1
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Dodds AC, Sansom HG, Magennis SW, Sutherland A. Synthesis of Thiazoloindole α-Amino Acids: Chromophores Amenable to One- and Two-Photon Induced Fluorescence. Org Lett 2023; 25:8942-8946. [PMID: 38055619 PMCID: PMC10729019 DOI: 10.1021/acs.orglett.3c03851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
Thiazoloindole α-amino acids have been synthesized in four steps from tryptophan using a dual-catalytic thiolation reaction and a copper-mediated intramolecular N-arylation process. Late-stage diversification of the thiazoloindole core with electron-deficient aryl substituents produced chromophores that on one-photon excitation displayed blue-green emission, mega-Stokes shifts, and high quantum yields. The thiazoloindole amino acids could also be excited via two-photon absorption in the near-infrared, demonstrating their potential for biomedical imaging applications.
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Affiliation(s)
- Amy C. Dodds
- School of Chemistry, The Joseph Black
Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Henry G. Sansom
- School of Chemistry, The Joseph Black
Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Steven W. Magennis
- School of Chemistry, The Joseph Black
Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Andrew Sutherland
- School of Chemistry, The Joseph Black
Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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2
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Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda DS, Steffen FD, Cordes T, Magennis SW, Lerner E. A new twist on PIFE: photoisomerisation-related fluorescence enhancement. Methods Appl Fluoresc 2023; 12:012001. [PMID: 37726007 PMCID: PMC10570931 DOI: 10.1088/2050-6120/acfb58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/24/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule. In this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turning PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Benjamin Ambrose
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Richard Börner
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Felix Erichson
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, United Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, United States of America
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ,85287, United States of America
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States of America
| | - Abhishek Mazumder
- CSIR-Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Fabio D Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Großhadernerstr. 2-4, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Eitan Lerner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
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3
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Nilsson JR, Benitez-Martin C, Sansom HG, Pfeiffer P, Baladi T, Le HN, Dahlén A, Magennis SW, Wilhelmsson LM. Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA. Phys Chem Chem Phys 2023. [PMID: 37475592 DOI: 10.1039/d3cp01147j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Fluorescent nucleobase analogues (FBAs) are established tools for studying oligonucleotide structure, dynamics and interactions, and have recently also emerged as an attractive option for labeling RNA-based therapeutics. A recognized drawback of FBAs, however, is that they typically require excitation in the UV region, which for imaging in biological samples may have disadvantages related to phototoxicity, tissue penetration, and out-of-focus photobleaching. Multiphoton excitation has the potential to alleviate these issues and therefore, in this work, we characterize the multiphoton absorption properties and detectability of the highly fluorescent quadracyclic adenine analogue 2CNqA as a ribonucleotide monomer as well as incorporated, at one or two positions, into a 16mer antisense oligonucleotide (ASO). We found that 2CNqA has a two-photon absorption cross section that, among FBAs, is exceptionally high, with values of σ2PA(700 nm) = 5.8 GM, 6.8 GM, and 13 GM for the monomer, single-, and double-labelled oligonucleotide, respectively. Using fluorescence correlation spectroscopy, we show that the 2CNqA has a high 2P brightness as the monomer and when incorporated into the ASO, comparing favorably to other FBAs. We furthermore demonstrate the usefulness of the 2P imaging mode for improving detectability of 2CNqA-labelled ASOs in live cells.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Carlos Benitez-Martin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Henry G Sansom
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Tom Baladi
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hoang-Ngoan Le
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
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4
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Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda DS, Steffen FD, Cordes T, Magennis SW, Lerner E. A new twist on PIFE: photoisomerisation-related fluorescence enhancement. ArXiv 2023:arXiv:2302.12455v2. [PMID: 36866225 PMCID: PMC9980184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis/trans photoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule and, in this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turn PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Benjamin Ambrose
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, UK, Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, UK
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Richard Börner
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Felix Erichson
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Achillefs N. Kapanidis
- Kavli Institute for Nanoscience Discovery, Department of Biological Physics, The University of Oxford, UK
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ, 85287, USA
| | - Timothy M. Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Abhishek Mazumder
- Kavli Institute for Nanoscience Discovery, Department of Biological Physics, The University of Oxford, UK
| | - David S. Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, UK, Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, UK
| | - Fabio D. Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr, 2-4, 82152 Planegg-Martinsried, Germany
| | - Steven W. Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, UK
| | - Eitan Lerner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem; Jerusalem 9190401, Israel, Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
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5
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Nobis D, Sansom HG, Magennis SW. Corrigendum: Pulse-shaped broadband multiphoton excitation for single-molecule fluorescence detection in the far field (2023 Methods Appl. Fluoresc.11017001). Methods Appl Fluoresc 2023; 11. [PMID: 37057756 DOI: 10.1088/2050-6120/acca63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/15/2023]
Affiliation(s)
- David Nobis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Henry G Sansom
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
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6
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Nobis D, Sansom HG, Magennis SW. Pulse-shaped broadband multiphoton excitation for single-molecule fluorescence detection in the far field. Methods Appl Fluoresc 2023; 11. [PMID: 36595246 DOI: 10.1088/2050-6120/aca87f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 12/01/2022] [Indexed: 12/04/2022]
Abstract
Multiphoton excitation of fluorescence has many potential advantages over resonant (one-photon) excitation, but the method has not found widespread use for ultrasensitive applications. We recently described an approach to the multiphoton excitation of single molecules that uses a pulse shaper to compress and tailor pulses from an ultrafast broadband laser in order to optimise the brightness and signal-to-background ratio following non-linear excitation. Here we provide a detailed description of the setup and illustrate its use and potential by optimising two-photon fluorescence of a common fluorophore, rhodamine 110, at the single-molecule level. We also show that a DNA oligonucleotide labelled with a fluorescent nucleobase analogue, tC, can be detected using two-photon FCS, whereas one-photon excitation causes rapid photobleaching. The ability to improve the signal-to-background ratio and to reduce the incident power required to attain a given brightness can be applied to the multiphoton excitation of any fluorescent species, from small molecules with low multiphoton cross sections to the brightest nanoparticles.
