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Special Issue "Single Molecules"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067).

Deadline for manuscript submissions: closed (30 November 2009)

Special Issue Editors

Guest Editor
Prof. Dr. Herbert Schneckenburger (Website)

Institute of Applied Research, Aalen University, Beethovenstr. 1, 73430 Aalen, Germany
Phone: +49 7361 576-3401
Interests: biomedical optics; microscopy; fluorescence; FRET
Guest Editor
Prof. Dr. Karl Otto Greulich (Website)

Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Abteilung Einzelzell- und Einzelmolekueltechniken, Beutenbergstr. 11, D-07745 Jena, Germany
Phone: 493641656400

Special Issue Information

Dear Colleagues,

With increasing sensitivity of optical detection systems single molecule measurements have gained considerable importance. Single molecules and ultra-weak fluorescence signals are now measured reliably in liquids, solids and biological systems upon selective excitation of thin layers by confocal, optical near field or evanescent wave excitation. Ultra-sensitive video detection, photon counting or correlation techniques are used to measure stationary or dynamic molecular events, whereas Förster resonance energy transfer (FRET) is used to probe intermolecular interactions. Contributions to this special issue may be dedicated to these or related techniques, including applications to fluorescent dyes, nano-beads, fluorescent proteins or further biomolecules with a diagnostic or analytical potential.

Herbert Schneckenburger
Guest Editor

Keywords

  • single molecules
  • confocal microscopy
  • optical near-field
  • evanescent waves
  • correlation spectroscopy
  • FRET

Published Papers (12 papers)

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Research

Jump to: Review

Open AccessArticle Reconsideration of Dynamic Force Spectroscopy Analysis of Streptavidin-Biotin Interactions
Int. J. Mol. Sci. 2010, 11(5), 2134-2151; doi:10.3390/ijms11052134
Received: 9 April 2010 / Revised: 3 May 2010 / Accepted: 6 May 2010 / Published: 13 May 2010
Cited by 10 | PDF Full-text (2108 KB) | HTML Full-text | XML Full-text
Abstract
To understand and design molecular functions on the basis of molecular recognition processes, the microscopic probing of the energy landscapes of individual interactions in a molecular complex and their dependence on the surrounding conditions is of great importance. Dynamic force spectroscopy (DFS) [...] Read more.
To understand and design molecular functions on the basis of molecular recognition processes, the microscopic probing of the energy landscapes of individual interactions in a molecular complex and their dependence on the surrounding conditions is of great importance. Dynamic force spectroscopy (DFS) is a technique that enables us to study the interaction between molecules at the single-molecule level. However, the obtained results differ among previous studies, which is considered to be caused by the differences in the measurement conditions. We have developed an atomic force microscopy technique that enables the precise analysis of molecular interactions on the basis of DFS. After verifying the performance of this technique, we carried out measurements to determine the landscapes of streptavidin-biotin interactions. The obtained results showed good agreement with theoretical predictions. Lifetimes were also well analyzed. Using a combination of cross-linkers and the atomic force microscope that we developed, site-selective measurement was carried out, and the steps involved in bonding due to microscopic interactions are discussed using the results obtained by site-selective analysis. Full article
(This article belongs to the Special Issue Single Molecules)
Open AccessArticle Light Dose is a Limiting Factor to Maintain Cell Viability in Fluorescence Microscopy and Single Molecule Detection
Int. J. Mol. Sci. 2010, 11(3), 956-966; doi:10.3390/ijms11030956
Received: 14 January 2010 / Revised: 20 February 2010 / Accepted: 21 February 2010 / Published: 8 March 2010
Cited by 26 | PDF Full-text (881 KB) | HTML Full-text | XML Full-text
Abstract
A test system for cell viability based on colony formation has been established and applied to high resolution fluorescence microscopy and single molecule detection. Living cells were irradiated either by epi-illumination or by total internal reflection (TIR) of a laser beam, and [...] Read more.
A test system for cell viability based on colony formation has been established and applied to high resolution fluorescence microscopy and single molecule detection. Living cells were irradiated either by epi-illumination or by total internal reflection (TIR) of a laser beam, and light doses where at least 90% of irradiated cells survived were determined. These light doses were in the range of a few J/cm2 up to about 200 J/cm2 depending on the wavelength of illumination as well as on the presence or absence of a fluorescent dye (e.g., the membrane marker laurdan). In general, cells were less sensitive to TIR than to epi-illumination. However, comparably high light doses needed for repetitive excitation of single molecules limit the application of super-resolution microscopy to living cells. Full article
(This article belongs to the Special Issue Single Molecules)
Figures

