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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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2
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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3
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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] [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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4
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Menges JA, Grandjean A, Clasen A, Jung G. Kinetics of Palladium(0)‐Allyl Interactions in the Tsuji‐Trost Reaction, derived from Single‐Molecule Fluorescence Microscopy. ChemCatChem 2020. [DOI: 10.1002/cctc.202000032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Johannes A. Menges
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Alexander Grandjean
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Anne Clasen
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
| | - Gregor Jung
- Department of Biophysical Chemistry Saarland University Building B2 2 66123 Saarbrücken Germany
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Halter O, Plenio H. Fluorescent Dyes in Organometallic Chemistry: Coumarin‐Tagged NHC–Metal Complexes. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800395] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Oliver Halter
- Organometallic Chemistry TU Darmstadt Alarich‐Weiss‐Str.12 64287 Darmstadt Germany
| | - Herbert Plenio
- Organometallic Chemistry TU Darmstadt Alarich‐Weiss‐Str.12 64287 Darmstadt Germany
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6
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Vasiuta R, Plenio H. Observing Initial Steps in Gold-Catalyzed Alkyne Transformations by Utilizing Bodipy-Tagged Phosphine-Gold Complexes. Chemistry 2016; 22:6353-60. [DOI: 10.1002/chem.201600264] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Roman Vasiuta
- Organometallic Chemistry; TU Darmstadt; Alarich-Weiss-Str. 12 64287 Darmstadt Germany
| | - Herbert Plenio
- Organometallic Chemistry; TU Darmstadt; Alarich-Weiss-Str. 12 64287 Darmstadt Germany
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7
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Kos P, Plenio H. Metal Complexes of a Boron-Dipyrromethene (BODIPY)-Tagged N-Heterocyclic Carbene (NHC) as Luminescent Carbon Monoxide Chemodosimeters. Chemistry 2014; 21:1088-95. [DOI: 10.1002/chem.201405316] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 01/05/2023]
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8
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Brox D, Schwering M, Engelhardt J, Herten DP. Reversible Chemical Reactions for Single-Color Multiplexing Microscopy. Chemphyschem 2014; 15:2331-6. [DOI: 10.1002/cphc.201402012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 11/09/2022]
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9
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Rybina A, Lang C, Wirtz M, Grußmayer K, Kurz A, Maier F, Schmitt A, Trapp O, Jung G, Herten DP. Direkte Beobachtung alternativer Reaktionswege an einzelnen Molekülen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300100] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Rybina A, Lang C, Wirtz M, Grußmayer K, Kurz A, Maier F, Schmitt A, Trapp O, Jung G, Herten DP. Distinguishing Alternative Reaction Pathways by Single-Molecule Fluorescence Spectroscopy. Angew Chem Int Ed Engl 2013; 52:6322-5. [DOI: 10.1002/anie.201300100] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 02/25/2013] [Indexed: 11/07/2022]
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11
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Schwering M, Kiel A, Kurz A, Lymperopoulos K, Sprödefeld A, Krämer R, Herten DP. Hochauflösende Mikroskopie mit reversiblen chemischen Reaktionen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Schwering M, Kiel A, Kurz A, Lymperopoulos K, Sprödefeld A, Krämer R, Herten DP. Far-field nanoscopy with reversible chemical reactions. Angew Chem Int Ed Engl 2011; 50:2940-5. [PMID: 21404374 DOI: 10.1002/anie.201006013] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Indexed: 02/06/2023]
Affiliation(s)
- Michael Schwering
- Cellnetworks Cluster & Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany
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13
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Hammerstein AF, Shin SH, Bayley H. Single-molecule kinetics of two-step divalent cation chelation. Angew Chem Int Ed Engl 2010; 49:5085-90. [PMID: 20572213 DOI: 10.1002/anie.200906601] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anne F Hammerstein
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
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14
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Vorfalt T, Wannowius KJ, Thiel V, Plenio H. How Important Is the Release–Return Mechanism in Olefin Metathesis? Chemistry 2010; 16:12312-5. [DOI: 10.1002/chem.201001832] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tim Vorfalt
- Organometallic Chemistry, TU Darmstadt, Petersenstrasse 18, 64287 Darmstadt (Germany)
| | - Klaus J. Wannowius
- Organometallic Chemistry, TU Darmstadt, Petersenstrasse 18, 64287 Darmstadt (Germany)
| | - Vasco Thiel
- Organometallic Chemistry, TU Darmstadt, Petersenstrasse 18, 64287 Darmstadt (Germany)
| | - Herbert Plenio
- Organometallic Chemistry, TU Darmstadt, Petersenstrasse 18, 64287 Darmstadt (Germany)
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15