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Affiliation(s)
- David Nobis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Henry G Sansom
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
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7
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Samaan GN, Wyllie MK, Cizmic JM, Needham LM, Nobis D, Ngo K, Andersen S, Magennis SW, Lee SF, Purse BW. Single-molecule fluorescence detection of a tricyclic nucleoside analogue. Chem Sci 2020; 12:2623-2628. [PMID: 34164030 PMCID: PMC8179283 DOI: 10.1039/d0sc03903a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C-linked 8-(diethylamino)benzo[b][1,8]naphthyridin-2(1H)-one nucleoside, which we name ABN, exhibits ε442 = 20 000 M−1 cm−1 and Φem,540 = 0.39 in water, increasing to Φem = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities. Fluorescent nucleoside analogue ABN is readily detected at the single-molecule level and retains a quantum yield >50% in duplex DNA oligonucleotides.![]()
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Affiliation(s)
- George N Samaan
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Mckenzie K Wyllie
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Julian M Cizmic
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Lisa-Maria Needham
- University of Cambridge, Chemistry Department Lensfield Road Cambridge CB2 1EW UK
| | - David Nobis
- School of Chemistry, University of Glasgow University Avenue Glasgow G12 8QQ UK
| | - Katrina Ngo
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Susan Andersen
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Steven W Magennis
- School of Chemistry, University of Glasgow University Avenue Glasgow G12 8QQ UK
| | - Steven F Lee
- University of Cambridge, Chemistry Department Lensfield Road Cambridge CB2 1EW UK
| | - Byron W Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
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8
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Morten MJ, Steinmark IE, Magennis SW. Probing DNA Dynamics: Stacking‐Induced Fluorescence Increase (SIFI) versus FRET. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael J. Morten
- School of ChemistryUniversity of Glasgow Joseph Black Building University Avenue Glasgow GA12 8QQ UK
| | - I. Emilie Steinmark
- School of ChemistryUniversity of Glasgow Joseph Black Building University Avenue Glasgow GA12 8QQ UK
| | - Steven W. Magennis
- School of ChemistryUniversity of Glasgow Joseph Black Building University Avenue Glasgow GA12 8QQ UK
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9
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Affiliation(s)
- Michael J. Morten
- School of ChemistryUniversity of Glasgow Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - I. Emilie Steinmark
- School of ChemistryUniversity of Glasgow Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Steven W. Magennis
- School of ChemistryUniversity of Glasgow Joseph Black Building University Avenue Glasgow G12 8QQ UK
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10
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Berrocal-Martin R, Sanchez-Cano C, Chiu CKC, Needham RJ, Sadler PJ, Magennis SW. Metallation-Induced Heterogeneous Dynamics of DNA Revealed by Single-Molecule FRET. Chemistry 2020; 26:4980-4987. [PMID: 31999015 DOI: 10.1002/chem.202000458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Indexed: 11/09/2022]
Abstract
The metallation of nucleic acids is key to wide-ranging applications, from anticancer medicine to nanomaterials, yet there is a lack of understanding of the molecular-level effects of metallation. Here, we apply single-molecule fluorescence methods to study the reaction of an organo-osmium anticancer complex and DNA. Individual metallated DNA hairpins are characterised using Förster resonance energy transfer (FRET). Although ensemble measurements suggest a simple two-state system, single-molecule experiments reveal an underlying heterogeneity in the oligonucleotide dynamics, attributable to different degrees of metallation of the GC-rich hairpin stem. Metallated hairpins display fast two-state transitions with a two-fold increase in the opening rate to ≈2 s-1 , relative to the unmodified hairpin, and relatively static conformations with long-lived open (and closed) states of 5 to ≥50 s. These studies show that a single-molecule approach can provide new insight into metallation-induced changes in DNA structure and dynamics.
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Affiliation(s)
- Raul Berrocal-Martin
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Carlos Sanchez-Cano
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Cookson K C Chiu
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Russell J Needham
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
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11
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Berrones‐Reyes JC, Muñoz‐Flores BM, Uscanga‐Palomeque AC, Santillán R, Del Angel‐Mosqueda C, Nobis D, Cochrane MA, Magennis SW, Jiménez‐Pérez VM. Two‐Photon Detection of Organotin Schiff Base Complexes in Cancer Cells. ChemistrySelect 2020. [DOI: 10.1002/slct.201904816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jessica C. Berrones‐Reyes
- Universidad Autónoma de Nuevo LeónFacultad de Ciencias Químicas Av. Pedro de Alba 66455 Nuevo León México
| | - Blanca M. Muñoz‐Flores
- Universidad Autónoma de Nuevo LeónFacultad de Ciencias Químicas Av. Pedro de Alba 66455 Nuevo León México
| | | | - Rosa Santillán
- Centro de Investigación y de Estudios Avanzados del IPNDepartamento de Química, A. P. 14-740, C. P. 07000 D. F. México
| | - Casiano Del Angel‐Mosqueda
- Universidad Autónoma de Nuevo LeónFacultad de Odontología Av. Dr. Eduardo Aguirre Pequeño 64460 Nuevo León México
| | - David Nobis
- University of GlasgowSchool of Chemistry, Joseph Black Building, University Place Glasgow G12 8QQ United Kingdom
| | - Max A. Cochrane
- University of GlasgowSchool of Chemistry, Joseph Black Building, University Place Glasgow G12 8QQ United Kingdom
| | - Steven W. Magennis
- University of GlasgowSchool of Chemistry, Joseph Black Building, University Place Glasgow G12 8QQ United Kingdom
| | - Víctor M. Jiménez‐Pérez
- Universidad Autónoma de Nuevo LeónFacultad de Ciencias Químicas Av. Pedro de Alba 66455 Nuevo León México
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12
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Bell JD, Harkiss AH, Nobis D, Malcolm E, Knuhtsen A, Wellaway CR, Jamieson AG, Magennis SW, Sutherland A. Conformationally rigid pyrazoloquinazoline α-amino acids: one- and two-photon induced fluorescence. Chem Commun (Camb) 2020; 56:1887-1890. [DOI: 10.1039/c9cc09064a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Conformationally rigid unnatural α-amino acids bearing a pyrazoloquinazoline ring system that are amenable to both one- and two-photon excitation have been developed as new fluorescent probes.
