ChemPhysChem

Cover image for Vol. 13 Issue 4

Special Issue: Single-Molecule Studies

March 2012

Volume 13, Issue 4

Pages 881–1095

  1. Cover Picture

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    1. Cover Picture: Linking Single-Molecule Blinking to Chromophore Structure and Redox Potentials (ChemPhysChem 4/2012) (page 881)

      Ingo H. Stein, Stella Capone, Jochem H. Smit, Fabian Baumann, Dr. Thorben Cordes and Prof. Dr. Philip Tinnefeld

      Article first published online: 15 MAR 2012 | DOI: 10.1002/cphc.201290016

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      Intensity fluctuations of individual fluorophores, also termed blinking, are studied at the single-molecule level by T. Cordes, P. Tinnefeld et al. on p. 931. Therefore, dye molecules of the homologous series of cyanines were immobilized through double-stranded DNA on BSA-coated cover slips. The OFF-times due to radical-ion formation increase for larger chromophore size and correlate with redox potentials. Cover artwork by Christoph Hohmann, Nanosystems Initiative Munich (NIM).

  2. Inside Cover

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    1. Inside Cover: Mapping of Surface-Enhanced Fluorescence on Metal Nanoparticles using Super-Resolution Photoactivation Localization Microscopy (ChemPhysChem 4/2012) (page 882)

      Dr. Hongzhen Lin, Dr. Silvia P. Centeno, Liang Su, Bart Kenens, Susana Rocha, Dr. Michel Sliwa, Prof. Dr. Johan Hofkens and Prof. Dr. Hiroshi Uji-i

      Article first published online: 7 MAR 2012 | DOI: 10.1002/cphc.201280402

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      Surface-enhanced fluorescence photo-activation localization microscopy reveals imaging of the point-spread-function and spatial distribution of individual fluorescent molecules near densely labeled metal nanostructures as shown by H. Uji-i et al. on p. 973.

  3. Editorial

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      A Man for Single Molecules (pages 883–884)

      Prof. Dr. Thomas Bein, Prof. Dr. Don C. Lamb and Prof. Dr. Jens Michaelis

      Article first published online: 15 MAR 2012 | DOI: 10.1002/cphc.201200095

  4. Graphical Abstract

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    1. Graphical Abstract: ChemPhysChem 4/2012 (pages 887–893)

      Article first published online: 15 MAR 2012 | DOI: 10.1002/cphc.201290017

  5. News

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    1. Spotlights on our sister journals: ChemPhysChem 4/2012 (pages 896–898)

      Article first published online: 15 MAR 2012 | DOI: 10.1002/cphc.201290018

    2. Complex Systems Made Easy (page 899)

      Article first published online: 15 MAR 2012 | DOI: 10.1002/cphc.201200174

  6. Concept

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    1. Chromophores in Conjugated Polymers—All Straight? (pages 901–907)

      Prof. John M. Lupton

      Article first published online: 16 DEC 2011 | DOI: 10.1002/cphc.201100770

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      What shape is it? Single-molecule and ensemble time-resolved studies support the notion that the π-bond in large macromolecules, such as conjugated polymers, is remarkably persistent in space: even individual chromophores can be bent and twisted, so that caution is warranted when interpreting a wide range of polarization-based spectroscopies.

  7. Communications

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    1. Photobleaching and Blinking of TAMRA Induced by Mn2+ (pages 909–913)

      Elana M. S. Stennett, Dr. Gerdenis Kodis and Prof. Dr. Marcia Levitus

      Article first published online: 1 FEB 2012 | DOI: 10.1002/cphc.201100781

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      Blinking and bleaching: Coordination of Mn2+ to DNA induces intersystem crossing, causing fluctuations in the fluorescence intensity and accelerated photobleaching.

