Special Issue "Single Molecules"

Guest Editor
Prof. Dr. Karl Otto Greulich
Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Abteilung Einzelzell- und Einzelmolekueltechniken, Beutenbergstr. 11, D-07745 Jena, Germany
Website: http://www.imb-jena.de/www_kog/staff/greulich.html
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Guest Editor
Prof. Dr. Herbert Schneckenburger
Institut für Angewandte Forschung, Hochschule Aalen, Anton-Huber-Str. 21, 73430 Aalen, Germany
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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.org. 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 Molecular Diversity Preservation International.

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).

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

Feature Papers

Type of Paper: Article
Title: Analysis of Specific Chromatin Regions@Single Molecule Resolution
Authors: Y. Weiland ¹, R. Kaufmann ¹, P. Lemmer ¹, R. Amberger ¹ and C. Cremer ^1,2,3,4,*
Affiliations: ¹ Kirchhoff-Institute for Physics
² Institute for Pharmacy and Molecular Biotechnology
³ Bioquant-Center, University Heidelberg
⁴ Institute for Molecular Biophysics, The Jackson Laboratory/University of Maine
* Author to whom correspondence should be addressed; E-mails: cremer@kip.uni-heidelberg.de; cremer@bmm.uni-heidelberg.de
Abstract: An essential problem to analyse nuclear chromatin nanostructures by far field light microscopy is the conventional optical resolution restricted to about 200 nm laterally and 600 nm axially. Various recently introduced laseroptical “nanoscopy” approaches such as Structured Illumination (SI), 4Pi- and Stimulated Emission Depletion (STED) Microscopy allowed to extend the spatial analysis far beyond these limits. Here we report on a novel method “Spectral Precision Distance/Position Determination Microscopy (SPDM) with Physically Modifiable Fluorochromes (SPDM_Phymod) to analyse the spatial distribution of single nuclear proteins and DNA sequences at the macromolecular optical resolution level. As other methods of “Spectrally Assigned Localization Microscopy” (SALM), SPDM_Phymod is based on labelling ‘point like’ objects (e.g. single molecules) with different spectral signatures, spectrally selective registration and high precision localization monitoring by far field fluorescence microscopy. The basic condition is that in a given observation volume, at a given time and for a given spectral registration mode, only one such object (e.g. a single molecule) is registered. In particular, SPDM_Phymod is based on excitation intensity dependent reversible photobleaching and stochastic induction of ‘fluorescent bursts’ of the excited molecules. This results in an observable fluorescence lifetime in the order of seconds; as a consequence, a large number of ‘spectral signatures’ is obtained described by the stochastic onset times of the single molecule fluorescence bursts. Presently, SPDM_Phymod techniques have been used to determine the intracellular spatial location of single histone molecules at a density up to ca. 1000 molecules/μm² of the same type with an estimated best localization precision in the few nm range (at an excitation wavelength of λ_exc = 488 nm); distances in the range of 15 – 30 nm were nanoscopically resolved between individual fluorescent histone molecules. Using synthetic fluorochromes in combination with Fluorescence-in situ Hybridization (FISH), it became possible to allow superresolved ‘nanoimaging’ of specific chromatin domains in human cell nuclei.
Reference: Lemmer, P.; Gunkel, M.; Baddeley, D.; Kaufmann, R.; Urich, A.; Weiland, Y.; Reymann, J.; Müller, P.; Hausmann, M.; Cremer, C. SPDM – Light Microscopy with Single Molecule Resolution at the Nanoscale. Applied Physics B 2008, 93, 1-12.

Regular Papers

Type of Paper: Review
Title: Chromatin Fiber Dynamics under Tension and Torsion
Authors: Christophe Lavelle ¹, Jean-Marc Victor ² and Jordanka Zlatanova ^3,*
Affiliations: ¹ Interdisciplinary Research Institute, CNRS USR 3078, Villeneuve d'Ascq F-59655 France
² Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Paris F-75005, France
³ Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
* Author to whom correspondence should be addressed; E-mail: jordanka@uwyo.edu; Tel. 307-766-2892
Abstract: The genetic and epigenetic information in eukaryotic cells is encoded in large, hierarchically folded chromatin fibers. Mechanical micromanipulation of individual chromatin fibers have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by chromatin structural changes. Indeed, magnetic and optical tweezers have open opportunities to handle single chromatin fibers and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors. These challenging technical approaches provide deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of gene expression.