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Calaça Serrão A, Wunnava S, Dass AV, Ufer L, Schwintek P, Mast CB, Braun D. High-Fidelity RNA Copying via 2',3'-Cyclic Phosphate Ligation. J Am Chem Soc 2024; 146:8887-8894. [PMID: 38503430 PMCID: PMC10995993 DOI: 10.1021/jacs.3c10813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Templated ligation offers an efficient approach to replicate long strands in an RNA world. The 2',3'-cyclic phosphate (>P) is a prebiotically available activation that also forms during RNA hydrolysis. Using gel electrophoresis and high-performance liquid chromatography, we found that the templated ligation of RNA with >P proceeds in simple low-salt aqueous solutions with 1 mM MgCl2 under alkaline pH ranging from 9 to 11 and temperatures from -20 to 25 °C. No additional catalysts were required. In contrast to previous reports, we found an increase in the number of canonical linkages to 50%. The reaction proceeds in a sequence-specific manner, with an experimentally determined ligation fidelity of 82% at the 3' end and 91% at the 5' end of the ligation site. With splinted oligomers, five ligations created a 96-mer strand, demonstrating a pathway for the ribozyme assembly. Due to the low salt requirements, the ligation conditions will be compatible with strand separation. Templated ligation mediated by 2',3'-cyclic phosphate in alkaline conditions therefore offers a performant replication and elongation reaction for RNA on early Earth.
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Affiliation(s)
- Adriana Calaça Serrão
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Sreekar Wunnava
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Avinash V. Dass
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
- Department
of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4M1, Canada
| | - Lennard Ufer
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Philipp Schwintek
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Christof B. Mast
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Dieter Braun
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
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2
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Monitoring Molecular Properties of a Fluorescence Light-Up Aptamer Using Fluorescence Cross-Correlation Spectroscopy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12042002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fluorescence light-up aptamers (FLAPs) are tools for RNA imaging, wherein the RNA of interest is appended with a FLAP sequence that can bind to a corresponding small-molecule fluorogen and enhance its fluorescence. The fluorescence properties of FLAPs have mostly been analyzed in bulk and described as the average of a large number of RNA–fluorogen complexes. In this study, we evaluated the feasibility of fluorescence correlation spectroscopy (FCS)- and fluorescence cross-correlation spectroscopy (FCCS)-based quantifications of FLAPs in a solution using Broccoli, a common FLAP, and its corresponding fluorogen, DFHBI-1T. We investigated the folding efficiency, photostability, and photophysical properties of the Broccoli–DFHBI-1T complex using their FCS/FCCS characteristics. With FCS, we observed that the fluorescence was affected by the affinity between Broccoli and DFHBI-1T and the folding (maturation) state of Broccoli RNA. Moreover, the FCCS measurement of ATTO647N-labeled Broccoli and its complex with DFHBI-1T revealed the proportion of the mature Broccoli–DFHBI-1T complex. The current FCS/FCCS-based study of Broccoli–DFHBI-1T provides a model for analyzing FLAPs and their fluorogen pairs at the single-molecule level.
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3
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Confocal Laser Scanning Microscopy and Fluorescence Correlation Methods for the Evaluation of Molecular Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1310:1-30. [PMID: 33834430 DOI: 10.1007/978-981-33-6064-8_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Confocal laser scanning microscopy (CLSM) and related microscopic techniques allow a unique and versatile approach to image and analyze living cells due to their specificity and high sensitivity. Among confocal related techniques, fluorescence correlation methods, such as fluorescence correlation spectroscopy (FCS) and dual-color fluorescence cross-correlation spectroscopy (FCCS), are highly sensitive biophysical methods for analyzing the complex dynamic events of molecular diffusion and interaction change in live cells as well as in solution by exploiting the characteristics of fluorescence signals. Analytical and quantitative information from FCS and FCCS coupled with fluorescence images obtained from CLSM can now be applied in convergence science such as drug delivery and nanomedicine, as well as in basic cell biology. In this chapter, a brief introduction into the physical parameters that can be obtained from FCS and FCCS is first provided. Secondly, experimental examples of the methods for evaluating the parameters is presented. Finally, two potential FCS and FCCS applications for convergence science are introduced in more detail.
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4
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Kawai K, Maruyama A. Kinetics of Photoinduced Reactions at the Single‐Molecule Level: The KACB Method. Chemistry 2020; 26:7740-7746. [DOI: 10.1002/chem.202000439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/20/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Atsushi Maruyama
- Department of Life Science and TechnologyTokyo Institute of Technology 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa 226-8501 Japan
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5
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Dietz MS, Wehrheim SS, Harwardt MLIE, Niemann HH, Heilemann M. Competitive Binding Study Revealing the Influence of Fluorophore Labels on Biomolecular Interactions. NANO LETTERS 2019; 19:8245-8249. [PMID: 31621335 DOI: 10.1021/acs.nanolett.9b03736] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fluorescence methods are important tools in modern biology. Direct labeling of biomolecules with a fluorophore might, however, change interaction surfaces. Here, we introduce a competitive binding assay in combination with fluorescence correlation spectroscopy that reports binding affinities of both labeled and unlabeled biomolecules to their binding target. We investigated how fluorophore labels at different positions of a DNA oligonucleotide affect hybridization to a complementary oligonucleotide and found dissociation constants varying within 2 orders of magnitude. We next demonstrated that placing a fluorophore label at position Leu280 in the protein ligand internalin B does not alter the binding affinity to the MET receptor tyrosine kinase, compared to unlabeled internalin B. Our approach is simple to implement and can be applied to investigate the influence of fluorophore labels in a large variety of biomolecular interactions.
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Affiliation(s)
- Marina S Dietz
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
| | - S Sophia Wehrheim
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
| | - Marie-Lena I E Harwardt
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
| | - Hartmut H Niemann
- Structural Biochemistry, Department of Chemistry , Bielefeld University , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Mike Heilemann
- Single-Molecule Biophysics, Institute of Physical and Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Straße 7 , 60438 Frankfurt/Main , Germany
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6
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Tamura T, Endo H, Suzuki A, Sato Y, Kato K, Ohtani M, Yamaguchi M, Demura T. Affinity-based high-resolution analysis of DNA binding by VASCULAR-RELATED NAC-DOMAIN7 via fluorescence correlation spectroscopy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:298-313. [PMID: 31313414 DOI: 10.1111/tpj.14443] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
VASCULAR-RELATED NAC-DOMAIN7 (VND7) is the master transcription factor for vessel element differentiation in Arabidopsis thaliana. To identify the cis-acting sequence(s) bound by VND7, we employed fluorescence correlation spectroscopy (FCS) to find VND7-DNA interactions quantitatively. This identified an 18-bp sequence from the promoter of XYLEM CYSTEINE PEPTIDASE1 (XCP1), a direct target of VND7. A quantitative assay for binding affinity between VND7 and the 18-bp sequence revealed the core nucleotides contributing to specific binding between VND7 and the 18-bp sequence. Moreover, by combining the systematic evolution of ligands by exponential enrichment (SELEX) technique with known consensus sequences, we defined a motif termed the Ideal Core Structure for binding by VND7 (ICSV). We also used FCS to search for VND7 binding sequences in the promoter regions of other direct targets. Taking these data together, we proposed that VND7 preferentially binds to the ICSV sequence. Additionally, we found that substitutions among the core nucleotides affected transcriptional regulation by VND7 in vivo, indicating that the core nucleotides contribute to vessel-element-specific gene expression. Furthermore, our results demonstrate that FCS is a powerful tool for unveiling the DNA-binding properties of transcription factors.
