL OF BIOMEDICAL OPTICS 2004; 9:395-403. [PMID: 15065907 DOI: 10.1117/1.1646416] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This study investigates the feasibility of using the enhanced cyan mutant of green fluorescent protein (ECFP) as a probe for two-photon fluorescence correlation spectroscopy (FCS). Molecular dynamics and other properties of ECFP and an ECFP-tubulin fusion protein were investigated in living Potorous tridactylis (PTK2) cells. ECFP has high molecular brightness in the nucleus (eta=3.3 kcpsm) and in the cytoplasm (3.2 kcpsm) under our experimental conditions. The diffusion constants of ECFP were determined to be 20+/-7 microm(2)/s in the nucleus and 21+/-8 microm(2)/s in the cytoplasm. ECFP has stable molecular characteristics with negligible photobleaching and photodynamic effects in our measurements. At the highest concentration of monomer ECFP (425 nM) the amount of dimer ECFP was estimated to be negligible ( approximately 1.8 nM), consistent with our data analysis using a single species model. ECFP-tubulin has a diffusion constant of 6 microm(2)/s in the living cells. In addition, we demonstrate that analysis of the molecular brightness can provide a new avenue for studying the polymerization state of tubulin. We suggest that the tubulin in the vicinity of the nucleus exists primarily as a heterodimer subunit while those in the area away from the nucleus (d>5 microm) are mostly oligomers. We conclude that ECFP is a useful genetic fluorescent probe for FCS studies of various cellular processes when in fusion to other biomolecules of interest.
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Affiliation(s)
- Zifu Wang
- Beckman Laser Institute, University of California at Irvine, Irvine, California 92612, USA
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138
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Kiesler E, Visa N. Intranuclear pre-mRNA trafficking in an insect model system. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2004; 35:99-118. [PMID: 15113081 DOI: 10.1007/978-3-540-74266-1_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Eva Kiesler
- Department of Molecular Biology and Functional Genomics, Stockholm University, 10961 Stockholm, Sweden
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139
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Chen Y, Wei LN, Müller JD. Probing protein oligomerization in living cells with fluorescence fluctuation spectroscopy. Proc Natl Acad Sci U S A 2003; 100:15492-7. [PMID: 14673112 PMCID: PMC307595 DOI: 10.1073/pnas.2533045100] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence fluctuation spectroscopy provides information about protein interactions in the intercellular environment from naturally occurring equilibrium fluctuations. We determine the molecular brightness of fluorescent proteins from the fluctuations by analyzing the photon counting histogram (PCH) or its moments and demonstrate the use of molecular brightness in probing the oligomerization state of proteins. We report fluorescence fluctuation measurements of enhanced GFP (EGFP) in cells up to concentrations of 10 microM by using an improved PCH theory. The molecular brightness of EGFP is constant in the concentration range studied. The brightness of a tandem EGFP construct, which carries two fluorophores, increases by a factor of two compared with EGFP alone, demonstrating the sensitivity of molecular brightness as a probe for protein complex formation. Oligomerization of nuclear receptors plays a crucial role in the regulation of gene expression. We probe the oligomerization state of the testicular receptor 4 and the ligand-binding domains of retinoid X receptor and retinoic acid receptor by observing molecular brightness changes as a function of protein concentration. The large concentration range accessible by experiment allows us to perform titration experiments on EGFP fusion proteins. An increase in the molecular brightness with protein concentration indicates the formation of homocomplexes. We observe the formation of homodimers of retinoid X receptor ligand binding domain upon addition of ligand. Resolving protein interactions in a cell is an important step in understanding cellular function on a molecular level. Brightness analysis promises to develop into an important tool for determining protein complex formation in cells.
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Affiliation(s)
- Yan Chen
- School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA
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140
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Politz JCR, Tuft RA, Pederson T. Diffusion-based transport of nascent ribosomes in the nucleus. Mol Biol Cell 2003; 14:4805-12. [PMID: 12960421 PMCID: PMC284785 DOI: 10.1091/mbc.e03-06-0395] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Revised: 07/18/2003] [Accepted: 08/08/2003] [Indexed: 11/11/2022] Open
Abstract
Although the complex process of ribosome assembly in the nucleolus is beginning to be understood, little is known about how the ribosomal subunits move from the nucleolus to the nuclear membrane for transport to the cytoplasm. We show here that large ribosomal subunits move out from the nucleolus and into the nucleoplasm in all directions, with no evidence of concentrated movement along directed paths. Mobility was slowed compared with that expected in aqueous solution in a manner consistent with anomalous diffusion. Once nucleoplasmic, the subunits moved in the same random manner and also sometimes visited another nucleolus before leaving the nucleus.