Open AccessArticle Electrostatic Interactions of Fluorescent Molecules with Dielectric Interfaces Studied by Total Internal Reflection Fluorescence Correlation Spectroscopy
Int. J. Mol. Sci. 2010, 11(2), 386-406; doi:10.3390/ijms11020386
Received: 23 November 2009 / Revised: 17 January 2010 / Accepted: 21 January 2010 / Published: 28 January 2010
Cited by 7 | PDF Full-text (355 KB) | HTML Full-text | XML Full-text
Abstract
Electrostatic interactions between dielectric surfaces and different fluorophores used in ultrasensitive fluorescence microscopy are investigated using objective-based Total Internal Reflection Fluorescence Correlation Spectroscopy (TIR-FCS). The interfacial dynamics of cationic rhodamine 123 and rhodamine 6G, anionic/dianionic fluorescein, zwitterionic rhodamine 110 and neutral ATTO [...] Read more.
Electrostatic interactions between dielectric surfaces and different fluorophores used in ultrasensitive fluorescence microscopy are investigated using objective-based Total Internal Reflection Fluorescence Correlation Spectroscopy (TIR-FCS). The interfacial dynamics of cationic rhodamine 123 and rhodamine 6G, anionic/dianionic fluorescein, zwitterionic rhodamine 110 and neutral ATTO 488 are monitored at various ionic strengths at physiological pH. As analyzed by means of the amplitude and time-evolution of the autocorrelation function, the fluorescent molecules experience electrostatic attraction or repulsion at the glass surface depending on their charges. Influences of the electrostatic interactions are also monitored through the triplet-state population and triplet relaxation time, including the amount of detected fluorescence or the count-rate-per-molecule parameter. These TIR-FCS results provide an increased understanding of how fluorophores are influenced by the microenvironment of a glass surface, and show a promising approach for characterizing electrostatic interactions at interfaces. Full article
(This article belongs to the Special Issue Single Molecules)
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Open AccessArticle Single Molecule Experiments Challenge the Strict Wave-Particle Dualism of Light
Int. J. Mol. Sci. 2010, 11(1), 304-311; doi:10.3390/ijms11010304
Received: 3 December 2009 / Revised: 11 January 2010 / Accepted: 12 January 2010 / Published: 21 January 2010
PDF Full-text (322 KB) | HTML Full-text | XML Full-text
Abstract
Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the “single photon limit” of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single [...] Read more.
Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the “single photon limit” of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. “Single photon detectors” do not meet their promise―only “photon number resolving single photon detectors” do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified. Full article
(This article belongs to the Special Issue Single Molecules)
Open AccessArticle Host-Guest Complexation Studied by Fluorescence Correlation Spectroscopy: Adamantane–Cyclodextrin Inclusion
Int. J. Mol. Sci. 2010, 11(1), 173-188; doi:10.3390/ijms11010173
Received: 1 December 2009 / Revised: 31 December 2009 / Accepted: 4 January 2010 / Published: 12 January 2010
Cited by 24 | PDF Full-text (474 KB) | HTML Full-text | XML Full-text
Abstract
The host-guest complexation between an Alexa 488 labelled adamantane derivative and β-cyclodextrin is studied by Fluorescence Correlation Spectroscopy (FCS). A 1:1 complex stoichiometry and a high association equilibrium constant of K = 5.2 × 104 M-1 are obtained in aqueous [...] Read more.
The host-guest complexation between an Alexa 488 labelled adamantane derivative and β-cyclodextrin is studied by Fluorescence Correlation Spectroscopy (FCS). A 1:1 complex stoichiometry and a high association equilibrium constant of K = 5.2 × 104 M-1 are obtained in aqueous solution at 25 °C and pH = 6. The necessary experimental conditions are discussed. FCS proves to be an excellent method for the determination of stoichiometry and association equilibrium constant of this type of complexes, where both host and guest are nonfluorescent and which are therefore not easily amenable to standard fluorescence spectroscopic methods. Full article
(This article belongs to the Special Issue Single Molecules)
Figures