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Affiliation(s)
- Taizo Tamura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hitoshi Endo
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Atsunobu Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yutaka Sato
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ko Kato
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama, 338-8570, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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7
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Su D, Hou Y, Dong C, Ren J. Fluctuation correlation spectroscopy and its applications in homogeneous analysis. Anal Bioanal Chem 2019; 411:4523-4540. [DOI: 10.1007/s00216-019-01884-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022]
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8
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Yamamoto J, Mikuni S, Kinjo M. Multipoint fluorescence correlation spectroscopy using spatial light modulator. BIOMEDICAL OPTICS EXPRESS 2018; 9:5881-5890. [PMID: 31065400 PMCID: PMC6491007 DOI: 10.1364/boe.9.005881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/11/2018] [Accepted: 10/28/2018] [Indexed: 06/09/2023]
Abstract
A multipoint holographic fluorescence correlation spectroscope (MP-hFCS) was successfully developed. The validity of the MP-hFCS was demonstrated using diffusion measurements of fluorescent dye solutions and of fluorescent proteins in single cells. Furthermore, the successful detection of the nuclear transport of a green fluorescent protein-tagged glucocorticoid receptor α indicates the possibility of being able to monitor directional molecular transport using the MP-hFCS. This allows multipoint analysis of the intermolecular interactions and molecular transport in living cells. Finally, the MP-hFCS can achieve multipoint diffusion measurements with high spatial and time resolution while maintaining a high photon detection sensitivity.
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Affiliation(s)
- Johtaro Yamamoto
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8568, Japan
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido, 001-0021, Japan
| | - Shintaro Mikuni
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido, 001-0021, Japan
| | - Masataka Kinjo
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido, 001-0021, Japan
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9
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Sasaki A, Yamamoto J, Kinjo M, Noda N. Absolute Quantification of RNA Molecules Using Fluorescence Correlation Spectroscopy with Certified Reference Materials. Anal Chem 2018; 90:10865-10871. [DOI: 10.1021/acs.analchem.8b02213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Akira Sasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Johtaro Yamamoto
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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10
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Peptide Self-Assembly Measured Using Fluorescence Correlation Spectroscopy. Methods Mol Biol 2018. [PMID: 29744833 DOI: 10.1007/978-1-4939-7811-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescence correlation spectroscopy (FCS) is a flexible and powerful technique to measure the diffusion of fluorescently labeled particles. It has been important in examining a range of biological processes, from intracellular transport, to DNA hybridization. It is particularly suited to measuring the assembly of peptides, since peptides are often too small to be detected by standard light scattering methods, or may not contain aromatic amino acid residues, which limits the use of other spectroscopic techniques. In this protocol, we describe state-of-the-art sample preparation for Aβ1-42 peptide solutions and the measurement and analysis of the self-assembly of the peptide to form fibrils via a number of intermediate states using FCS.
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11
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Potentials and pitfalls of inverse fluorescence correlation spectroscopy. Methods 2018; 140-141:23-31. [DOI: 10.1016/j.ymeth.2018.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 12/19/2017] [Accepted: 01/12/2018] [Indexed: 11/21/2022] Open
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12
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Schwille P. There and back again: from the origin of life to single molecules. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:493-498. [PMID: 29569181 PMCID: PMC5982444 DOI: 10.1007/s00249-018-1295-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/08/2018] [Accepted: 03/13/2018] [Indexed: 11/27/2022]
Abstract
What is life? There is hardly a more fundamental question raised by aspiring researchers, and one less prone to ever be answered in a scientifically satisfying way. In the long, productive and highly influential period of research following his Nobel-recognised work on relaxation kinetics, Manfred Eigen made seminal contributions towards a quantifiable definition of life, with a strong focus on its evolutionary character. In the last years of his time as an active researcher, however, he devoted himself to another, purely experimental topic: the detection and analysis of single biomolecules in aqueous solution. In this short review, I will give an overview of the groundbreaking contributions to the field of single molecule research made by Eigen and coworkers, and show that both, in its intrinsic motivation, and in its consequences, single molecule research strongly relates to the question of the physical-chemical essence of life. In fact, research on living systems with single molecule sensitivity will always refer the researcher to the question of the simplest possible representation, and thus the origin, of any biological phenomenon.
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Affiliation(s)
- Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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13
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Midelet J, El-Sagheer AH, Brown T, Kanaras AG, Débarre A, Werts MHV. Spectroscopic and Hydrodynamic Characterisation of DNA-Linked Gold Nanoparticle Dimers in Solution using Two-Photon Photoluminescence. Chemphyschem 2018; 19:827-836. [PMID: 29465817 DOI: 10.1002/cphc.201701228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 01/08/2023]
Abstract
Two-photon photoluminescence (TPPL) emission spectra of DNA-gold nanoparticle (AuNP) monoconjugates and the corresponding DNA-linked AuNP dimers are obtained by photon time-of-flight spectroscopy. This technique is combined with two-photon photoluminescence fluctuation correlation spectroscopy (TPPL-FCS) to simultaneously monitor the optical and hydrodynamic behaviour of these nano-assemblies in solution, with single-particle sensitivity and microsecond temporal resolution. In this study, the AuNPs have an average core diameter of 12 nm, which renders their dark-field plasmonic light scattering too weak for single-particle imaging. Moreover, as a result of the lack of plasmonic coupling in the dimers, the optical extinction, scattering and photoluminescence spectra of the DNA-AuNP complexes are not sufficiently different to distinguish between monomers and dimers. The use of TPPL-FCS successfully addresses these bottlenecks and enables the distinction between AuNP monomers and AuNP dimers in solution by measurement of their hydrodynamic rotational and translational diffusion.