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Affiliation(s)
- Joan C Ritland Politz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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141
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Clamme JP, Krishnamoorthy G, Mély Y. Intracellular dynamics of the gene delivery vehicle polyethylenimine during transfection: investigation by two-photon fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2003; 1617:52-61. [PMID: 14637019 DOI: 10.1016/j.bbamem.2003.09.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Though polyethylenimine (PEI) is one of the most efficient nonviral vectors, one concern is the significant cytotoxicity of free PEI that represents about 80% of the PEI molecules in PEI/DNA mixtures used for transfection. In this respect, the aim of this work was to further investigate the intracellular fate of PEI during transfection of L929 fibroblasts. To this end, we analyzed by fluorescence correlation spectroscopy (FCS) using two-photon excitation the intracellular concentration and diffusion properties of labeled PEI and PEI/DNA complexes in various compartments of L929 cells. High initial fluorescence intensity, rapid photobleaching and the absence of measurable autocorrelation curves in most selected locations in cytoplasm suggest that PEI/DNA complexes and PEI accumulate (up to 30 times the concentration in the extracellular medium) in late endosomes bound to the inner membrane face. This feature, together with membrane destabilizing properties of PEI, may explain the release of PEI into cytoplasm and subsequent diffusion into the nucleus. In the nucleus, the concentration of PEI was found to be about 2.5- to 3.5-fold higher than the one in the incubation medium. Moreover, autocorrelation curves obtained in the nuclear compartment can be analyzed with either a two-component model (with the major fraction undergoing free Brownian diffusion) or an anomalous diffusion model. Both the endosomal disruption and the large intranuclear PEI concentration may contribute to PEI cytotoxicity.
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Affiliation(s)
- Jean-Pierre Clamme
- UMR 7034 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74 Route du Rhin, B.P. 24, F-67401 Cedex Illkirch, France
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142
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Pederson T. Nuclear impressionism: how the active genome creates the very canvas on which gene expression is painted. J Appl Biomed 2003. [DOI: 10.32725/jab.2003.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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143
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Abstract
Intense research in recent years has shown that many pre-mRNA processing events are co-transcriptional or at least begin during RNA synthesis by RNA polymerase II (Pol II). But is it important that pre-mRNA processing occurs co-transcriptionally? Whereas Pol II directs 5' capping of mRNA by binding to and recruiting all three capping activities to transcription units, co-transcriptional splicing is not obligatory. In some cases, such as alternative splicing, splicing may occur post-transcriptionally owing to the slower kinetics of splicing unfavorable introns. Despite recent models in which splicing factors are bound directly to the C-terminal domain (CTD) of Pol II, little evidence supports that view. Instead, interactions between snRNPs and transcription elongation factors provide the strongest molecular evidence for a physical link between transcription and splicing. Transcription termination depends on polyadenylation signals, but, like splicing, polyadenylation per se probably begins co-transcriptionally and continues post-transcriptionally. Nascent RNA plays an important role in determining which transcripts are polyadenylated and which alternative terminal exon is used. A recent addition to co-transcriptional RNA processing is a possible RNA surveillance step prior to release of the mRNP from the transcription unit, which appears to coordinate nuclear transport with mRNA processing and may be mediated by components of the nuclear exosome.
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Affiliation(s)
- Karla M Neugebauer
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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144
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Knemeyer JP, Herten DP, Sauer M. Detection and identification of single molecules in living cells using spectrally resolved fluorescence lifetime imaging microscopy. Anal Chem 2003; 75:2147-53. [PMID: 12720354 DOI: 10.1021/ac026333r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The detection of single mRNA molecules tagged by microinjected, singly fluorescently labeled oligo(dT) 43-mer molecules in living cells in quasi-natural surrounding, that is, cell culture medium, is demonstrated. Single-stranded oligonucleotides were labeled at the 5'-end with a red-absorbing oxazine derivative (MR121) and excited by a pulsed laser diode emitting at 635 nm with a repetition rate of 64 MHz. Spectrally resolved fluorescence lifetime imaging microscopy (SFLIM) on untreated living 3T3 mouse fibroblast cells reveals autofluorescence signals found predominately in the cytoplasm with fluorescence lifetimes of approximately 1.3 ns and emission maximums of approximately 665-670 nm. Hence, fluorescence signals of single MR121-labeled oligonucleotide molecules that exhibit a fluorescence lifetime of 2.8 ns and a fluorescence emission maximum of 685 nm can be easily discriminated against autofluorescence. MR121-labeled oligonucleotides were microinjected into the cytoplasm or nucleus of living 3T3 mouse fibroblast cells using a micropipet. Since the micropipet exhibits an inner diameter of 500 +/- 200 nm at the very end of the tip-comparable to the diameter of the detection volume applied-the number of molecules delivered into the cell via the micropipet can be counted. Furthermore, the presented technique enables the quantitative detection and time-resolved identification of single molecules in living cells as a result of their characteristic emission maximums and fluorescence lifetime. The results obtained from single-molecule studies demonstrate for the first time that 10-30% of the microinjected oligo(dT) 43-mer molecules cannot diffuse freely inside of the nucleus but, rather, are tethered to immobile elements of the transcriptional, splicing, or polyadenylation machinery.