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Affiliation(s)
- Jonathan D. Bell
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
| | - Alexander H. Harkiss
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
| | - David Nobis
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
| | - Eilidh Malcolm
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
| | - Astrid Knuhtsen
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
| | | | - Andrew G. Jamieson
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
| | - Steven W. Magennis
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
| | - Andrew Sutherland
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow
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13
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Nobis D, Fisher RS, Simmermacher M, Hopkins PA, Tor Y, Jones AC, Magennis SW. Single-Molecule Detection of a Fluorescent Nucleobase Analogue via Multiphoton Excitation. J Phys Chem Lett 2019; 10:5008-5012. [PMID: 31397575 PMCID: PMC7024020 DOI: 10.1021/acs.jpclett.9b02108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The ability to routinely detect fluorescent nucleobase analogues at the single-molecule level would create a wealth of opportunities to study nucleic acids. We report the multiphoton-induced fluorescence and single-molecule detection of a dimethylamine-substituted extended-6-aza-uridine (DMAthaU). We show that DMAthaU can exist in a highly fluorescent form, emitting strongly in the visible region (470-560 nm). Using pulse-shaped broadband Ti:sapphire laser excitation, DMAthaU undergoes two-photon (2P) absorption at low excitation powers, switching to three-photon (3P) absorption at high incident intensity. The assignment of a 3P process is supported by cubic response calculations. Under both 2P and 3P excitation, the single-molecule brightness was over an order of magnitude higher than reported previously for any fluorescent base analogue, which facilitated the first single-molecule detection of an emissive nucleoside with multiphoton excitation.
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Affiliation(s)
- David Nobis
- WestCHEM School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Rachel S. Fisher
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Mats Simmermacher
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Patrycja A. Hopkins
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Anita C. Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
- Corresponding Authors (A.C.J.)., (S.W.M.)
| | - Steven W. Magennis
- WestCHEM School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
- Corresponding Authors (A.C.J.)., (S.W.M.)
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14
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Morten MJ, Lopez SG, Steinmark IE, Rafferty A, Magennis SW. Stacking-induced fluorescence increase reveals allosteric interactions through DNA. Nucleic Acids Res 2019; 46:11618-11626. [PMID: 30277520 PMCID: PMC6265455 DOI: 10.1093/nar/gky887] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/19/2018] [Indexed: 12/14/2022] Open
Abstract
From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye–DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids.
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Affiliation(s)
- Michael J Morten
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Sergio G Lopez
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - I Emilie Steinmark
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Aidan Rafferty
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Steven W Magennis
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
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15
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Fisher RS, Nobis D, Füchtbauer AF, Bood M, Grøtli M, Wilhelmsson LM, Jones AC, Magennis SW. Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity. Phys Chem Chem Phys 2018; 20:28487-28498. [PMID: 30412214 DOI: 10.1039/c8cp05496g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorescent nucleobase analogues (FBAs) have many desirable features in comparison to extrinsic fluorescent labels, but they are yet to find application in ultrasensitive detection. Many of the disadvantages of FBAs arise from their short excitation wavelengths (often in the ultraviolet), making two-photon excitation a potentially attractive approach. Pentacyclic adenine (pA) is a recently developed FBA that has an exceptionally high two-photon brightness. We have studied the two-photon-excited fluorescence properties of pA and how they are affected by incorporation in DNA. We find that pA is more photostable under two-photon excitation than via resonant absorption. When incorporated in an oligonucleotide, pA has a high two-photon cross section and emission quantum yield, varying with sequence context, resulting in the highest reported brightness for such a probe. The use of a two-photon microscope with ultrafast excitation and pulse shaping has allowed the detection of pA-containing oligonucleotides in solution with a limit of detection of ∼5 molecules, demonstrating that practical single-molecule detection of FBAs is now within reach.
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Affiliation(s)
- Rachel S Fisher
- EaStCHEM School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, UK.
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16
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Baltierra-Jasso LE, Morten MJ, Magennis SW. Sub-Ensemble Monitoring of DNA Strand Displacement Using Multiparameter Single-Molecule FRET. Chemphyschem 2018; 19:551-555. [PMID: 29316151 DOI: 10.1002/cphc.201800012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Indexed: 11/09/2022]
Abstract
Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here, we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of 10 m-1 s-1 . We also followed the displacement from a DNA three-way junction (3WJ) by ssDNA. The presence of three internal mismatched bases in the middle of the invading strand did not prevent displacement from the 3WJ, but reduced the second-order rate constant by about 50 %. We attribute strand exchange in the dsDNA and 3WJ to a zero-toehold pathway from the blunt-ended duplex arms. The single-molecule approach demonstrated here will be useful for studying complex DNA networks.
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Affiliation(s)
- Laura E Baltierra-Jasso
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Michael J Morten
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Steven W Magennis
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
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17
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Baltierra-Jasso LE, Morten MJ, Magennis SW. Cover Feature: Sub-Ensemble Monitoring of DNA Strand Displacement Using Multiparameter Single-Molecule FRET (ChemPhysChem 5/2018). Chemphyschem 2018. [DOI: 10.1002/cphc.201800146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Michael J. Morten
- WestCHEM School of Chemistry; University of Glasgow; University Avenue Glasgow G12 8QQ UK
| | - Steven W. Magennis
- WestCHEM School of Chemistry; University of Glasgow; University Avenue Glasgow G12 8QQ UK
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18
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Bood M, Füchtbauer AF, Wranne MS, Ro JJ, Sarangamath S, El-Sagheer AH, Rupert DLM, Fisher RS, Magennis SW, Jones AC, Höök F, Brown T, Kim BH, Dahlén A, Wilhelmsson LM, Grøtli M. Pentacyclic adenine: a versatile and exceptionally bright fluorescent DNA base analogue. Chem Sci 2018; 9:3494-3502. [PMID: 29780479 PMCID: PMC5934695 DOI: 10.1039/c7sc05448c] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 03/01/2018] [Indexed: 12/16/2022] Open
Abstract
A highly fluorescent, non-perturbing, pentacyclic adenine analog was designed, synthesized, incorporated into DNA and photophysical evaluated.
Emissive base analogs are powerful tools for probing nucleic acids at the molecular level. Herein we describe the development and thorough characterization of pentacyclic adenine (pA), a versatile base analog with exceptional fluorescence properties. When incorporated into DNA, pA pairs selectively with thymine without perturbing the B-form structure and is among the brightest nucleobase analogs reported so far. Together with the recently established base analog acceptor qAnitro, pA allows accurate distance and orientation determination via Förster resonance energy transfer (FRET) measurements. The high brightness at emission wavelengths above 400 nm also makes it suitable for fluorescence microscopy, as demonstrated by imaging of single liposomal constructs coated with cholesterol-anchored pA–dsDNA, using total internal reflection fluorescence microscopy. Finally, pA is also highly promising for two-photon excitation at 780 nm, with a brightness (5.3 GM) that is unprecedented for a base analog.