Open AccessArticle Identification of Different Donor-Acceptor Structures via Förster Resonance Energy Transfer (FRET) in Quantum-Dot-Perylene Bisimide Assemblies
Int. J. Mol. Sci. 2009, 10(12), 5239-5256; doi:10.3390/ijms10125239
Received: 21 October 2009 / Revised: 23 November 2009 / Accepted: 27 November 2009 / Published: 1 December 2009
Cited by 17 | PDF Full-text (1537 KB) | HTML Full-text | XML Full-text
Abstract
Nanoassemblies are formed via self-assembly of ZnS capped CdSe quantum dots (QD) and perylene bisimide (PBI) dyes. Upon assembly formation the QD photoluminescence is quenched, as can be detected both via single particle detection and ensemble experiments in solution. Quenching has been [...] Read more.
Nanoassemblies are formed via self-assembly of ZnS capped CdSe quantum dots (QD) and perylene bisimide (PBI) dyes. Upon assembly formation the QD photoluminescence is quenched, as can be detected both via single particle detection and ensemble experiments in solution. Quenching has been assigned to FRET and NON-FRET processes. Analysis of FRET allows for a distinction between different geometries of the QD dye assemblies. Time-resolved single molecule spectroscopy reveals intrinsic fluctuations of the PBI fluorescence lifetime and spectrum, caused by rearrangement of the phenoxy side groups. The distribution of such molecular conformations and their changed dynamics upon assembly formation are discussed in the scope of FRET efficiency and surface ligand density. Full article
(This article belongs to the Special Issue Single Molecules)
Open AccessCommunication Molecule Non-Radiative Coupling to a Metallic Nanosphere: An Optical Theorem Treatment
Int. J. Mol. Sci. 2009, 10(9), 3931-3936; doi:10.3390/ijms10093931
Received: 10 July 2009 / Revised: 1 September 2009 / Accepted: 4 September 2009 / Published: 8 September 2009
Cited by 4 | PDF Full-text (152 KB) | HTML Full-text | XML Full-text
Abstract
The non-radiative coupling of a molecule to a metallic spherical particle is approximated by a sum involving particle quasistatic polarizabilities. We demonstrate that energy transfer from molecule to particle satisfies the optical theorem if size effects corrections are properly introduced into the [...] Read more.
The non-radiative coupling of a molecule to a metallic spherical particle is approximated by a sum involving particle quasistatic polarizabilities. We demonstrate that energy transfer from molecule to particle satisfies the optical theorem if size effects corrections are properly introduced into the quasistatic polarizabilities. We hope that this simplified model gives valuable information on the coupling mechanism between molecule and metallic nanostructures available for, e.g., surface enhanced spectroscopy signal analysis. Full article
(This article belongs to the Special Issue Single Molecules)
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Review

Jump to: Research

Open AccessReview Chromatin Fiber Dynamics under Tension and Torsion
Int. J. Mol. Sci. 2010, 11(4), 1557-1579; doi:10.3390/ijms11041557
Received: 3 December 2009 / Revised: 20 February 2010 / Accepted: 19 March 2010 / Published: 12 April 2010
Cited by 27 | PDF Full-text (1356 KB) | HTML Full-text | XML Full-text
Abstract
Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome [...] Read more.
Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome and chromatin structural changes. Indeed, magnetic and optical tweezers have allowed opportunities to handle single nucleosomal particles or nucleosomal arrays and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors acting on the DNA. These challenging technical approaches provide us with deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of cellular metabolism. Full article
(This article belongs to the Special Issue Single Molecules)
Figures