    2. Peptide–Antibody Complex as Handle for Single-Molecule Cut & Paste (pages 914–917)

      Mathias Strackharn, Stefan W. Stahl, Philip M. D. Severin, Thomas Nicolaus and Prof. Dr. Hermann E. Gaub

      Article first published online: 19 DEC 2011 | DOI: 10.1002/cphc.201100765

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      Molecule-by-molecule arrangement of proteins, for example, in enzymatic networks of predefined composition and proximity, is a major goal that may be accomplished by the single-molecule cut-and-paste technique (SMC&P). For this purpose, co-expressed anchors and handles as protein tags should be employed. As a first step in this direction, the authors develop an SMC&P design which exploits an antibody–peptide complex as a molecular handle.

    3. A Protein Biosensor That Relies on Bending of Single DNA Molecules (pages 918–922)

      Dr. Robert Crawford, Douglas J. Kelly and Dr. Achillefs N. Kapanidis

      Article first published online: 24 FEB 2012 | DOI: 10.1002/cphc.201100881

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      A “bendy” protein sensor: A DNA-based sensor that uses folded DNA (through DNA kinks) and protein-induced bending to detect DNA-binding proteins is presented. Single-molecule sensing of a transcriptional activator (catabolite activator protein, CAP, which bends its DNA site by 80°) is demonstrated in solution and on surfaces, both in buffers and in cell lysates. The method should allow detection of a wide range of DNA-bending proteins.

    4. Ortho-Functionalized Perylenediimides for Highly Fluorescent Water-Soluble Dyes (pages 923–926)

      Glauco Battagliarin, Melari Davies, Dr. Stephan Mackowiak, Dr. Chen Li and Prof. Klaus Müllen

      Article first published online: 13 JAN 2012 | DOI: 10.1002/cphc.201100833

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      Clearly visible: A water-soluble and highly fluorescent perylenediimide is synthesized via ruthenium-catalyzed alkylation with outstanding yields (see scheme). For the first time, the possibility to use phosphonate derivatives in a Murai-type reaction is demonstrated.

    5. Tip-Enhanced Near-Field Optical Microscopy of Quasi-1 D Nanostructures (pages 927–929)

      Miriam Böhmler and Prof. Dr. Achim Hartschuh

      Article first published online: 8 DEC 2011 | DOI: 10.1002/cphc.201100670

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      High-resolution imaging and spectroscopy of single CdSe nanowires and carbon nanotubes using tip-enhanced near-field optical microscopy increases the optical excitation and emission rates within a nanoscale sample volume. The resulting signal enhancement for Raman scattering and photoluminescence as well as the tip–sample-distance dependence are investigated.

  8. Articles

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Concept
    8. Communications
    9. Articles
    10. Preview
    1. Linking Single-Molecule Blinking to Chromophore Structure and Redox Potentials (pages 931–937)

      Ingo H. Stein, Stella Capone, Jochem H. Smit, Fabian Baumann, Dr. Thorben Cordes and Prof. Dr. Philip Tinnefeld

      Article first published online: 8 DEC 2011 | DOI: 10.1002/cphc.201100820

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      The missing link: Blinking of three dyes from a homologous series (Cy3, Cy5, Cy7) is studied (see picture). The underlying radical anion states are induced by controlling the oxygen concentration and by adding the reductant ascorbic acid. For different conditions the OFF-state lifetime always increases in the order Cy3<Cy5<Cy7. Off-state lifetimes are related to higher reduction potentials as well as chromophore size.

    2. Probing the Electronic State of a Single Coronene Molecule by the Emission from Proximate Fluorophores (pages 938–945)

      Dr. Burkhard Fückel, Dr. Gerald Hinze, Prof. Dr. Jishan Wu, Prof. Dr. Klaus Müllen and Prof. Dr. Thomas Basché

      Article first published online: 17 JAN 2012 | DOI: 10.1002/cphc.201100785

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      Long time, no see: The long triplet state lifetime of hexa-peri-hexabenzocoronene (blue) appears as dark states in the emission of the perylenemonoimide periphery (green).