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Affiliation(s)
- Mattias Bood
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden .
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Jong Jin Ro
- Department of Chemistry , Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , South Korea
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Afaf H El-Sagheer
- Chemistry Branch , Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Déborah L M Rupert
- Division of Biological Physics , Department of Physics , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Rachel S Fisher
- School of Chemistry , University of Edinburgh , The King's Buildings , Edinburgh EH9 3JJ , UK
| | - Steven W Magennis
- WestCHEM , School of Chemistry , University of Glasgow , Glasgow , G12 8QQ , UK
| | - Anita C Jones
- School of Chemistry , University of Edinburgh , The King's Buildings , Edinburgh EH9 3JJ , UK
| | - Fredrik Höök
- Division of Biological Physics , Department of Physics , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Tom Brown
- Department of Chemistry , Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK
| | - Byeang Hyean Kim
- Department of Chemistry , Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , South Korea
| | - Anders Dahlén
- AstraZeneca R&D , Innovative Medicines , Cardiovascular & Metabolic Diseases (CVMD) , Pepparedsleden 1, SE-431 83 Mölndal , Gothenburg , Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden .
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19
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Venkatesh V, Berrocal-Martin R, Wedge CJ, Romero-Canelón I, Sanchez-Cano C, Song JI, Coverdale JPC, Zhang P, Clarkson GJ, Habtemariam A, Magennis SW, Deeth RJ, Sadler PJ. Mitochondria-targeted spin-labelled luminescent iridium anticancer complexes. Chem Sci 2017; 8:8271-8278. [PMID: 29568475 PMCID: PMC5857930 DOI: 10.1039/c7sc03216a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/11/2017] [Indexed: 11/30/2022] Open
Abstract
Mitochondria generate energy but malfunction in many cancer cells, hence targeting mitochondrial metabolism is a promising approach for cancer therapy. Here we have designed cyclometallated iridium(iii) complexes, containing one TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) spin label [C43H43N6O2Ir1·PF6]˙ (Ir-TEMPO1) and two TEMPO spin labels [C52H58N8O4Ir1·PF6]˙ (Ir-TEMPO2). Electron paramagnetic resonance (EPR) spectroscopy revealed spin-spin interactions between the TEMPO units in Ir-TEMPO2. Both Ir-TEMPO1 and Ir-TEMPO2 showed bright luminescence with long lifetimes (ca. 35-160 ns); while Ir-TEMPO1 displayed monoexponential decay kinetics, the biexponential decays measured for Ir-TEMPO2 indicated the presence of more than one energetically-accessible conformation. This observation was further supported by density functional theory (DFT) calculations. The antiproliferative activity of Ir-TEMPO2 towards a range of cancer cells was much greater than that of Ir-TEMPO1, and also the antioxidant activity of Ir-TEMPO2 is much higher against A2780 ovarian cancer cells when compared with Ir-TEMPO1. Most notably Ir-TEMPO2 was particularly potent towards PC3 human prostate cancer cells (IC50 = 0.53 μM), being ca. 8× more active than the clinical drug cisplatin, and ca. 15× more selective towards cancer cells versus normal cells. Confocal microscopy showed that both Ir-TEMPO1 and Ir-TEMPO2 localise in the mitochondria of cancer cells.
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Affiliation(s)
- V Venkatesh
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore-560012 , India
| | | | - Christopher J Wedge
- Department of Chemical Sciences , University of Huddersfield , Huddersfield HD1 3DH , UK .
| | - Isolda Romero-Canelón
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
- School of Pharmacy , University of Birmingham , Edgbaston B15 2TT , UK
| | | | - Ji-Inn Song
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
| | | | - Pingyu Zhang
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
| | - Guy J Clarkson
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
| | - Abraha Habtemariam
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
| | - Steven W Magennis
- School of Chemistry , WestCHEM , University of Glasgow , Glasgow G12 8QQ , UK .
| | - Robert J Deeth
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
| | - Peter J Sadler
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK .
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20
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Toulmin A, Baltierra-Jasso LE, Morten MJ, Sabir T, McGlynn P, Schröder GF, Smith BO, Magennis SW. Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint. Biochemistry 2017; 56:4985-4991. [PMID: 28820590 DOI: 10.1021/acs.biochem.7b00677] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully complementary 3WJ and found that it contained unpaired bases at the branchpoint, which is consistent with previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule Förster resonance energy transfer, molecular modeling, time-resolved ensemble fluorescence spectroscopy, and the first 19F nuclear magnetic resonance observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint. A 3WJ with a GC-rich branchpoint adopts an open conformation with unpaired bases at the branch and at least one additional conformation with an increased number of base interactions at the branchpoint. This structural diversity has implications for branch interactions and processing in vivo and for technological applications.
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Affiliation(s)
- Anita Toulmin
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Laura E Baltierra-Jasso
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K.,School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Michael J Morten
- School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Tara Sabir
- The School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K.,The Photon Science Institute, The University of Manchester , Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Peter McGlynn
- Department of Biology, University of York , Wentworth Way, York YO10 5DD, U.K
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich , 52425 Jülich, Germany.,Physics Department, Heinrich-Heine Universität Düsseldorf , Düsseldorf, Germany
| | - Brian O Smith
- Institute of Molecular, Cell and Systems Biology, University of Glasgow , Glasgow G12 8QQ, U.K
| | - Steven W Magennis
- School of Chemistry, WestCHEM, University of Glasgow , Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
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21
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Quinn SD, Magennis SW. Optical detection of gadolinium(iii) ions via quantum dot aggregation. RSC Adv 2017; 7:24730-24735. [PMID: 29308186 PMCID: PMC5735353 DOI: 10.1039/c7ra03969g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/28/2017] [Indexed: 11/21/2022] Open
Abstract
A rapid, sensitive and selective optical readout of the presence of gadolinium(iii) ions would have a wide range of applications for clinical and environmental monitoring. We demonstrate that water-soluble CdTe quantum dots (QDs) are induced to aggregate by Gd3+ ions in aqueous solution. By using a combination of photoluminescence spectroscopy, dynamic light scattering and fluorescence correlation spectroscopy (FCS) to monitor quantum dot aggregation kinetics, we correlate the efficiency of the self-quenching process with the degree of aggregation across a broad range of conditions, including different sizes of QDs. We attribute the aggregation to metal binding to the QD's surface ligands and the quenching to intra-aggregate energy transfer between QDs. When the strategy was applied to additional trivalent ions, the aggregation rate varied according to the particular trivalent metal ion used, suggesting that the selectivity can be enhanced and controlled by appropriate design of the capping ligands and solution conditions.