Open AccessReview Anchoring of a Single Molecular Rotor and Its Array on Metal Surfaces using Molecular Design and Self-Assembly
Int. J. Mol. Sci. 2010, 11(2), 656-671; doi:10.3390/ijms11020656
Received: 14 January 2010 / Revised: 26 January 2010 / Accepted: 1 February 2010 / Published: 9 February 2010
Cited by 4 | PDF Full-text (3632 KB) | HTML Full-text | XML Full-text
Abstract
Functionalizing of single molecules on surfaces has manifested great potential for bottom-up construction of complex devices on a molecular scale. We discuss the growth mechanism for the initial layers of polycyclic aromatic hydrocarbons on metal surfaces and we review our recent progress [...] Read more.
Functionalizing of single molecules on surfaces has manifested great potential for bottom-up construction of complex devices on a molecular scale. We discuss the growth mechanism for the initial layers of polycyclic aromatic hydrocarbons on metal surfaces and we review our recent progress on molecular machines, and present a molecular rotor with a fixed off-center axis formed by chemical bonding. These results represent important advances in molecular-based nanotechnology. Full article
(This article belongs to the Special Issue Single Molecules)
Figures

Open AccessReview Recent Developments in Fluorescence Correlation Spectroscopy for Diffusion Measurements in Planar Lipid Membranes
Int. J. Mol. Sci. 2010, 11(2), 427-457; doi:10.3390/ijms11020427
Received: 3 December 2009 / Revised: 11 January 2010 / Accepted: 15 January 2010 / Published: 28 January 2010
Cited by 21 | PDF Full-text (712 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as [...] Read more.
Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support. Full article
(This article belongs to the Special Issue Single Molecules)
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Open AccessReview Photonic Methods to Enhance Fluorescence Correlation Spectroscopy and Single Molecule Fluorescence Detection
Int. J. Mol. Sci. 2010, 11(1), 206-221; doi:10.3390/ijms11010206
Received: 24 November 2009 / Revised: 4 January 2010 / Accepted: 8 January 2010 / Published: 13 January 2010
Cited by 23 | PDF Full-text (4123 KB) | HTML Full-text | XML Full-text
Abstract
Recent advances in nanophotonics open the way for promising applications towards efficient single molecule fluorescence analysis. In this review, we discuss how photonic methods bring innovative solutions for two essential questions: how to detect a single molecule in a highly concentrated solution, [...] Read more.
Recent advances in nanophotonics open the way for promising applications towards efficient single molecule fluorescence analysis. In this review, we discuss how photonic methods bring innovative solutions for two essential questions: how to detect a single molecule in a highly concentrated solution, and how to enhance the faint optical signal emitted per molecule? The focus is set primarily on the widely used technique of fluorescence correlation spectroscopy (FCS), yet the discussion can be extended to other single molecule detection methods. Full article
(This article belongs to the Special Issue Single Molecules)
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Open AccessReview Occurence and Bioactivities of Funicone-Related Compounds
Int. J. Mol. Sci. 2009, 10(4), 1430-1444; doi:10.3390/ijms10041430
Received: 22 January 2009 / Revised: 23 March 2009 / Accepted: 26 March 2009 / Published: 30 March 2009
Cited by 12 | PDF Full-text (147 KB) | HTML Full-text | XML Full-text
Abstract
Studies on production of secondary metabolites by fungi have received a substantial boost lately, particularly with reference to applications of their biological properties in human medicine. Funicones represent a series of related compounds for which there is accumulating evidence supporting their possible [...] Read more.
Studies on production of secondary metabolites by fungi have received a substantial boost lately, particularly with reference to applications of their biological properties in human medicine. Funicones represent a series of related compounds for which there is accumulating evidence supporting their possible use as pharmaceuticals. This paper provides a review on the current status of knowledge on these fungal extrolites, with special reference to aspects concerning their molecular structures and biological activities. Full article
(This article belongs to the Special Issue Single Molecules)

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