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Affiliation(s)
- Johanna Midelet
- Physics and Astronomy, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Antonios G Kanaras
- Physics and Astronomy, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Anne Débarre
- Lab. Aimé-Cotton and PPSM, École Normale Supérieure de Cachan, CNRS, 61 Av. du Président Wilson, 94235, Cachan, France
| | - Martinus H V Werts
- Univ Rennes, CNRS, SATIE-UMR8029, 35000, Rennes, France.,École Normale Supérieure de Rennes, Av. R. Schuman, Campus de Ker Lann, 35170, Bruz, France
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14
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Tiwari M, Oasa S, Yamamoto J, Mikuni S, Kinjo M. A Quantitative Study of Internal and External Interactions of Homodimeric Glucocorticoid Receptor Using Fluorescence Cross-Correlation Spectroscopy in a Live Cell. Sci Rep 2017; 7:4336. [PMID: 28659593 PMCID: PMC5489515 DOI: 10.1038/s41598-017-04499-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/18/2017] [Indexed: 01/16/2023] Open
Abstract
Glucocorticoid receptor (GRα) is a well-known ligand-dependent transcription-regulatory protein. The classic view is that unliganded GRα resides in the cytoplasm, relocates to the nucleus after ligand binding, and then associates with a specific DNA sequence, namely a glucocorticoid response element (GRE), to activate a specific gene as a homodimer. It is still a puzzle, however, whether GRα forms the homodimer in the cytoplasm or in the nucleus before DNA binding or after that. To quantify the homodimerization of GRα, we constructed the spectrally different fluorescent protein tagged hGRα and applied fluorescence cross-correlation spectroscopy. First, the dissociation constant (Kd) of mCherry2-fused hGRα or EGFP-fused hGRα was determined in vitro. Then, Kd of wild-type hGRα was found to be 3.00 μM in the nucleus, which was higher than that in vitro. Kd of a DNA-binding-deficient mutant was 3.51 μM in the nucleus. This similarity indicated that GRα homodimerization was not necessary for DNA binding but could take place on GRE by means of GRE as a scaffold. Moreover, cytoplasmic homodimerization was also observed using GRα mutated in the nuclear localization signal. These findings support the existence of a dynamic monomer pathway and regulation of GRα function both in the cytoplasm and nucleus.
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Affiliation(s)
- Manisha Tiwari
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Sho Oasa
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan.
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15
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Rosa AMM, Prazeres DMF, Paulo PMR. Fluorescence correlation spectroscopy study of the complexation of DNA hybrids, IgG antibody, and a chimeric protein of IgG-binding ZZ domains fused with a carbohydrate binding module. Phys Chem Chem Phys 2017; 19:16606-16614. [DOI: 10.1039/c7cp00662d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) was used to characterize the molecular interactions between the four components of a DNA recognition system.
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Affiliation(s)
- A. M. M. Rosa
- iBB – Institute for Bioengineering and Biosciences
- Department of Bioengineering
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisbon
| | - D. M. F. Prazeres
- iBB – Institute for Bioengineering and Biosciences
- Department of Bioengineering
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisbon
| | - P. M. R. Paulo
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisbon
- Portugal
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16
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Wulf V, Knoch F, Speck T, Sönnichsen C. Gold Nanorods as Plasmonic Sensors for Particle Diffusion. J Phys Chem Lett 2016; 7:4951-4955. [PMID: 27934054 DOI: 10.1021/acs.jpclett.6b02165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plasmonic gold nanoparticles are normally used as sensor to detect analytes permanently bound to their surface. If the interaction between the analyte and the nanosensor surface is negligible, it only diffuses through the sensor's sensing volume, causing a small temporal shift of the plasmon resonance position. By using a very sensitive and fast detection scheme, we are able to detect these small fluctuations in the plasmon resonance. With the help of a theoretical model consistent with our detection geometry, we determine the analyte's diffusion coefficient. The method is verified by observing the trends upon changing diffusor size and medium viscosity, and the diffusion coefficients obtained were found to reflect reduced diffusion close to a solid interface. Our method, which we refer to as NanoPCS (for nanoscale plasmon correlation spectroscopy), is of practical importance for any application involving the diffusion of analytes close to nanoparticles.
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Affiliation(s)
- Verena Wulf
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
| | - Fabian Knoch
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
| | - Thomas Speck
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
| | - Carsten Sönnichsen
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
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17
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Oura M, Yamamoto J, Ishikawa H, Mikuni S, Fukushima R, Kinjo M. Polarization-dependent fluorescence correlation spectroscopy for studying structural properties of proteins in living cell. Sci Rep 2016; 6:31091. [PMID: 27489044 PMCID: PMC4973283 DOI: 10.1038/srep31091] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/14/2016] [Indexed: 11/10/2022] Open
Abstract
Rotational diffusion measurement is predicted as an important method in cell biology because the rotational properties directly reflect molecular interactions and environment in the cell. To prove this concept, polarization-dependent fluorescence correlation spectroscopy (pol-FCS) measurements of purified fluorescent proteins were conducted in viscous solution. With the comparison between the translational and rotational diffusion coefficients obtained from pol-FCS measurements, the hydrodynamic radius of an enhanced green fluorescent protein (EGFP) was estimated as a control measurement. The orientation of oligomer EGFP in living cells was also estimated by pol-FCS and compared with Monte Carlo simulations. The results of this pol-FCS experiment indicate that this method allows an estimation of the molecular orientation using the characteristics of rotational diffusion. Further, it can be applied to analyze the degree of molecular orientation and multimerization or detection of tiny aggregation of aggregate-prone proteins.
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Affiliation(s)
- Makoto Oura
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Hideto Ishikawa
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Ryousuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
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18
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Junager NPL, Kongsted J, Astakhova K. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes. SENSORS 2016; 16:s16081173. [PMID: 27472344 PMCID: PMC5017339 DOI: 10.3390/s16081173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 01/08/2023]
Abstract
Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.
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Affiliation(s)
- Nina P L Junager
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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19
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Raster image cross-correlation analysis for spatiotemporal visualization of intracellular degradation activities against exogenous DNAs. Sci Rep 2015; 5:14428. [PMID: 26400011 PMCID: PMC4585853 DOI: 10.1038/srep14428] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/28/2015] [Indexed: 11/09/2022] Open
Abstract
Reducing intracellular DNA degradation is critical to enhance the efficiency of gene therapy. Exogenous DNA incorporation into cells is strictly blocked by the defense machinery of intracellular nuclease activity. Raster image correlation spectroscopy (RICS) and raster image cross-correlation spectroscopy (cross-correlation RICS; ccRICS) are image-based correlation methods. These powerful tools allow the study of spatiotemporal molecular dynamics. Here we performed spatiotemporal ccRICS analyses of fluorescent DNA and directly monitored the process of exogenous DNA degradation in living cell cytoplasm. Such direct monitors of DNA degradation allow us to determine the fate of the exogenous DNA in living cells. On comparing the process in living cells, our study shows that cytoplasmic nuclease activity differs between cell lines; therefore, we propose that the difference of nuclease activity in cytoplasm dictates a different resistance to exogenous DNA incorporation. New insight on efficient gene delivery can be provided with our study.
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Hu H, Huang X, Ren J. Studies on the formation and stability of triplex DNA using fluorescence correlation spectroscopy. LUMINESCENCE 2015; 31:830-6. [DOI: 10.1002/bio.3030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Hongyan Hu
- College of Chemistry & Chemical Engineering; Shanghai Jiao Tong University; Shanghai People's Republic of China
| | - Xiangyi Huang
- College of Chemistry & Chemical Engineering; Shanghai Jiao Tong University; Shanghai People's Republic of China
| | - Jicun Ren
- College of Chemistry & Chemical Engineering; Shanghai Jiao Tong University; Shanghai People's Republic of China
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21
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Zheng Z, Jing B, Sorci M, Belfort G, Zhu Y. Accelerated insulin aggregation under alternating current electric fields: Relevance to amyloid kinetics. BIOMICROFLUIDICS 2015; 9:044123. [PMID: 26339322 PMCID: PMC4552700 DOI: 10.1063/1.4928767] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/07/2015] [Indexed: 06/05/2023]
Abstract
The time-dependent nucleation phase is critical to amyloid fibrillation and related to many pathologies, in which the conversion from natively folded amyloidogenic proteins to oligomers via nucleation is often hypothesized as a possible underlying mechanism. In this work, non-uniform AC-electric fields across two asymmetric electrodes were explored to control and examine the aggregation of insulin, a model amyloid protein, in aqueous buffer solution at constant temperature (20 °C) by fluorescence correlation spectroscopy and fluorescence microscopy. Insulin was rapidly concentrated in a strong AC-field by imposed AC-electroosmosis flow over an optimal frequency range of 0.5-2 kHz. In the presence of an AC-field, direct fibrillation from insulin monomers without the formation of oligomer precursors was observed. Once the insulin concentration had nearly doubled its initial concentration, insulin aggregates were observed in solution. The measured lag time for the onset of insulin aggregation, determined from the abrupt reduction in insulin concentration in solution, was significantly shortened from months or years in the absence of AC-fields to 1 min-3 h under AC-fields. The ability of external fields to alter amyloid nucleation kinetics provides insights into the onset of amyloid fibrillation.