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Hammerstein A, Shin SH, Bayley H. Single-Molecule Kinetics of Two-Step Divalent Cation Chelation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Lymperopoulos K, Kiel A, Seefeld A, Stöhr K, Herten DP. Fluorescent probes and delivery methods for single-molecule experiments. Chemphyschem 2010; 11:43-53. [PMID: 19960557 DOI: 10.1002/cphc.200900359] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The recent explosion in papers utilising single-molecule experiments pushes the envelope further for increased spatial and temporal resolution. In order to achieve this, a combination of novel fluorescent probes and spectroscopy techniques are required. Herein, we provide an overview on our contribution to developments in the field of fluorescent probes along with a palette of alternative delivery methods for introducing the probes into living cells. We discuss probe requirements arising from the use of single-molecule spectroscopy methods and the customisation of probes that depends on the target molecule, the chemical state of the molecule as well as the distance and the type of interaction between sensor and ligand. We explain how Förster resonance energy transfer (FRET) and photon-induced electron transfer (PET) can increase the probe customisation. We also discuss additional requirements that arise when performing experiments in living cells like toxicity and cell permeability. Regarding the latter, we devote a special paragraph on the different ways to introduce the desired probe into the cell and how the different properties of each probe and cell type may require different delivery methods. We offer insights based on our experience working with a variety of single-molecule methods, fluorescent probes and delivery systems. Overall, we encompass the latest developments on probe design and delivery and illustrate that the wealth of information provided by single-molecule studies goes along with increased complexity.
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Affiliation(s)
- Konstantinos Lymperopoulos
- Cellnetworks Cluster and Institute for Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany.
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Sashuk V, Peeck L, Plenio H. [(NHC)(NHCewg)RuCl2(CHPh)] Complexes with Modified NHCewg Ligands for Efficient Ring-Closing Metathesis Leading to Tetrasubstituted Olefins. Chemistry 2010; 16:3983-93. [DOI: 10.1002/chem.200903275] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Jäger M, Kiel A, Herten DP, Hamprecht FA. Analysis of single-molecule fluorescence spectroscopic data with a Markov-modulated Poisson process. Chemphyschem 2009; 10:2486-95. [PMID: 19644999 DOI: 10.1002/cphc.200900331] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a photon-by-photon analysis framework for the evaluation of data from single-molecule fluorescence spectroscopy (SMFS) experiments using a Markov-modulated Poisson process (MMPP). A MMPP combines a discrete (and hidden) Markov process with an additional Poisson process reflecting the observation of individual photons. The algorithmic framework is used to automatically analyze the dynamics of the complex formation and dissociation of Cu2+ ions with the bidentate ligand 2,2'-bipyridine-4,4'dicarboxylic acid in aqueous media. The process of association and dissociation of Cu2+ ions is monitored with SMFS. The dcbpy-DNA conjugate can exist in two or more distinct states which influence the photon emission rates. The advantage of a photon-by-photon analysis is that no information is lost in preprocessing steps. Different model complexities are investigated in order to best describe the recorded data and to determine transition rates on a photon-by-photon basis. The main strength of the method is that it allows to detect intermittent phenomena which are masked by binning and that are difficult to find using correlation techniques when they are short-lived.
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Affiliation(s)
- Mark Jäger
- Philips Research, High Tech Campus 34, 5656AE Eindhoven, The Netherlands
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Elemans J, Lei S, De Feyter S. Molekulare und supramolekulare Netzwerke auf Oberflächen: vom zweidimensionalen Kristall-Engineering bis zur Reaktivität. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806339] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Elemans J, Lei S, De Feyter S. Molecular and Supramolecular Networks on Surfaces: From Two-Dimensional Crystal Engineering to Reactivity. Angew Chem Int Ed Engl 2009; 48:7298-332. [DOI: 10.1002/anie.200806339] [Citation(s) in RCA: 576] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Vogelsang J, Kasper R, Steinhauer C, Person B, Heilemann M, Sauer M, Tinnefeld P. A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes. Angew Chem Int Ed Engl 2008; 47:5465-9. [PMID: 18601270 DOI: 10.1002/anie.200801518] [Citation(s) in RCA: 416] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jan Vogelsang
- Angewandte Physik-Biophysik, and Center for NanoScience, Ludwig-Maximilians-Universität, Amalienstrasse 54, 80799 München, Germany
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Vogelsang J, Kasper R, Steinhauer C, Person B, Heilemann M, Sauer M, Tinnefeld P. Ein System aus Reduktions‐ und Oxidationsmittel verringert Photobleichen und Blinken von Fluoreszenzfarbstoffen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801518] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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