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Affiliation(s)
- Jens-Peter Knemeyer
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, Germany
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145
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Wachsmuth M, Weidemann T, Müller G, Hoffmann-Rohrer UW, Knoch TA, Waldeck W, Langowski J. Analyzing intracellular binding and diffusion with continuous fluorescence photobleaching. Biophys J 2003; 84:3353-63. [PMID: 12719264 PMCID: PMC1302895 DOI: 10.1016/s0006-3495(03)70059-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of approximately 13 s.
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Affiliation(s)
- Malte Wachsmuth
- Division Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany
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146
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Kuthan H. A mathematical model of single target site location by Brownian movement in subcellular compartments. J Theor Biol 2003; 221:79-87. [PMID: 12634045 DOI: 10.1006/jtbi.2003.3172] [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: 11/22/2022]
Abstract
The location of distinct sites is mandatory for many cellular processes. In the subcompartments of the cell nucleus, only very small numbers of diffusing macromolecules and specific target sites of some types may be present. In this case, we are faced with the Brownian movement of individual macromolecules and their "random search" for single/few specific target sites, rather than bulk-averaged diffusion and multiple sites. In this article, I consider the location of a distant central target site, e.g. a globular protein, by individual macromolecules executing unbiased (i.e. drift-free) random walks in a spherical compartment. For this walk-and-capture model, the closed-form analytic solution of the first passage time probability density function (p.d.f.) has been obtained as well as the first and second moment. In the limit of a large ratio of the radii of the spherical diffusion space and central target, well-known relations for the variance and the first two moments for the exponential p.d.f. were found to hold with high accuracy. These calculations reinforce earlier numerical results and Monte Carlo simulations. A major implication derivable from the model is that non-directed random movement is an effective means for locating single sites in submicron-sized compartments, even when the diffusion coefficients are comparatively small and the diffusing species are present in one copy only. These theoretical conclusions are underscored numerically for effective diffusion constants ranging from 0.5 to 10.0 microm(2) s(-1), which have been reported for a couple of nuclear proteins in their physiological environment. Spherical compartments of submicron size are, for example, the Cajal bodies (size: 0.1-1.0 microm), which are present in 1-5 copies in the cell nucleus. Within a small Cajal body of radius 0.1 microm a single diffusing protein molecule (with D=0.5 microm(2) s(-1)) would encounter a medium-sized protein of radius 2.5 nm within 1 s with a probability near certainty (p=0.98).
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147
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Fradin C, Abu-Arish A, Granek R, Elbaum M. Fluorescence correlation spectroscopy close to a fluctuating membrane. Biophys J 2003; 84:2005-20. [PMID: 12609903 PMCID: PMC1302770 DOI: 10.1016/s0006-3495(03)75009-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Compartmentalization of the cytoplasm by membranes should have a strong influence on the diffusion of macromolecules inside a cell, and we have studied how this could be reflected in fluorescence correlation spectroscopy (FCS) experiments. We derived the autocorrelation function measured by FCS for fluorescent particles diffusing close to a soft membrane, and show it to be the sum of two contributions: short timescale correlations come from the diffusion of the particles (differing from free diffusion because of the presence of an obstacle), whereas long timescale correlations arise from fluctuations of the membrane itself (which create intensity fluctuations by modulating the number of detected particles). In the case of thermal fluctuations this second type of correlation depends on the elasticity of the membrane. To illustrate this calculation, we report the results of FCS experiments carried out close to a vesicle membrane. The measured autocorrelation functions display very distinctly the two expected contributions, and allow both to recover the diffusion coefficient of the fluorophore and to characterize the membrane fluctuations in term of a bending rigidity. Our results show that FCS measurements inside cells can lead to erroneous values of the diffusion coefficient if the influence of membranes is not recognized.
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Affiliation(s)
- Cécile Fradin
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel.