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Affiliation(s)
- Zhongli Zheng
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Benxin Jing
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Mirco Sorci
- Howard P. Isermann Department of Chemical and Biological Engineering and The Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, USA
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and The Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, USA
| | - Yingxi Zhu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
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22
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Ruan L, Su D, Shao C, Wang J, Dong C, Huang X, Ren J. A sensitive and microscale method for drug screening combining affinity probes and single molecule fluorescence correlation spectroscopy. Analyst 2015; 140:1207-14. [DOI: 10.1039/c4an01816h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The theoretical model of drug screening method based on competitive reaction and fluorescence correlation spectroscopy.
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Affiliation(s)
- Lingao Ruan
- College of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiaotong University
- Shanghai 200240
- People's Republic of China
| | - Di Su
- College of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiaotong University
- Shanghai 200240
- People's Republic of China
| | - Chang Shao
- Shanghai Laiyi Center for Biopharmaceutical R&D
- Shanghai 201203
- People's Republic of China
| | - Jinjie Wang
- College of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiaotong University
- Shanghai 200240
- People's Republic of China
| | - Chaoqing Dong
- College of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiaotong University
- Shanghai 200240
- People's Republic of China
| | - Xiangyi Huang
- College of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiaotong University
- Shanghai 200240
- People's Republic of China
| | - Jicun Ren
- College of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiaotong University
- Shanghai 200240
- People's Republic of China
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23
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Hein PP, Kolb KE, Windgassen T, Bellecourt MJ, Darst SA, Mooney RA, Landick R. RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement. Nat Struct Mol Biol 2014; 21:794-802. [PMID: 25108353 PMCID: PMC4156911 DOI: 10.1038/nsmb.2867] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/03/2014] [Indexed: 12/11/2022]
Abstract
The rates of RNA synthesis and the folding of nascent RNA into biologically active structures are linked via pausing by RNA polymerase (RNAP). Structures that form within the RNA-exit channel can either increase pausing by interacting with RNAP or decrease pausing by preventing backtracking. Conversely, pausing is required for proper folding of some RNAs. Opening of the RNAP clamp domain has been proposed to mediate some effects of nascent-RNA structures. However, the connections among RNA structure formation and RNAP clamp movement and catalytic activity remain uncertain. Here, we assayed exit-channel structure formation in Escherichia coli RNAP with disulfide cross-links that favor closed- or open-clamp conformations and found that clamp position directly influences RNA structure formation and RNAP catalytic activity. We report that exit-channel RNA structures slow pause escape by favoring clamp opening through interactions with the flap that slow translocation.
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Affiliation(s)
- Pyae P. Hein
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - Kellie E. Kolb
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - Tricia Windgassen
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - Michael J. Bellecourt
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Rachel A. Mooney
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI 53706, USA
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24
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Qi J, Zeng J, Zhao F, Lin SH, Raja B, Strych U, Willson RC, Shih WC. Label-free, in situ SERS monitoring of individual DNA hybridization in microfluidics. NANOSCALE 2014; 6:8521-6. [PMID: 24953169 DOI: 10.1039/c4nr01951b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We present label-free, in situ monitoring of individual DNA hybridization in microfluidics. By immobilizing molecular sentinel probes on nanoporous gold disks, we demonstrate sensitivity approaching the single-molecule limit via surface-enhanced Raman scattering which provides robust signals without photobleaching for more than an hour. We further demonstrate that a target concentration as low as 20 pM can be detected within 10 min under diffusion-limited transport.
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Affiliation(s)
- Ji Qi
- Department of Electrical and Computer Engineering, USA.
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25
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Bacia K, Haustein E, Schwille P. Fluorescence correlation spectroscopy: principles and applications. Cold Spring Harb Protoc 2014; 2014:709-25. [PMID: 24987147 DOI: 10.1101/pdb.top081802] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is used to study the movements and the interactions of biomolecules at extremely dilute concentrations, yielding results with good spatial and temporal resolutions. Using a number of technical developments, FCS has become a versatile technique that can be used to study a variety of sample types and can be advantageously combined with other methods. Unlike other fluorescence-based techniques, the analysis of FCS data is not based on the average intensity of the fluorescence emission but examines the minute intensity fluctuations caused by spontaneous deviations from the mean at thermal equilibrium. These fluctuations can result from variations in local concentrations owing to molecular mobility or from characteristic intermolecular or intramolecular reactions of fluorescently labeled biomolecules present at low concentrations. Here, we provide a basic introduction to FCS, including its technical development and theoretical basis, experimental setup of an FCS system, adjustment of a setup, data acquisition, and analysis of FCS measurements. Finally, the application of FCS to the study of lipid bilayer membranes and to living cells is discussed.
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26
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Bulseco DA, Wolf DE. Fluorescence correlation spectroscopy: molecular complexing in solution and in living cells. Methods Cell Biol 2014; 114:489-524. [PMID: 23931520 DOI: 10.1016/b978-0-12-407761-4.00021-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
This chapter describes how the microscope can be used to measure a fluorescence signal from a small, confined volume of the sample-the confocal volume-and how these measurements are used to quantitate the dynamics and complexing of molecules, the technique of fluorescence correlation spectroscopy (FCS). FCS represents a significant example of how the microscope can be used to extract information beyond the resolution limit of classical optics. FCS enables studying events at the level of single molecules. With FCS, one can measure the diffusion times and the interaction of macromolecules, the absolute concentration of fluorescently labeled particles, and the kinetics of chemical reactions. Practical applications of FCS include studies on ligand-receptor binding, protein-protein and protein-DNA interactions, and the aggregation of fluorescently labeled particles. The chapter focuses on the principles of FCS, demonstrates how FCS is used to study macromolecular interactions in solution and in living cells, and examines critical experimental parameters that must be considered. The chapter also discusses the minimum requirements for building a microscope-based FCS instrument and illustrates the key criteria for both instrument sensitivity and analysis of FCS data. It can be used to study single molecules both in solution and in living cells and can be used to monitor a 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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28
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Abstract
Dual-color cross-correlation spectroscopy is a special kind of fluctuation analysis which selectively probes the formation or deletion of linkages between two different fluorescently labeled molecules at extremely low concentrations. Two-photon excitation can, under certain circumstances, significantly simplify this method if different probe molecules with distinct emission properties are accessible by a common IR excitation wavelength.
