http://www.mdpi.com/journal/ijms/special_issues/single-molecules/ 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 Submission All papers should be submitted to ijms@mdpi.com. To be published continuously until the deadline and papers will be listed together at the special issue website. Submitted papers should not have been published previously, nor be under consideration for publication elsewhere. All papers are refereed through a peer-review process. A guide for authors is available on the Instructions for Authors page. The International Journal of Molecular Sciences is an international peer-reviewed monthly journal published by MDPI. Open Access publication fees are 800 CHF per paper. English correction fees and/or formatting fees (250 CHF) will be added in certain cases (1050 CHF per paper for those papers that require extensive additional formatting and/or English corrections). http://www.mdpi.com/1422-0067/11/5/2134/ 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. http://www.mdpi.com/1422-0067/11/5/2134/ Thu, 13 May 2010 00:00:00 CEST International Journal of Molecular Sciences 2010-05-13 11 5 Article 2134 2151 1422-0067 Reconsideration of Dynamic Force Spectroscopy Analysis of Streptavidin-Biotin Interactions 2010-05-13 doi: 10.3390/ijms11052134 Taninaka Takeuchi Shigekawa http://www.mdpi.com/1422-0067/11/4/1557/ 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. http://www.mdpi.com/1422-0067/11/4/1557/ Mon, 12 Apr 2010 00:00:00 CEST International Journal of Molecular Sciences 2010-04-12 11 4 Review 1557 1579 1422-0067 Chromatin Fiber Dynamics under Tension and Torsion 2010-04-12 doi: 10.3390/ijms11041557 Lavelle Victor Zlatanova http://www.mdpi.com/1422-0067/11/3/956/ 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. http://www.mdpi.com/1422-0067/11/3/956/ Mon, 08 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-08 11 3 Article 956 966 1422-0067 Light Dose is a Limiting Factor to Maintain Cell Viability in Fluorescence Microscopy and Single Molecule Detection 2010-03-08 doi: 10.3390/ijms11030956 Michael Wagner Petra Weber Thomas Bruns Wolfgang S. L. Strauss Rainer Wittig Herbert Schneckenburger http://www.mdpi.com/1422-0067/11/2/656/ 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. http://www.mdpi.com/1422-0067/11/2/656/ Tue, 09 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-09 11 2 Review 656 671 1422-0067 Anchoring of a Single Molecular Rotor and Its Array on Metal Surfaces using Molecular Design and Self-Assembly 2010-02-09 doi: 10.3390/ijms11020656 Li Gao Shi-Xuan Du Hong-Jun Gao http://www.mdpi.com/1422-0067/11/2/427/ 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. http://www.mdpi.com/1422-0067/11/2/427/ Thu, 28 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-28 11 2 Review 427 457 1422-0067 Recent Developments in Fluorescence Correlation Spectroscopy for Diffusion Measurements in Planar Lipid Membranes 2010-01-28 doi: 10.3390/ijms11020427 Radek Macháň Martin Hof http://www.mdpi.com/1422-0067/11/2/386/ 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. http://www.mdpi.com/1422-0067/11/2/386/ Thu, 28 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-28 11 2 Article 386 406 1422-0067 Electrostatic Interactions of Fluorescent Molecules with Dielectric Interfaces Studied by Total Internal Reflection Fluorescence Correlation Spectroscopy 2010-01-28 doi: 10.3390/ijms11020386 Hans Blom Kai Hassler Andriy Chmyrov Jerker Widengren http://www.mdpi.com/1422-0067/11/1/304/ 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. http://www.mdpi.com/1422-0067/11/1/304/ Thu, 21 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-21 11 1 Article 304 311 1422-0067 Single Molecule Experiments Challenge the Strict Wave-Particle Dualism of Light 2010-01-21 doi: 10.3390/ijms11010304 Karl Otto Greulich http://www.mdpi.com/1422-0067/11/1/206/ 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. http://www.mdpi.com/1422-0067/11/1/206/ Wed, 13 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-13 11 1 Review 206 221 1422-0067 Photonic Methods to Enhance Fluorescence Correlation Spectroscopy and Single Molecule Fluorescence Detection 2010-01-13 doi: 10.3390/ijms11010206 Jérome Wenger Hervé Rigneault http://www.mdpi.com/1422-0067/11/1/173/ 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. http://www.mdpi.com/1422-0067/11/1/173/ Tue, 12 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-12 11 1 Article 173 188 1422-0067 Host-Guest Complexation Studied by Fluorescence Correlation Spectroscopy: Adamantane–Cyclodextrin Inclusion 2010-01-12 doi: 10.3390/ijms11010173 Daniel Granadero Jorge Bordello Maria Jesus Pérez-Alvite Mercedes Novo Wajih Al-Soufi http://www.mdpi.com/1422-0067/10/12/5239/ 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. http://www.mdpi.com/1422-0067/10/12/5239/ Tue, 01 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-01 10 12 Article 5239 5256 1422-0067 Identification of Different Donor-Acceptor Structures via Förster Resonance Energy Transfer (FRET) in Quantum-Dot-Perylene Bisimide Assemblies 2009-12-01 doi: 10.3390/ijms10125239 Danny Kowerko Stefan Krause Nicole Amecke Mohamed Abdel-Mottaleb Jörg Schuster Christian Von Borczyskowski http://www.mdpi.com/1422-0067/10/9/3931/ 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. http://www.mdpi.com/1422-0067/10/9/3931/ Tue, 08 Sep 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-09-08 10 9 Communication 3931 3936 1422-0067 Molecule Non-Radiative Coupling to a Metallic Nanosphere: An Optical Theorem Treatment 2009-09-08 doi: 10.3390/ijms10093931 Gérard Colas Des Francs http://www.mdpi.com/1422-0067/10/4/1430/ 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. http://www.mdpi.com/1422-0067/10/4/1430/ Mon, 30 Mar 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-03-30 10 4 Review 1430 1444 1422-0067 Occurence and Bioactivities of Funicone-Related Compounds 2009-03-30 doi: 10.3390/ijms10041430 Rosario Nicoletti Emiliano Manzo Maria Letizia Ciavatta