    3. Absorption, Luminescence, and Sizing of Organic Dye Nanoparticles and of Patterns Formed Upon Dewetting (pages 946–951)

      Dr. Alexander Gaiduk, Mustafa Yorulmaz, Prof. Dr. Eléna Ishow and Prof. Dr. Michel Orrit

      Article first published online: 19 DEC 2011 | DOI: 10.1002/cphc.201100788

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      Labyrinthine: Quantitative insight into phototphysics of organic dye nanoparticles and the dewetting induced patterns formed from a push–pull triarylamine dye is obtained by using simultaneous absorption and fluorescence microscopy (see picture). The quantum yield of organic nanoparticles and the number of molecules forming the nanoparticles and patterns are deduced.

    4. Polarization-Dependent SERS at Differently Oriented Single Gold Nanorods (pages 952–958)

      Jiqing Jiao, Xiao Wang, Frank Wackenhut, Anke Horneber, Prof. Liuping Chen, Dr. Antonio Virgilio Failla, Prof. Alfred J. Meixner and Dr. Dai Zhang

      Article first published online: 29 FEB 2012 | DOI: 10.1002/cphc.201100718

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      Influential nanorods: Polarization-dependent enhanced Raman spectra of non-resonant adenine molecules are obtained using single gold nanorods and a parabolic mirror-assisted optical microscope with higher-order laser beams. The influence of the three-dimensional orientation of individual gold nanorods on the Raman enhancement and the nanorod excitation are discussed.

    5. Formation Principles and Ligand Dynamics of Nanoassemblies of CdSe Quantum Dots and Functionalised Dye Molecules (pages 959–972)

      Dr. Thomas Blaudeck, Prof. Dr. Eduard I. Zenkevich, Prof. Dr. Mohamed Abdel-Mottaleb, Klementyna Szwaykowska, Dr. Danny Kowerko, Prof. Dr. Frank Cichos and Prof. Dr. Christian von Borczyskowski

      Article first published online: 23 DEC 2011 | DOI: 10.1002/cphc.201100711

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      Quenching the glow! The size-dependent photoluminescence quenching of semiconductor quantum dots by functionalised dye molecules in solution is analysed with respect to Förster resonance energy transfer (FRET) and non-FRET contributions (see picture). By this approach, assembly formation and ligand dynamics can be studied at extremely low concentrations of quantum dots and dye molecules.

    6. Mapping of Surface-Enhanced Fluorescence on Metal Nanoparticles using Super-Resolution Photoactivation Localization Microscopy (pages 973–981)

      Dr. Hongzhen Lin, Dr. Silvia P. Centeno, Liang Su, Bart Kenens, Susana Rocha, Dr. Michel Sliwa, Prof. Dr. Johan Hofkens and Prof. Dr. Hiroshi Uji-i

      Article first published online: 19 DEC 2011 | DOI: 10.1002/cphc.201100743

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      Maps on metals: Photoactivation localization microscopy (PALM) is applied to study suface-enhanced fluorescence (SEF) on metal nanostructures (SEF-PALM), see picture. The detection of fluorescence from individual single molecules can be used to image the point-spread function and spatial distribution of the fluorescence emitted in the vicinity of a metal surface.

    7. The Effect of Temperature on Single-Polypeptide Adsorption (pages 982–989)

      Sandra Kienle, Susanne Liese, Nadine Schwierz, Prof. Dr. Roland R. Netz and Prof. Dr. Thorsten Hugel

      Article first published online: 31 JAN 2012 | DOI: 10.1002/cphc.201100776

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      Compensating Mechanisms: The temperature-dependent desorption of single polypeptides from hydrophobic surfaces, studied by means of atomic force microscopy and molecular dynamics simulations, shows a strong compensation mechanism between the different contributions to the desorption force. This is reminiscent of the protein-folding process, where large entropic and enthalpic contributions compensate each other, resulting in a small free-energy difference between the folded and unfolded states.