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Affiliation(s)
- P Schwille
- Experimental Biophysics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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29
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Dietz MS, Fricke F, Krüger CL, Niemann HH, Heilemann M. Receptor-Ligand Interactions: Binding Affinities Studied by Single-Molecule and Super-Resolution Microscopy on Intact Cells. Chemphyschem 2013; 15:671-6. [DOI: 10.1002/cphc.201300755] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Harada K, Mikuni S, Beppu H, Niimi H, Abe S, Hano N, Yamagata K, Kinjo M, Kitajima I. A rapid and high-throughput quantitation assay of the nuclear factor κB activity using fluorescence correlation spectroscopy in the setting of clinical laboratories. PLoS One 2013; 8:e75579. [PMID: 24124497 PMCID: PMC3790820 DOI: 10.1371/journal.pone.0075579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 11/30/2022] Open
Abstract
Background Transcription factor nuclear factor-κB (NF-κB) plays a key role in the regulation of immune responses to inflammation. However, convenient assay systems to quantitate the NF-κB activity level in a timely manner are not available in the setting of clinical laboratories. Therefore, we developed a novel and high-throughput quantitative assay based on fluorescence correlation spectroscopy (FCS) to detect the NF-κB activity level in cellular nuclear extracts and evaluated the performance of this method. The basic principle of this assay is to calculate the binding fraction of NF-κB to fluorescent-labeled DNA probes, which contain NF-κB binding sites. Methods Non-fluorescent competitive probes are employed to normalize the influence of the viscosity of the nuclear extracts between samples and to eliminate the influence of nonspecific binding of the fluorescent probes. To confirm accurate quantitation, human recombinant NF-κB p50 was mixed into U937 cell nuclear extracts, and the binding fraction of the fluorescent probes to NF-κB in the mixture was calculated for quantitation. To evaluate whether this method can be applied to measure the NF-κB activity in human lymphocytes, the NF-κB activity levels of systemic inflammatory response syndrome patients during perioperative periods were measured. Results The percentage recovery was 88.9%. The coefficients of variation of the intra-assay were approximately 10%. NF-κB activity levels during the perioperative period can were successfully measured. The assay time for the FCS measurement was within 20 minutes. Conclusions This assay system can be used to quantitate NF-κB activity levels in a timely manner in the setting of hospital laboratories.
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Affiliation(s)
- Kenu Harada
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
| | - Shintaro Mikuni
- Department of Advanced Optical Imaging Research, Research Center for Cooperative Projects, Graduated School of Medicine, Hokkaido University, Sapporo, Japan
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Hideyuki Beppu
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
| | - Shigeki Abe
- Sysmex Corporation BMA Laboratory, Kobe, Japan
| | - Nobuko Hano
- Sysmex Corporation BMA Laboratory, Kobe, Japan
| | | | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Isao Kitajima
- Department of Clinical Laboratory and Molecular Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Toyama, Japan
- * E-mail:
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31
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Brinkmeier M, Dörre K, Stephan J, Eigen M. Two-beam cross-correlation: a method to characterize transport phenomena in micrometer-sized structures. Anal Chem 2012; 71:609-16. [PMID: 21662718 DOI: 10.1021/ac980820i] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To determine flow properties, namely, the velocity and angle of the flow in microstructured channels, an experimental realization based on fluorescence correlation spectroscopy is described. For this purpose, two micrometer-sized spatially separated volume elements have been created. The cross-correlation signal from these has been recorded and evaluated mathematically. In addition to previous results, two-beam cross-correlation allows for fast and easy determination of even small (down to 200 μm/s) flow velocities, as well as simultaneous measurement of diffusion properties of single dye molecules within a rather short detection time of 5-100 s and an error rate of less than 20%. The spatial flow resolution is around 1-2 μm, limited by the diameter of the volume element. Furthermore, vectorial flow data can be obtained and evaluated. A discussion of the theoretical background and an experimental verification of the theoretical results is performed. The feasibility of fast and easy data processing is shown if the flow time is the only desired information. Possible applications of this precise and simple method are the determination of transportation effects within artificial microstructures for CE and HPLC, fast chemical kinetics, and high-throughput screening.
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Affiliation(s)
- M Brinkmeier
- Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077 Göttingen, Germany
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32
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Ridgeway WK, Millar DP, Williamson JR. Quantitation of ten 30S ribosomal assembly intermediates using fluorescence triple correlation spectroscopy. Proc Natl Acad Sci U S A 2012; 109:13614-9. [PMID: 22869699 PMCID: PMC3427059 DOI: 10.1073/pnas.1204620109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The self-assembly of bacterial 30S ribosomes involves a large number of RNA folding and RNA-protein binding steps. The sequence of steps determines the overall assembly mechanism and the structure of the mechanism has ramifications for the robustness of biogenesis and resilience against kinetic traps. Thermodynamic interdependencies of protein binding inferred from omission-reconstitution experiments are thought to preclude certain assembly pathways and thus enforce ordered assembly, but this concept is at odds with kinetic data suggesting a more parallel assembly landscape. A major challenge is deconvolution of the statistical distribution of intermediates that are populated during assembly at high concentrations approaching in vivo assembly conditions. To specifically resolve the intermediates formed by binding of three ribosomal proteins to the full length 16S rRNA, we introduce Fluorescence Triple-Correlation Spectroscopy (F3CS). F3CS identifies specific ternary complexes by detecting coincident fluctuations in three-color fluorescence data. Triple correlation integrals quantify concentrations and diffusion kinetics of triply labeled species, and F3CS data can be fit alongside auto-correlation and cross-correlation data to quantify the populations of 10 specific ribosome assembly intermediates. The distribution of intermediates generated by binding three ribosomal proteins to the entire native 16S rRNA included significant populations of species that were not previously thought to be thermodynamically accessible, questioning the current interpretation of the classic omission-reconstitution experiments. F3CS is a general approach for analyzing assembly and function of macromolecular complexes, especially those too large for traditional biophysical methods.
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Affiliation(s)
- William K. Ridgeway
- Departments of Molecular Biology and
- Chemistry, and
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | | | - James R. Williamson
- Departments of Molecular Biology and
- Chemistry, and
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
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A rule of seven in Watson-Crick base-pairing of mismatched sequences. Nat Struct Mol Biol 2012; 19:623-7. [PMID: 22580558 PMCID: PMC3372693 DOI: 10.1038/nsmb.2294] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 04/04/2012] [Indexed: 12/18/2022]
Abstract
Sequence recognition through base pairing is essential for DNA repair and gene regulation but the basic rules governing this process remain elusive. In particular, the kinetics of annealing between two imperfectly matched strands is not well characterized despite its potential importance in nucleic acids-based biotechnologies and gene silencing. Here we use single molecule fluorescence to visualize the multiple annealing and melting reactions of two untethered strands inside a porous vesicle, allowing us to quantify precisely the annealing and melting rates. The data as a function of mismatch position suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA. This phenomenological rule of seven may underlie the requirement of seven nucleotides complementarity to seed gene silencing by small non-coding RNA and may help guide performance improvement in DNA and RNA-based bio- and nano-technologies where off-target effects can be detrimental.