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Affiliation(s)
- Steven D Quinn
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.
| | - Steven W Magennis
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.
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22
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Dalton CE, Quinn SD, Rafferty A, Morten MJ, Gardiner JM, Magennis SW. Single-Molecule Fluorescence Detection of a Synthetic Heparan Sulfate Disaccharide. Chemphyschem 2016; 17:3442-3446. [PMID: 27538128 PMCID: PMC5111599 DOI: 10.1002/cphc.201600750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Indexed: 11/11/2022]
Abstract
The first single-molecule fluorescence detection of a structurally-defined synthetic carbohydrate is reported: a heparan sulfate (HS) disaccharide fragment labeled with Alexa488. Single molecules have been measured whilst freely diffusing in solution and controlled encapsulation in surface-tethered lipid vesicles has allowed extended observations of carbohydrate molecules down to the single-molecule level. The diverse and dynamic nature of HS-protein interactions means that new tools to investigate pure HS fragments at the molecular level would significantly enhance our understanding of HS. This work is a proof-of-principle demonstration of the feasibility of single-molecule studies of synthetic carbohydrates which offers a new approach to the study of pure glycosaminoglycan (GAG) fragments.
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Affiliation(s)
- Charlotte E Dalton
- The School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Steven D Quinn
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, UK
| | - Aidan Rafferty
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, UK
| | - Michael J Morten
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, UK
| | - John M Gardiner
- The School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Steven W Magennis
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, UK
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23
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Toulmin A, Morten MJ, Sabir T, Baltierra-Jasso LE, McGlynn P, Schröder GF, Smith B, Magennis SW. Branchpoint Structure of DNA Threeway Junctions. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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24
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Baltierra-Jasso LE, Morten MJ, Laflör L, Quinn SD, Magennis SW. DNA Hairpin Dynamics under Molecular Crowding Conditions. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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25
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Quinn SD, Dalton CE, Jeanneret RA, Gardiner JM, Magennis SW. Single-Molecule Studies of Fluorescently-Labelled Polysaccharides. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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26
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Affiliation(s)
- Laura E. Baltierra-Jasso
- The School of Chemistry and The Photon
Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, U.K
| | - Michael J. Morten
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, U.K
| | - Linda Laflör
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, U.K
| | - Steven D. Quinn
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, U.K
| | - Steven W. Magennis
- WestCHEM, School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, U.K
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27
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Abstract
Five isomorphic fluorescent uridine mimics have been subjected to two-photon (2P) excitation analysis to investigate their potential applicability as non-perturbing probes for the single-molecule detection of nucleic acids. We find that small structural differences can cause major changes in the 2P excitation probability, with the 2P cross sections varying by over one order of magnitude. Two of the probes, both thiophene-modified uridine analogs, have the highest 2P cross sections (3.8 GM and 7.6 GM) reported for nucleobase analogs, using a conventional Ti:sapphire laser for excitation at 690 nm; they also have the lowest emission quantum yields. In contrast, the analogs with the highest reported quantum yields have the lowest 2P cross sections. The structure-photophysical property relationship presented here is a first step towards the rational design of emissive nucleobase analogs with controlled 2P characteristics. The results demonstrate the potential for major improvements through judicious structural modifications.
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Affiliation(s)
- Richard S K Lane
- School of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL (UK)
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28
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Abstract
Ensemble-based measurements of kinetic isotope effects (KIEs) have advanced physical understanding of enzyme-catalyzed reactions, but controversies remain. KIEs are used as reporters of rate-limiting H-transfer steps, quantum mechanical tunnelling, dynamics and multiple reactive states. Single molecule (SM) enzymatic KIEs could provide new information on the physical basis of enzyme catalysis. Here, single pair fluorescence energy transfer (spFRET) was used to measure SM enzymatic KIEs on the H-transfer catalyzed by the enzyme pentaerythritol tetranitrate reductase. We evaluated a range of methods for extracting the SM KIE from single molecule spFRET time traces. The SM KIE enabled separation of contributions from nonenzymatic protein and fluorophore processes and H-transfer reactions. Our work demonstrates SM KIE analysis as a new method for deconvolving reaction chemistry from intrinsic dynamics.
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Affiliation(s)
- Christopher R Pudney
- Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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29
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Sabir T, Toulmin A, Ma L, Jones AC, McGlynn P, Schröder GF, Magennis SW. Branchpoint expansion in a fully complementary three-way DNA junction. J Am Chem Soc 2012; 134:6280-5. [PMID: 22329743 DOI: 10.1021/ja211802z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Branched nucleic acid molecules serve as key intermediates in DNA replication, recombination, and repair; architectural elements in RNA; and building blocks and functional components for nanoscience applications. Using a combination of high-resolution single-molecule FRET, time-resolved spectroscopy, and molecular modeling, we have probed the local and global structure of a DNA three-way junction (3WJ) in solution. We found that it adopts a Y-shaped, pyramidal structure, in which the bases adjacent to the branchpoint are unpaired, despite the full Watson-Crick complementarity of the molecule. The unpairing allows a nanoscale cavity to form at the junction center. Our structure accounts for earlier observations made of the structure, flexibility, and reactivity of 3WJs. We anticipate that these results will guide the development of new DNA-based supramolecular receptors and nanosystems.
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Affiliation(s)
- Tara Sabir
- The School of Chemistry, Alan Turing Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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30
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Sabir T, Schröder GF, Toulmin A, McGlynn P, Magennis SW. Global Structure of Forked DNA in Solution Revealed by High-Resolution Single-Molecule FRET. J Am Chem Soc 2010; 133:1188-91. [DOI: 10.1021/ja108626w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tara Sabir
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- The Photon Science Institute, The University of Manchester, Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Gunnar F. Schröder
- Institute of Structural Biology and Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Anita Toulmin
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- The Photon Science Institute, The University of Manchester, Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
| | - Peter McGlynn
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, U.K
| | - Steven W. Magennis
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- The Photon Science Institute, The University of Manchester, Alan Turing Building, Oxford Road, Manchester M13 9PL, U.K
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31
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Graham EM, Iwai K, Uchiyama S, de Silva AP, Magennis SW, Jones AC. Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy. Lab Chip 2010; 10:1267-73. [PMID: 20445879 DOI: 10.1039/b924151e] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The use of a water-soluble, thermo-responsive polymer as a highly sensitive fluorescence-lifetime probe of microfluidic temperature is demonstrated. The fluorescence lifetime of poly(N-isopropylacrylamide) labelled with a benzofurazan fluorophore is shown to have a steep dependence on temperature around the polymer phase transition and the photophysical origin of this response is established. The use of this unusual fluorescent probe in conjunction with fluorescence lifetime imaging microscopy (FLIM) enables the spatial variation of temperature in a microfluidic device to be mapped, on the micron scale, with a resolution of less than 0.1 degrees C. This represents an increase in temperature resolution of an order of magnitude over that achieved previously by FLIM of temperature-sensitive dyes.