    8. Lipid Diffusion within Black Lipid Membranes Measured with Dual-Focus Fluorescence Correlation Spectroscopy (pages 990–1000)

      Kerstin Weiß and Prof. Dr. Jörg Enderlein

      Article first published online: 17 JAN 2012 | DOI: 10.1002/cphc.201100680

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      Watch them glow: A description and theoretical evaluation of dual-focus fluorescence correlation spectroscopy as a tool for measuring diffusion within lipid bilayers is presented (see picture). The method is applied to a study of the dependence of lipid diffusion on lipid and buffer composition with regard to the ionic strength of the buffer, particularly concerning the influence of mono- and divalent ions.

    9. Long-Range Transport of Giant Vesicles along Microtubule Networks (pages 1001–1006)

      Christoph Herold, Dr. Cécile Leduc, Robert Stock, Prof. Dr. Stefan Diez and Prof. Dr. Petra Schwille

      Article first published online: 23 DEC 2011 | DOI: 10.1002/cphc.201100669

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      Moving giant vesicles: In a biomimetic assay, giant unilamellar vesicles with membrane-anchored kinesin-1 motor proteins are transported along a two-dimensional microtubule network (see picture). In this assay, cooperatively acting motor proteins enable long traveling distances up to the millimeter range.

    10. Three-Dimensional Super-Resolution Imaging of the Midplane Protein FtsZ in Live Caulobacter crescentus Cells Using Astigmatism (pages 1007–1012)

      Dr. Julie S. Biteen, Dr. Erin D. Goley, Prof. Lucy Shapiro and Prof. W. E. Moerner

      Article first published online: 20 JAN 2012 | DOI: 10.1002/cphc.201100686

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      3D is here to stay: Three-dimensional super-resolution astigmatic optical imaging provides images of the FtsZ Z-ring in bacterial cells in various stages of the cell cycle. The picture shows, left to right: live stalked cell, live pre-divisional cell, fixed stalked cell, fixed pre-divisional cell. Scale bar: 200 nm.

    11. Bayesian-Inference-Based Fluorescence Correlation Spectroscopy and Single-Molecule Burst Analysis Reveal the Influence of Dye Selection on DNA Hairpin Dynamics (pages 1013–1022)

      Wolfgang Kügel, Dr. Adam Muschielok and Prof. Dr. Jens Michaelis

      Article first published online: 25 JAN 2012 | DOI: 10.1002/cphc.201100720

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      Dynamic studies: Fluorescence correlation spectroscopy (FCS) data are globally analyzed using the Bayesian inference. This approach is applied, in combination with the results from single-molecule burst analysis, to investigate the influence of various labels on DNA hairpin kinetics as a function of the salt concentration.

    12. Optical Modulation and Selective Recovery of Cy5 Fluorescence (pages 1023–1029)

      Dr. Chaoyang Fan, Jung-Cheng Hsiang and Prof. Dr. Robert M. Dickson

      Article first published online: 15 NOV 2011 | DOI: 10.1002/cphc.201100671

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      Photoinduced isomerization of Cy5 from trans to cis can be quickly reversed with long-wavelength secondary illumination. Modulating this co-illumination directly encodes the modulation waveform on the higher energy Cy5 fluorescence, enabling its selective recovery even in the presence of overwhelming background. This low-energy, reversible, long-lived dark state makes Cy5 an excellent dye for synchronously amplified fluorescence image recovery (SAFIRe).

    13. Integration of Organic Fluorophores in the Surface of Polymer-Coated Colloidal Nanoparticles for Sensing the Local Polarity of the Environment (pages 1030–1035)

      Faheem Amin, Dr. Dmytro A. Yushchenko, Dr. Jose M. Montenegro and Prof. Dr. Wolfgang J. Parak

      Article first published online: 1 MAR 2012 | DOI: 10.1002/cphc.201100901

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      Let it shine: Gold nanoparticles (see picture) are decorated with an organic fluorophore that possesses fluorescence sensitive to the polarity and hydrogen-bonding properties of the surrounding local environment.