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Perevoshchikova IV, Kotova EA, Antonenko YN. Fluorescence correlation spectroscopy in biology, chemistry, and medicine. BIOCHEMISTRY (MOSCOW) 2011; 76:497-516. [PMID: 21639831 DOI: 10.1134/s0006297911050014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.
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Affiliation(s)
- I V Perevoshchikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
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35
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Kawai K, Matsutani E, Maruyama A, Majima T. Probing the Charge-Transfer Dynamics in DNA at the Single-Molecule Level. J Am Chem Soc 2011; 133:15568-77. [DOI: 10.1021/ja206325m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Eri Matsutani
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Atsushi Maruyama
- Institute for Materials Chemistry and Engineering, Kyushu University, Motooka 744-CE11, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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36
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Umezu T, Ohyashiki K, Ohyashiki JH. Detection method for quantifying global DNA methylation by fluorescence correlation spectroscopy. Anal Biochem 2011; 415:145-50. [PMID: 21600184 DOI: 10.1016/j.ab.2011.04.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/16/2011] [Accepted: 04/21/2011] [Indexed: 12/27/2022]
Abstract
A method for quantifying global DNA methylation using fluorescence correlation spectroscopy (FCS) has been established. The single-molecule methylation assay (SMMA) is based on two methodologies. One methodology, FCS, estimates the translational diffusion coefficient of molecules in solution, whereas the other methodology uses the high affinity of methyl-CpG-binding domain protein 2 (MBD2) to bind specifically to methylated DNA. We studied the specific binding rates of fluorescence-labeled MBD2 and methylated DNA from biological samples using the automated FCS system. Using a standard curve with methylated control DNA, we developed the SMMA index to assess the global DNA methylation level of the biological samples. A marked decrease in the SMMA index was observed when human leukemia cell lines (U937 and K562) were cultured with DNA demethylating agents. Our findings clearly indicate the applicability of SMMA as a simple and rapid tool for quantifying global DNA methylation. SMMA may prove useful for genome-wide comparative methylation analyses of malignancies and as an indicator of the demethylation effects of epigenetic drugs.
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Affiliation(s)
- Tomohiro Umezu
- Department of Molecular Science, Tokyo Medical University, Tokyo 160-0023, Japan.
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Tian Y, Martinez MM, Pappas D. Fluorescence correlation spectroscopy: a review of biochemical and microfluidic applications. APPLIED SPECTROSCOPY 2011; 65:115A-124A. [PMID: 21396180 PMCID: PMC3071976 DOI: 10.1366/10-06224] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Over the years fluorescence correlation spectroscopy (FCS) has proven to be a useful technique that has been utilized in several fields of study. Although FCS initially suffered from poor signal-to-noise ratios, the incorporation of confocal microscopy has overcome this drawback and transformed FCS into a sensitive technique with high figures of merit. In addition, tandem methods have evolved to include dual-color cross-correlation, total internal reflection fluorescence correlation, and fluorescence lifetime correlation spectroscopy combined with time-correlated single-photon counting. In this review, we discuss several applications of FSC for biochemical, microfluidic, and cellular investigations.
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Affiliation(s)
- Yu Tian
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Michelle M. Martinez
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Dimitri Pappas
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
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Oliver PM, Park JS, Vezenov D. Quantitative High-Resolution Sensing of DNA Hybridization Using Magnetic Tweezers with Evanescent Illumination. NANOSCALE 2011; 3:581-91. [PMID: 21103547 PMCID: PMC3379821 DOI: 10.1039/c0nr00479k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We applied the combined approach of evanescent nanometry and force spectroscopy using magnetic tweezers to quantify the degree of hybridization of a single synthetic single-stranded DNA oligomer to a resolution approaching a single-base. In this setup, the 200 nucleotide long DNA was covalently attached to the surface of an optically transparent solid support at one end and to the surface of a superparamagnetic fluorescent microsphere (force probe) at the other end. The force was applied to the probes using an electromagnet. The end-to-end molecular distance (i.e. out-of-image-plane position of the force probe) was determined from the intensity of the probe fluorescent image observed with total-internal reflectance microscopy. An equation of state for single stranded DNA molecules under tension (extensible freely jointed chain) was used to derive the penetration depth of the evanescent field and to calibrate the magnetic properties of the force probes. The parameters of the magnetic response of the force probes obtained from the equation of state remained constant when changing the penetration depth, indicating a robust calibration procedure. The results of such a calibration were also confirmed using independently measured probe-surface distances for probes mounted onto cantilevers of an atomic force microscope. Upon hybridization of the complementary 50 nucleotide-long oligomer to the surface-bound 200-mer, the changes in the force-distance curves were consistent with the quantitative conversion of 25% of the original single-stranded DNA to its double-stranded form, which was modeled as an elastic rod. The method presented here for quantifying the hybridization state of the single DNA molecules has potential for determining the degree of hybridization of individual molecules in a single molecule array with high accuracy.
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Gao T, Blanchette CD, He W, Bourguet F, Ly S, Katzen F, Kudlicki WA, Henderson PT, Laurence TA, Huser T, Coleman MA. Characterizing diffusion dynamics of a membrane protein associated with nanolipoproteins using fluorescence correlation spectroscopy. Protein Sci 2011; 20:437-47. [PMID: 21280134 PMCID: PMC3048428 DOI: 10.1002/pro.577] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 11/29/2010] [Accepted: 12/01/2010] [Indexed: 01/28/2023]
Abstract
Nanolipoprotein particles (NLPs) represent a unique nanometer-sized scaffold for supporting membrane proteins (MP). Characterization of their dynamic shape and association with MP in solution remains a challenge. Here, we present a rapid method of analysis by fluorescence correlation spectroscopy (FCS) to characterize bacteriorhodopsin (bR), a membrane protein capable of forming a NLP complex. By selectively labeling individual components of NLPs during cell-free synthesis, FCS enabled us to measure specific NLP diffusion times and infer size information for different NLP species. The resulting bR-loaded NLPs were shown to be dynamically discoidal in solution with a mean diameter of 7.8 nm. The insertion rate of bR in the complex was ∼55% based on a fit model incorporating two separate diffusion properties to best approximate the FCS data. More importantly, based on these data, we infer that membrane protein associated NLPs are thermodynamically constrained as discs in solution, while empty NLPs appear to be less constrained and dynamically spherical.