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Affiliation(s)
- Emmelyn M Graham
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
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Kalinin S, Sisamakis E, Magennis SW, Felekyan S, Seidel CAM. On the Origin of Broadening of Single-Molecule FRET Efficiency Distributions beyond Shot Noise Limits. J Phys Chem B 2010; 114:6197-206. [DOI: 10.1021/jp100025v] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Evangelos Sisamakis
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Steven W. Magennis
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
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Natrajan LS, Toulmin A, Chew A, Magennis SW. Two-photon luminescence from polar bis-terpyridyl-stilbene derivatives of Ir(iii) and Ru(ii). Dalton Trans 2010; 39:10837-46. [DOI: 10.1039/c0dt00750a] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Channon KJ, Devlin GL, Magennis SW, Finlayson CE, Tickler AK, Silva C, MacPhee CE. Modification of Fluorophore Photophysics through Peptide-Driven Self-Assembly. J Am Chem Soc 2008; 130:5487-91. [DOI: 10.1021/ja710310c] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kevin J. Channon
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, U.K., CB3 0HE, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, U.K., CB2 1EW, SUPA, School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, U.K., EH9 3JZ, and Départment de Physique, Université de Montréal, C. P. 6128 succ. centre-ville, Montréal, Québec, Canada, H3C 3J7
| | - Glyn L. Devlin
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, U.K., CB3 0HE, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, U.K., CB2 1EW, SUPA, School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, U.K., EH9 3JZ, and Départment de Physique, Université de Montréal, C. P. 6128 succ. centre-ville, Montréal, Québec, Canada, H3C 3J7
| | - Steven W. Magennis
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, U.K., CB3 0HE, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, U.K., CB2 1EW, SUPA, School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, U.K., EH9 3JZ, and Départment de Physique, Université de Montréal, C. P. 6128 succ. centre-ville, Montréal, Québec, Canada, H3C 3J7
| | - Chris E. Finlayson
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, U.K., CB3 0HE, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, U.K., CB2 1EW, SUPA, School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, U.K., EH9 3JZ, and Départment de Physique, Université de Montréal, C. P. 6128 succ. centre-ville, Montréal, Québec, Canada, H3C 3J7
| | - Anna K. Tickler
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, U.K., CB3 0HE, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, U.K., CB2 1EW, SUPA, School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, U.K., EH9 3JZ, and Départment de Physique, Université de Montréal, C. P. 6128 succ. centre-ville, Montréal, Québec, Canada, H3C 3J7
| | - Carlos Silva
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, U.K., CB3 0HE, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, U.K., CB2 1EW, SUPA, School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, U.K., EH9 3JZ, and Départment de Physique, Université de Montréal, C. P. 6128 succ. centre-ville, Montréal, Québec, Canada, H3C 3J7
| | - Cait E. MacPhee
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, U.K., CB3 0HE, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, U.K., CB2 1EW, SUPA, School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh, U.K., EH9 3JZ, and Départment de Physique, Université de Montréal, C. P. 6128 succ. centre-ville, Montréal, Québec, Canada, H3C 3J7
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Abstract
To explore the effect of intermolecular interactions on the photophysics of 2-aminopurine (2AP) in a well-defined environment, we have investigated the fluorescence properties of single 2AP crystals, having determined their X-ray structure. In the crystal, 2AP is subject to base-stacking and hydrogen-bonding interactions similar to those found in DNA. The crystal shows dual fluorescence: pi-stacked molecules in the bulk of the lattice have redshifted excitation and emission spectra, while molecules at defect sites have spectra similar to those of 2AP in solution or in DNA. Heterogeneous intermolecular interactions in the crystal give rise to multiexponential fluorescence decay characteristics similar to those observed for 2AP-labelled DNA. The presence of about 13 % of the 7H tautomer in the crystal confirms that 9H-7H tautomerisation of 2AP occurs in the ground state. Long-wavelength excitation of a 2AP-labelled oligonucleotide duplex produced redshifted emission similar to that observed in the crystal, indicating that pi-stacking interaction of 2AP with nucleobases gives rise to a low energy excited state.
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Affiliation(s)
- Robert K Neely
- School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
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Magennis SW, Habtemariam A, Novakova O, Henry JB, Meier S, Parsons S, Oswald IDH, Brabec V, Sadler PJ. Dual triggering of DNA binding and fluorescence via photoactivation of a dinuclear ruthenium(II) arene complex. Inorg Chem 2007; 46:5059-68. [PMID: 17497848 DOI: 10.1021/ic062111q] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The dinuclear RuII arene complexes [{(eta6-arene)RuCl}2(mu-2,3-dpp)](PF6)2, arene=indan (1), benzene (2), p-cymene (3), or hexamethylbenzene (4) and 2,3-dpp=2,3-bis(2-pyridyl)pyrazine, have been synthesized and characterized. Upon irradiation with UVA light, complexes 1 and 2 readily underwent arene loss, while complexes 3 and 4 did not. The photochemistry of 1 was studied in detail. In the X-ray structure of [{(eta6-indan)RuCl}2(mu-2,3-dpp)](PF6)2 (1), 2,3-dpp bridges two RuII centers 6.8529(6) A apart. In water, aquation of 1 in the dark occurs with replacement of chloride with biexponential kinetics and decay constants of 100+/-1 min-1 and 580+/-11 min-1. This aquation was suppressed by 0.1 M NaCl. UV or visible irradiation of 1 in aqueous or methanolic solution led to arene loss. The fluorescence of the unbound arene is approximately 40 times greater than when it is complexed. Irradiation of 1 also had a significant effect on its interactions with DNA. The DNA binding of 1 is increased after irradiation. The non-irradiated form of 1 preferentially formed DNA adducts that only weakly blocked RNA polymerase, while irradiation of 1 transformed the adducts into stronger blocks for RNA polymerase. The efficiency of irradiated 1 to form DNA interstrand cross-links was slightly greater than that of cisplatin in both 10 mM NaClO4 and 0.1 M NaCl. In contrast, the interstrand cross-linking efficiency of non-irradiated 1 in 10 mM NaClO4 was relatively low. An intermediate amount of cross-linking was observed when the sample of DNA already modified by non-irradiated 1 was irradiated. DNA unwinding measurements supported the conclusion that both mono- and bifunctional adducts with DNA can form. These results show that photoactivation of dinuclear RuII arene complexes can simultaneously produce a highly reactive ruthenium species that can bind to DNA and a fluorescent marker (the free arene). Importantly, the mechanism of photoreactivity is also independent of oxygen. These complexes, therefore, have the potential to combine both photoinduced cell death and fluorescence imaging of the location and efficiency of the photoactivation process.