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148
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Haupts U, Rüdiger M, Ashman S, Turconi S, Bingham R, Wharton C, Hutchinson J, Carey C, Moore KJ, Pope AJ. Single-molecule detection technologies in miniaturized high-throughput screening: fluorescence intensity distribution analysis. JOURNAL OF BIOMOLECULAR SCREENING 2003; 8:19-33. [PMID: 12854995 DOI: 10.1177/1087057102239669] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Single-molecule detection technologies are becoming a powerful readout format to support ultra-high-throughput screening. These methods are based on the analysis of fluorescence intensity fluctuations detected from a small confocal volume element. The fluctuating signal contains information about the mass and brightness of the different species in a mixture. The authors demonstrate a number of applications of fluorescence intensity distribution analysis (FIDA), which discriminates molecules by their specific brightness. Examples for assays based on brightness changes induced by quenching/dequenching of fluorescence, fluorescence energy transfer, and multiple-binding stoichiometry are given for important drug targets such as kinases and proteases. FIDA also provides a powerful method to extract correct biological data in the presence of compound fluorescence.
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149
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Calapez A, Pereira HM, Calado A, Braga J, Rino J, Carvalho C, Tavanez JP, Wahle E, Rosa AC, Carmo-Fonseca M. The intranuclear mobility of messenger RNA binding proteins is ATP dependent and temperature sensitive. J Cell Biol 2002; 159:795-805. [PMID: 12473688 PMCID: PMC2173399 DOI: 10.1083/jcb.200203046] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
After being released from transcription sites, messenger ribonucleoprotein particles (mRNPs) must reach the nuclear pore complexes in order to be translocated to the cytoplasm. Whether the intranuclear movement of mRNPs results largely from Brownian motion or involves molecular motors remains unknown. Here we have used quantitative photobleaching techniques to monitor the intranuclear mobility of protein components of mRNPs tagged with GFP. The results show that the diffusion coefficients of the poly(A)-binding protein II (PABP2) and the export factor TAP are significantly reduced when these proteins are bound to mRNP complexes, as compared with nonbound proteins. The data further show that the mobility of wild-type PABP2 and TAP, but not of a point mutant variant of PABP2 that fails to bind to RNA, is significantly reduced when cells are ATP depleted or incubated at 22 degrees C. Energy depletion has only minor effects on the intranuclear mobility of a 2,000-kD dextran (which corresponds approximately in size to 40S mRNP particles), suggesting that the reduced mobility of PABP2 and TAP is not caused by a general alteration of the nuclear environment. Taken together, the data suggest that the mobility of mRNPs in the living cell nucleus involves a combination of passive diffusion and ATP-dependent processes.
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Affiliation(s)
- Alexandre Calapez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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150
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Ruan Q, Chen Y, Gratton E, Glaser M, Mantulin WW. Cellular characterization of adenylate kinase and its isoform: two-photon excitation fluorescence imaging and fluorescence correlation spectroscopy. Biophys J 2002; 83:3177-87. [PMID: 12496087 PMCID: PMC1302395 DOI: 10.1016/s0006-3495(02)75320-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Adenylate kinase (AK) is a ubiquitous enzyme that regulates the homeostasis of adenine nucleotides in the cell. AK1beta (long form) from murine cells shares the same protein sequence as AK1 (short form) except for the addition of 18 amino acid residues at its N-terminus. It is hypothesized that these residues serve as a signal for protein lipid modification and targeting of the protein to the plasma membrane. To better understand the cellular function of these AK isoforms, we have used several modern fluorescence techniques to characterize these two isoforms of AK enzyme. We fused cytosolic adenylate kinase (AK1) and its isoform (AK1beta) with enhanced green fluorescence protein (EGFP) and expressed the chimera proteins in HeLa cells. Using two-photon excitation scanning fluorescence imaging, we were able to directly visualize the localization of AK1-EGFP and AK1beta-EGFP in live cells. AK1beta-EGFP mainly localized on the plasma membrane, whereas AK1-EGFP distributed throughout the cell except for trace amounts in the nuclear membrane and some vesicles. We performed fluorescence correlation spectroscopy measurements and photon-counting histogram analysis in specific domains of live cells. For AK1-EGFP, we observed only one diffusion component in the cytoplasm. For AK1beta-EGFP, we observed two distinct diffusion components on the plasma membrane. One corresponded to the free diffusing protein, whereas the other represented the membrane-bound AK1beta-EGFP. The diffusion rate of AK1-EGFP was slowed by a factor of 1.8 with respect to that of EGFP, which was 50% more than what we would expect for a free diffusing AK1-EGFP. To rule out the possibility of oligomer formation, we performed photon-counting histogram analysis to direct analyze the brightness difference between AK1-EGFP and EGFP. From our analysis, we concluded that cytoplasmic AK1-EGFP is monomeric. fluorescence correlation spectroscopy proved to be a powerful technique for quantitatively studying the mobility of the target protein in live cells. This technology offers advantages in studying protein interactions and function in the cell.
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Affiliation(s)
- Qiaoqiao Ruan
- Laboratory for Fluorescence Dynamics, Department, University of Illinois in Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA
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