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Affiliation(s)
- Tingjuan Gao
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Craig D Blanchette
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
| | - Wei He
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Feliza Bourguet
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
| | - Sonny Ly
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | | | | | - Paul T Henderson
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Ted A Laurence
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
| | - Thomas Huser
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
| | - Matthew A Coleman
- NSF Center for Biophotonics Science and Technology, School of Medicine, University of California DavisSacramento, California 95817
- Lawrence Livermore National Laboratory, Physics and Life SciencesLivermore, California 94550
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Mazouchi A, Liu B, Bahram A, Gradinaru CC. On the performance of bioanalytical fluorescence correlation spectroscopy measurements in a multiparameter photon-counting microscope. Anal Chim Acta 2011; 688:61-9. [PMID: 21296206 DOI: 10.1016/j.aca.2011.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/10/2010] [Accepted: 01/04/2011] [Indexed: 11/26/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) data acquisition and analysis routines were developed and implemented in a home-built, multiparameter photon-counting microscope. Laser excitation conditions were investigated for two representative fluorescent probes, Rhodamine110 and enhanced green fluorescent protein (EGFP). Reliable local concentrations and diffusion constants were obtained by fitting measured FCS curves, provided that the excitation intensity did not exceed 20% of the saturation level for each fluorophore. Accurate results were obtained from FCS measurements for sample concentrations varying from pM to μM range, as well as for conditions of high background signals. These experimental constraints were found to be determined by characteristics of the detection system and by the saturation behavior of the fluorescent probes. These factors actually limit the average number of photons that can be collected from a single fluorophore passing through the detection volume. The versatility of our setup and the data analysis capabilities were tested by measuring the mobility of EGFP in the nucleus of Drosophila cells under conditions of high concentration and molecular crowding. As a bioanalytical application, we studied by FCS the binding affinity of a novel peptide-based drug to the cancer-regulating STAT3 protein and corroborated the results with fluorescence polarization analysis derived from the same photon data.
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Affiliation(s)
- Amir Mazouchi
- Department of Physics, Institute for Optical Sciences, University of Toronto, Toronto, Canada
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41
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Fluorescence Correlation and Cross-Correlation Spectroscopy Using Fluorescent Proteins for Measurements of Biomolecular Processes in Living Organisms. FLUORESCENT PROTEINS II 2011. [DOI: 10.1007/4243_2011_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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42
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Mitsuhashi M, Sakata H, Kinjo M, Yazawa M, Takahashi M. Dynamic assembly properties of nonmuscle myosin II isoforms revealed by combination of fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy. J Biochem 2010; 149:253-63. [PMID: 21106542 DOI: 10.1093/jb/mvq134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Myosin II molecules assemble into filaments through their C-terminal rod region, and are responsible for several cellular motile activities. Three isoforms of nonmuscle myosin II (IIA, IIB and IIC) are expressed in mammalian cells. However, little is known regarding the isoform composition in filaments. To obtain new insight into the assembly properties of myosin II isoforms, especially regarding the isoform composition in filaments, we performed a combination analysis of fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS), which enables us to acquire information on both the interaction and the size of each molecule simultaneously. Using C-terminal rod fragments of IIA and IIB (ARF296 and BRF305) labelled with different fluorescent probes, we demonstrated that hetero-assemblies were formed from a mixture of ARF296 and BRF305, and that dynamic exchange of rod fragments occurred between preformed homo-assemblies of each isoform in an isoform-independent manner. We also showed that Mts1 (S100A4) specifically stripped ARF296 away from the hetero-assemblies, and consequently, homo-assemblies of BRF305 were formed. These results suggest that IIA and IIB can form hetero-filaments in an isoform-independent manner, and that a factor like Mts1 can remove one isoform from the hetero-filament, resulting in a formation of homo-filaments consisting of another isoform.
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Affiliation(s)
- Mariko Mitsuhashi
- Division of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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43
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Mikuni J, Kato M, Taruya S, Tsuganezawa K, Mori M, Ogawa N, Honma T, Yokoyama S, Kojima H, Okabe T, Nagano T, Tanaka A. A fluorescence correlation spectroscopy-based assay for fragment screening of slowly inhibiting protein–peptide interaction inhibitors. Anal Biochem 2010; 402:26-31. [DOI: 10.1016/j.ab.2010.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 03/12/2010] [Accepted: 03/12/2010] [Indexed: 10/19/2022]
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Richards CI, Hsiang JC, Khalil AM, Hull NP, Dickson RM. FRET-enabled optical modulation for high sensitivity fluorescence imaging. J Am Chem Soc 2010; 132:6318-23. [PMID: 20397664 PMCID: PMC2874320 DOI: 10.1021/ja100175r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence resonance energy transfer is utilized to engineer donor photophysics for facile signal amplification and selective fluorescence recovery from high background. This is generalized such that many different fluorophores can be used in optical modulation schemes to drastically improve fluorescence imaging sensitivity. Dynamic, simultaneous, and direct excitation of the acceptor brightens and optically modulates higher energy donor emission. The externally imposed modulation waveform enables selective donor fluorescence extraction through demodulation. By incorporating an acceptor with significant, spectrally shifted, dark-state population, necessary excitation intensities are quite low and agree well with simulated enhancements. Enhancement versus modulation frequency directly yields dark-state lifetimes in a simple ensemble measurement. Using the long-lived Cy5 dark state in conjunction with Cy3 donors, we demonstrate image extraction from a large background to yield >>10-fold sensitivity improvements through synchronously amplified fluorescence image recovery (SAFIRe).
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Affiliation(s)
- Chris I. Richards
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Jung-Cheng Hsiang
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Andrew M. Khalil
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Nathan P. Hull
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Robert M. Dickson
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
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Xu F, Dong C, Xie C, Ren J. Ultrahighly sensitive homogeneous detection of DNA and microRNA by using single-silver-nanoparticle counting. Chemistry 2010; 16:14225. [PMID: 19938021 DOI: 10.1002/chem.200902555] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA and RNA analysis is of high importance for clinical diagnoses, forensic analysis, and basic studies in the biological and biomedical fields. In this paper, we report the ultrahighly sensitive homogeneous detection of DNA and microRNA by using a novel single-silver-nanoparticle counting (SSNPC) technique. The principle of SSNPC is based on the photon-burst counting of single silver nanoparticles (Ag NPs) in a highly focused laser beam (about 0.5 fL detection volume) due to Brownian motion and the strong resonance Rayleigh scattering of single Ag NPs. We first investigated the performance of the SSNPC system and then developed an ultrasensitive homogeneous detection method for DNA and microRNA based on this single-nanoparticle technique. Sandwich nucleic acid hybridization models were utilized in the assays. In the hybridization process, when two Ag-NP-oligonucleotide conjugates were mixed in a sample containing DNA (or microRNA) targets, the binding of the targets caused the Ag NPs to form dimers (or oligomers), which led to a reduction in the photon-burst counts. The SSNPC method was used to measure the change in the photon-burst counts. The relationship between the change of the photon-burst counts and the target concentration showed a good linearity. This method was used for the assay of sequence-specific DNA fragments and microRNAs. The detection limits were at about the 1 fM level, which is 2-5 orders of magnitude more sensitive than current homogeneous methods.