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Affiliation(s)
- Steven W Magennis
- School of Physics and the Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK.
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Millington M, Grindlay GJ, Altenbach K, Neely RK, Kolch W, Bencina M, Read ND, Jones AC, Dryden DTF, Magennis SW. High-precision FLIM–FRET in fixed and living cells reveals heterogeneity in a simple CFP–YFP fusion protein. Biophys Chem 2007; 127:155-64. [PMID: 17336446 DOI: 10.1016/j.bpc.2007.01.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 01/23/2007] [Accepted: 01/24/2007] [Indexed: 11/18/2022]
Abstract
We have used widefield photon-counting FLIM to study FRET in fixed and living cells using control FRET pairs. We have studied fixed mammalian cells expressing either cyan fluorescent protein (CFP) or a fusion of CFP and yellow fluorescent protein (YFP), and living fungal cells expressing either Cerulean or a Cerulean-Venus fusion protein. We have found the fluorescence behaviour to be essentially identical in the mammalian and fungal cells. Importantly, the high-precision FLIM data is able to reproducibly resolve multiple fluorescence decays, thereby revealing new information about the fraction of the protein population that undergoes FRET and reducing error in the measurement of donor-acceptor distances. Our results for this simple control system indicate that the in vivo FLIM-FRET studies of more complex protein-protein interactions would benefit greatly from such quantitative measurements.
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Affiliation(s)
- Michael Millington
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK
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Affiliation(s)
- Steven W Magennis
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre and the School of Chemistry, The University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK
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Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimašauskas S, Jones AC. Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucleic Acids Res 2005; 33:6953-60. [PMID: 16340006 PMCID: PMC1310896 DOI: 10.1093/nar/gki995] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 Å resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (∼100 ps) decay component and the large increase in the amplitude of the long (∼10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA–enzyme complexes that cannot be discerned from the present X-ray structures.
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Affiliation(s)
- Robert K. Neely
- School of Chemistry, The University of EdinburghWest Mains Road, Edinburgh EH9 3JJ, UK
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
| | - Dalia Daujotyte
- Laboratory of Biological DNA Modification, Institute of BiotechnologyLT-02241 Vilnius, Lithuania
| | - Saulius Grazulis
- Laboratory of DNA–Protein Interactions, Institute of BiotechnologyLT-02241 Vilnius, Lithuania
| | - Steven W. Magennis
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
| | - David T. F. Dryden
- School of Chemistry, The University of EdinburghWest Mains Road, Edinburgh EH9 3JJ, UK
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
| | - Saulius Klimašauskas
- Laboratory of Biological DNA Modification, Institute of BiotechnologyLT-02241 Vilnius, Lithuania
- Department of Biochemistry and Biophysics, Faculty of Natural Sciences, Vilnius UniversityLT-2009 Vilnius, Lithuania
| | - Anita C. Jones
- School of Chemistry, The University of EdinburghWest Mains Road, Edinburgh EH9 3JJ, UK
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
- To whom correspondence should be addressed. Tel: +44 131 6506449; Fax: +44 131 6504743;
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Bassett AP, Magennis SW, Glover PB, Lewis DJ, Spencer N, Parsons S, Williams RM, De Cola L, Pikramenou Z. Highly luminescent, triple- and quadruple-stranded, dinuclear Eu, Nd, and Sm(III) lanthanide complexes based on bis-diketonate ligands. J Am Chem Soc 2004; 126:9413-24. [PMID: 15281834 DOI: 10.1021/ja048022z] [Citation(s) in RCA: 268] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bis(beta-diketone) ligands 1,3-bis(3-phenyl-3-oxopropanoyl)benzene, H(2)L(1) and 1,3-bis(3-phenyl-3-oxopropanoyl) 5-ethoxy-benzene, H(2)L(2), have been prepared for the examination of dinuclear lanthanide complex formation and investigation of their properties as sensitizers for lanthanide luminescence. The ligands bear two conjugated diketonate binding sites linked by a 1,3-phenylene spacer. The ligands bind to lanthanide(III) or yttrium(III) ions to form neutral homodimetallic triple stranded complexes [M(2)L(1)(3)] where M = Eu, Nd, Sm, Y, Gd and [M(2)L(2)(3)], where M = Eu, Nd or anionic quadruple-stranded dinuclear lanthanide units, [Eu(2)L(1)(4)](2-). The crystal structure of the free ligand H(2)L(1) has been determined and shows a twisted arrangement of the two binding sites around the 1,3-phenylene spacer. The dinuclear complexes have been isolated and fully characterized. Detailed NMR investigations of the complexes confirm the formation of a single complex species, with high symmetry; the complexes show clear proton patterns with chemical shifts of a wide range due to the lanthanide paramagnetism. Addition of Pirkle's reagent to solutions of the complexes leads to splitting of the peaks, confirming the chiral nature of the complexes. Electrospray and MALDI mass spectrometry have been used to identify complex formulation and characteristic isotope patterns for the different lanthanide complexes have been obtained. The complexes have high molar absorption coefficients (around 13 x 10(4) M(-1)cm(-1)) and display strong visible (red or pink) or NIR luminescence upon irradiation at the ligand band around 350 nm, depending on the choice of the lanthanide. Emission quantum yield experiments have been performed and the luminescence signals of the dinuclear complexes have been found to be up to 11 times more intense than the luminescence signals of the mononuclear analogues. The emission quantum yields and the luminescence lifetimes are determined to be 5% and 220 micros for [Eu(2)L(1)(3)], 0.16% and 13 micros for [Sm(2)L(1)(3)], and 0.6% and 1.5 micros for [Nd(2)L(1)(3)]. The energy level of the ligand triplet state was determined from the 77 K spectrum of [Gd(2)L(1)(3)]. The bis-diketonate ligand is shown to be an efficient sensitizer, particularly for Sm and Nd. Photophysical studies of the europium complexes at room temperature and 77 K show the presence of a thermally activated deactivation pathway, which we attribute to ligand-to-metal charge transfer (LMCT). Quenching of the luminescence from this level seems to be operational for the Eu(III) complex but not for complexes of Sm(III) and Nd(III), which exhibit long lifetimes. The quadruple-stranded europium complex has been isolated and characterized as the piperidinium salt of [Eu(2)L(1)(4)](2-). Compared with the triple-stranded Eu(III) complex in the solid state, the quadruple-stranded complex displays a more intense emission signal with a distinct emission pattern indicating the higher symmetry of the quadruple-stranded complex.