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      Filtered FCS: Species Auto- and Cross-Correlation Functions Highlight Binding and Dynamics in Biomolecules (pages 1036–1053)

      Dr. Suren Felekyan, Dr. Stanislav Kalinin, Dr. Hugo Sanabria, Dr. Alessandro Valeri and Prof. Dr. Claus A. M. Seidel

      Article first published online: 7 MAR 2012 | DOI: 10.1002/cphc.201100897

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      Lifetime and polarization filtered fluorescence correlation spectroscopy, referred to as filtered FCS (fFCS), allows one to study dynamic binding equilibria sensed, for example, by anisotropy in the 2D diagram. The species-specific auto- (SACF) and cross-correlation (SCCF) functions for species (1) and (2) allow one to characterize the equilibrium via the relaxation time for interconversion (gray bar) and the corresponding species fractions (black arrow).

    15. Label-Free Live-Cell Imaging of Nucleic Acids Using Stimulated Raman Scattering Microscopy (pages 1054–1059)

      Xu Zhang, Dr. Maarten B. J. Roeffaers, Srinjan Basu, Joseph R. Daniele, Dr. Dan Fu, Dr. Christian W. Freudiger, Dr. Gary R. Holtom and Prof. X. Sunney Xie

      Article first published online: 24 FEB 2012 | DOI: 10.1002/cphc.201100890

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      Imaging nucleic acids: Label-free optical imaging of nucleic acids in live cells is demonstrated using highly sensitive stimulated Raman scattering (SRS) microscopy. This technique allows in vivo imaging of DNA condensation associated with cell division.

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      Combining MFD and PIE for Accurate Single-Pair Förster Resonance Energy Transfer Measurements (pages 1060–1078)

      Dr. Volodymyr Kudryavtsev, Dr. Martin Sikor, Dr. Stanislav Kalinin, Dr. Dejana Mokranjac, Prof. Dr. Claus A. M. Seidel and Prof. Don C. Lamb

      Article first published online: 1 MAR 2012 | DOI: 10.1002/cphc.201100822

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      In one fell swoop: By combining pulsed interleaved excitation with multiparameter fluorescence detection in burst analysis experiments, all information necessary for an accurate spFRET experiment can be collected in a single measurement (see picture for experimental setup). In addition, artifacts can be detected and often corrected.

    17. Hidden Markov Analysis of Trajectories in Single-Molecule Experiments and the Effects of Missed Events (pages 1079–1086)

      Johannes Stigler and Prof. Dr. Matthias Rief

      Article first published online: 5 MAR 2012 | DOI: 10.1002/cphc.201100814

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      Complex fluctuation patterns discovered by single-molecule experiments require statistical methods to analyze long multistate hopping traces. The authors give an introduction on how to implement hidden Markov modeling for this purpose and test the method on a calcium binding protein.

    18. Spectroscopic Properties of Gold Nanoparticles at the Single-Particle Level in Biological Environments (pages 1087–1092)

      Dr. Laura C. Estrada and Dr. Enrico Gratton

      Article first published online: 1 FEB 2012 | DOI: 10.1002/cphc.201100771

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      Trap and track: The orbital tracking method (OTM) allows us to simultaneously track single nanoparticles (NPs) and spectroscopically characterize their emission while diffusing even inside cells. As the NPs are always trapped by the laser, a detail spectroscopic characterization of the NPs can be done, even if the NPs are moving in three dimensions and along microns (see picture).

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Concept
    8. Communications
    9. Articles
    10. Preview
    1. You have free access to this content
      Preview: ChemPhysChem 5/2012 (page 1095)

      Article first published online: 15 MAR 2012 | DOI: 10.1002/cphc.201290015

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