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Affiliation(s)
- Fagong Xu
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, PR China
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46
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Zhou X, Xing D, Tang Y, Chen WR. PCR-free detection of genetically modified organisms using magnetic capture technology and fluorescence cross-correlation spectroscopy. PLoS One 2009; 4:e8074. [PMID: 19956680 PMCID: PMC2778010 DOI: 10.1371/journal.pone.0008074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 10/28/2009] [Indexed: 11/25/2022] Open
Abstract
The safety of genetically modified organisms (GMOs) has attracted much attention recently. Polymerase chain reaction (PCR) amplification is a common method used in the identification of GMOs. However, a major disadvantage of PCR is the potential amplification of non-target DNA, causing false-positive identification. Thus, there remains a need for a simple, reliable and ultrasensitive method to identify and quantify GMO in crops. This report is to introduce a magnetic bead-based PCR-free method for rapid detection of GMOs using dual-color fluorescence cross-correlation spectroscopy (FCCS). The cauliflower mosaic virus 35S (CaMV35S) promoter commonly used in transgenic products was targeted. CaMV35S target was captured by a biotin-labeled nucleic acid probe and then purified using streptavidin-coated magnetic beads through biotin-streptavidin linkage. The purified target DNA fragment was hybridized with two nucleic acid probes labeled respectively by Rhodamine Green and Cy5 dyes. Finally, FCCS was used to detect and quantify the target DNA fragment through simultaneously detecting the fluorescence emissions from the two dyes. In our study, GMOs in genetically engineered soybeans and tomatoes were detected, using the magnetic bead-based PCR-free FCCS method. A detection limit of 50 pM GMOs target was achieved and PCR-free detection of GMOs from 5 microg genomic DNA with magnetic capture technology was accomplished. Also, the accuracy of GMO determination by the FCCS method is verified by spectrophotometry at 260 nm using PCR amplified target DNA fragment from GM tomato. The new method is rapid and effective as demonstrated in our experiments and can be easily extended to high-throughput and automatic screening format. We believe that the new magnetic bead-assisted FCCS detection technique will be a useful tool for PCR-free GMOs identification and other specific nucleic acids.
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Affiliation(s)
- Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yonghong Tang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Wei R. Chen
- Department of Engineering and Physics College of Mathematics and Science, University of Central Oklahoma, Edmond, Oklahoma, United States of America
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47
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Sikorav JL, Orland H, Braslau A. Mechanism of thermal renaturation and hybridization of nucleic acids: Kramers' process and universality in Watson-Crick base pairing. J Phys Chem B 2009; 113:3715-25. [PMID: 19673131 DOI: 10.1021/jp807096z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions of single-stranded chains, in the presence of molar concentrations of monovalent salts and at elevated temperatures). The mechanism follows a Kramers' process, whereby the complementary chains overcome a potential barrier through Brownian motion. The barrier originates from a single rate-limiting nucleation event in which the first complementary base pairs are formed. The reaction then proceeds through a fast growth of the double helix. For the DNA of bacteriophages T7, T4, and phiX174, as well as for Escherichia coli DNA, the bimolecular rate k2 of the reaction increases as a power law of the average degree of polymerization <N> of the reacting single-strands: k2 is proportional to <N> alpha. This relationship holds for 100 < or = <N> < or = 50,000 with an experimentally determined exponent alpha = 0.51 +/- 0.01. The length dependence results from a thermodynamic excluded-volume effect. The reacting single-stranded chains are predicted to be in universal good solvent conditions, and the scaling law is determined by the relevant equilibrium monomer contact probability. The value theoretically predicted for the exponent is alpha = 1 - nutheta2, where nu is Flory's swelling exponent (nu approximately equal 0.588), and theta2 is a critical exponent introduced by des Cloizeaux (theta2 approximately equal 0.82), yielding alpha = 0.52 +/- 0.01, in agreement with the experimental results.
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Affiliation(s)
- Jean-Louis Sikorav
- DSM, Institut de Physique Théorique, IPhT, CNRS, MPPU, URA2306, Gif-sur-Yvette, France.
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48
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Kobayashi T, Yoshimori A, Kino K, Komori R, Miyazawa H, Tanuma SI. A new small molecule that directly inhibits the DNA binding of NF-kappaB. Bioorg Med Chem 2009; 17:5293-7. [PMID: 19539480 DOI: 10.1016/j.bmc.2009.05.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 05/11/2009] [Accepted: 05/12/2009] [Indexed: 12/21/2022]
Abstract
Nuclear factor-kappaB (NF-kappaB) has been considered as a good target for the treatment of many diseases. Although a lot of NF-kappaB inhibitors have already been reported, many of them have several common problems. Thus, we attempted to identify novel NF-kappaB inhibitors to be unique lead compounds for creating new pharmaceuticals. In the present study, we screened our chemical library for compounds that directly inhibit the DNA binding of NF-kappaB by using fluorescence correlation spectroscopy (FCS). Consequently, we identified a promising compound, 4,6-dichloro-N-phenyl-1,3,5-triazin-2-amine, referred to as NI241. It mediated a dose-dependent inhibition of the DNA binding of NF-kappaB p50. Its analogues also showed dose-dependent inhibition and their inhibitory effects were altered by the substituents on the N-phenyl group. Furthermore, we predicted the binding mode of NI241 with p50 in silico. In this model, NI241 forms three hydrogen bonds with Tyr60, His144, and Asp242 on p50, which are important amino acid residues for the interaction with DNA. These results suggest that NI241 with structural novelty may serve as a useful scaffold for the creation of new NF-kappaB inhibitors by rational optimization.
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Affiliation(s)
- Takanobu Kobayashi
- Laboratory of Molecular Biology, Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
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49
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Octeau V, Cognet L, Duchesne L, Lasne D, Schaeffer N, Fernig DG, Lounis B. Photothermal absorption correlation spectroscopy. ACS NANO 2009; 3:345-350. [PMID: 19236070 DOI: 10.1021/nn800771m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a popular technique, complementary to cell imaging for the investigation of dynamic processes in living cells. Based on fluorescence, this single molecule method suffers from artifacts originating from the poor fluorophore photophysics: photobleaching, blinking, and saturation. To circumvent these limitations we present here a new correlation method called photothermal absorption correlation spectroscopy (PhACS) which relies on the absorption properties of tiny nano-objects. PhACS is based on the photothermal heterodyne detection technique and measures akin FCS, the time correlation function of the detected signals. Application of this technique to the precise determination of the hydrodynamic sizes of different functionalized gold nanoparticles are presented, highlighting the potential of this method.
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Affiliation(s)
- Vivien Octeau
- Centre de Physique Moleculaire Optique et Hertzienne, Universite de Bordeaux and CNRS, 351 cours de la Liberation, Talence, F-33405, France
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50
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Wenger J, Gérard D, Aouani H, Rigneault H. Nanoaperture-enhanced signal-to-noise ratio in fluorescence correlation spectroscopy. Anal Chem 2009; 81:834-9. [PMID: 19099408 DOI: 10.1021/ac8024015] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fluorescence enhancement found in gold nanoapertures is demonstrated to increase the signal-to-noise ratio (SNR) in fluorescence correlation spectroscopy (FCS). Starting from a general discussion on noise in FCS experiments, we show that fluorescence enhancement leads to a dramatic increase in the SNR. This prediction is confirmed by experiments where we report an experimental gain in SNR of about 1 order of magnitude, corresponding to a 100-fold reduction of the experiment duration. This technique is then applied to monitor the kinetics of a fast enzymatic cleavage reaction. This set of experiments evidence the feasibility of FCS analysis with fast integration times of about 1 s, opening the way to the monitoring of a variety of biochemical reactions at reduced time scales.
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Affiliation(s)
- Jérôme Wenger
- Institut Fresnel, Aix-Marseille Université, CNRS, Domaine Universitaire de Saint-Jérôme, 13397 Marseille Cedex 20, France
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