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Affiliation(s)
- Andrew P Bassett
- School of Chemistry, The University of Birmingham, Edgbaston, B15 2TT, United Kingdom
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Affiliation(s)
- Robert K. Neely
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
| | - Steven W. Magennis
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
| | - David T. F. Dryden
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
| | - Anita C. Jones
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
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Brancaleon L, Magennis SW, Samuel IDW, Namdas E, Lesar A, Moseley H. Characterization of the photoproducts of protoporphyrin IX bound to human serum albumin and immunoglobulin G. Biophys Chem 2004; 109:351-60. [PMID: 15110933 DOI: 10.1016/j.bpc.2003.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2003] [Revised: 12/17/2003] [Accepted: 12/19/2003] [Indexed: 10/26/2022]
Abstract
Clinically useful photosensitisers (PSs) are likely bound to subcellular and molecular targets during phototherapy. Binding to a macromolecule has the potential to change the photophysical and photochemical characteristics of the PSs that are crucial for their phototoxicity and cell-killing activity. We investigated the effects of binding of a specific PS (protoporphyrin IX or PPIX) to two proteins, human serum albumin (HSA) and a commercially available immunoglobulin (IgG). These two proteins provide two different environments for PPIX. The albumin binds PPIX in hydrophobic binding sites located in subdomain IIA and IIIA, conversely IgG leaves PPIX exposed to the solvent. We show that photophysical parameters such as emission maxima and fluorescence lifetime depend on the binding site. Our results indicate that the different binding site yields very different rates of formation of photoproducts (more than three times higher for PPIX bound to HSA than to IgG) and that different mechanisms of formation may be occurring. Our characterization shows the relevance of protein binding for the photochemistry and ultimately the phototoxicity of PSs.
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Affiliation(s)
- Lorenzo Brancaleon
- The Scottish PDT Centre, Department of Dermatology and Photobiology Unit, Ninewells Hospital and Medical School, Dundee, UK.
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Abstract
Time-resolved fluorescence spectroscopy of the solvent-sensitive molecule 1,8-anilinonaphthalene sulfonate (ANS) is used to probe the structure and dynamics of an aqueous methanol solution (mole fraction = 0.5). The intensity decay of ANS in the mixed solvent displays single exponential kinetics under ambient conditions. At low temperature, a simple two-state solvent relaxation model describes the fluorescence decay for ANS in both methanol and the mixed solvent. The temperature dependence of ANS fluorescence in the mixed solvent is attributed to the onset of glassy dynamics in the aqueous component at higher temperature, implying a partial demixing of the water and methanol due to self-association. We discuss the absence of more complicated fluorescence decays in such a heterogeneous solvent system.
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Affiliation(s)
- Lorna Dougan
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK
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Magennis SW, Craig J, Gardner A, Fucassi F, Cragg PJ, Robertson N, Parsons S, Pikramenou Z. Crown ether lanthanide complexes as building blocks for luminescent ternary complexes. Polyhedron 2003. [DOI: 10.1016/s0277-5387(02)01405-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Frampton MJ, Magennis SW, Pillow JNG, Burn PL, Samuel IDW. The effect of intermolecular interactions on the electro-optical properties of porphyrin dendrimers with conjugated dendrons. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b209910c] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Luminescent lanthanide complexes have been developed, based on the assembly of bulky ligands around the lanthanide ion, to provide shell-type protection of the ion from coordinated solvent molecules. Aryl-functionalised imidodiphosphinate ligands (tpip and Metpip) provide a bidentate anionic site that leads to hexa-coordinate lanthanide complexes in which the aryl groups surround the ion. There are twelve phenyl groups around the lanthanide that act as "remote" (from the binding site) sensitisers for the metal ion. It is shown that these ligands are suitable for sensitising luminescence for all the lanthanides that emit in the visible range, namely, SmIII, EuIII, TbIII, DyIII. A "builtin" shield on the ligand is designed to provide a complete block of the approach of water to the lanthanide ion. The synthesis of the ligands and their lanthanides complexes as well as detailed photophysical studies of the complexes in solution and in the solid-state are presented.
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Affiliation(s)
- Steven W Magennis
- Department of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JJ, UK
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Pålsson LO, Beavington R, Frampton MJ, Lupton JM, Magennis SW, Markham JPJ, Pillow JNG, Burn PL, Samuel IDW. Synthesis and Excited State Spectroscopy of Tris(distyrylbenzenyl)amine-cored Electroluminescent Dendrimers. Macromolecules 2002. [DOI: 10.1021/ma011996g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lars-Olof Pålsson
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - Richard Beavington
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - Michael J. Frampton
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - John M. Lupton
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - Steven W. Magennis
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - Jonathan P. J. Markham
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - Jonathan N. G. Pillow
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - Paul L. Burn
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
| | - Ifor D. W. Samuel
- Department of Physics, University of Durham, South Road, Durham, DH1 3LE, U.K.; The Dyson Perrins Laboratory, Oxford University, South Parks Road, OX1 3QY, Oxford, U.K.; and Organic Semiconductor Centre, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9SS, U.K
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Ingham SL, Magennis SW. The synthesis, structure and selected reactivity of a series of tricarbonyl ruthenium complexes with 1,3-dienes and heterodienes. J Organomet Chem 1999. [DOI: 10.1016/s0022-328x(98)00950-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Magennis SW, Parsons S, Pikramenou Z, Corval A, Derek Woollins J. Imidodiphosphinate ligands as antenna units in luminescent lanthanide complexes. Chem Commun (Camb) 1999. [DOI: 10.1039/a808046a] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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