Analysis of fluorescent nanostructures in biological systems by means of Spectral Position Determination Microscopy (SPDM)

# PM and YW contributed equally to this work. Localization microscopy (LM) has become an established technique that enables effective optical resolutions in the nanometre range. In principle LM is based on the concept of optical isolation of the diffraction patterns of individual point emitters and assignment of their spatial positions to a joint localization map. A very effective method of optical isolation of molecules of the same type has been to use fluorophores that can be switched between two different spectral states to achieve a temporal isolation and thus a spatial separation of signals. A subsequent computational calculation allows determining the positions of individual fluorophores and their spatial distances even if they are below the conventional optical resolution limit. This review summarises various results of nanostructural investigations for biological applications dealing with protein distribution, distance- and cluster analysis of proteins as well as analyses of deoxyribonucleic acid (DNA) loci. All the data presented here, were received by Spectral Position Determination Microscopy (SPDM) and contain structural information far below the conventional diffraction limit of light microscopy. These analyses will improve the understanding of the dynamics and arrangement of proteins and chromatin in human cells leading to new insights into cellular functioning.

[1]  Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung , 1873 .

[2]  I. Hassinen,et al.  Oxidation-reduction midpoint potentials of mitochondrial flavoproteins and their intramitochondrial localization , 1978, Journal of bioenergetics and biomembranes.

[3]  G. V. Miller,et al.  Calibration of microspectrophotometers as it applies to the detection of lipofuscin and the blue- and yellow-emitting fluorophores in situ. , 1984, Methods in enzymology.

[4]  W. Kunz,et al.  Contribution of different enzymes to flavoprotein fluorescence of isolated rat liver mitochondria. , 1985, Biochimica et biophysica acta.

[5]  M Tsuchida,et al.  Lipofuscin and lipofuscin-like substances. , 1987, Chemistry and physics of lipids.

[6]  M. Schmid,et al.  Organization of DYZ2 repetitive DNA on the human Y chromosome. , 1990, Genomics.

[7]  David H. L. Bishop,et al.  The International Committee on Taxonomy of Viruses , 1995 .

[8]  Cremer,et al.  High‐precision distance measurements and volume‐conserving segmentation of objects near and below the resolution limit in three‐dimensional confocal fluorescence microscopy , 1998 .

[9]  B. Jähne,et al.  Handbook of Computer Vision and Applications: Volume 1: From Scenes to Images , 1999 .

[10]  Christoph Cremer,et al.  Spectral precision distance confocal microscopy for the analysis of molecular nuclear structure , 1999 .

[11]  N. Kanomata,et al.  Mammary carcinoma with prominent cytoplasmic lipofuscin granules mimicking melanocytic differentiation , 2000, Histopathology.

[12]  C Cremer,et al.  Three‐dimensional spectral precision distance microscopy of chromatin nanostructures after triple‐colour DNA labelling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome , 2000, Journal of microscopy.

[13]  Y. Matsumoto.  Lipofuscin pigmentation in pleomorphic adenoma of the palate. , 2001, Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics.

[14]  Tobias Knoch,et al.  Approaching the three-dimensional organization of the human genome: structural-, scaling- and dynamic properties in the simulation of interphase chromosomes and cell nuclei, long-range correlations in complete genomes, in vivo quantification of the chromat , 2002 .

[15]  George H. Patterson,et al.  A Photoactivatable GFP for Selective Photolabeling of Proteins and Cells , 2002, Science.

[16]  Rainer Heintzmann,et al.  High-resolution colocalization of single dye molecules by fluorescence lifetime imaging microscopy. , 2002, Analytical chemistry.

[17]  Christoph Cremer,et al.  Spatially modulated illumination microscopy allows axial distance resolution in the nanometer range. , 2002, Applied optics.

[18]  M. Reddehase,et al.  Two Antigenic Peptides from Genes m123 and m164 of Murine Cytomegalovirus Quantitatively Dominate CD8 T-Cell Memory in the H-2d Haplotype , 2002, Journal of Virology.

[19]  Christoph Cremer,et al.  COMBO-FISH: specific labeling of nondenatured chromatin targets by computer-selected DNA oligonucleotide probe combinations. , 2003, BioTechniques.

[20]  J. Schmidtke,et al.  Characterisation of a human Y chromosome repeated sequence and related sequences in higher primates , 2004, Chromosoma.

[21]  Lord Rayleigh,et al.  On the Theory of Optical Images, with Special Reference to the Microscope , 1903 .

[22]  Michael Schaefer,et al.  Reversible photobleaching of enhanced green fluorescent proteins. , 2005, Biochemistry.

[23]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[24]  H. Shimasaki,et al.  Isolation and analysis of age-related fluorescent substances in rat testes , 1980, Lipids.

[25]  Michael D. Mason,et al.  Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. , 2006, Biophysical journal.

[26]  Michael J Rust,et al.  Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) , 2006, Nature Methods.

[27]  Caitlin Smith.  Keeping tabs on fluorescent tags , 2007, Nature Methods.

[28]  David Baddeley,et al.  Nanostructure analysis using spatially modulated illumination microscopy , 2003, Nature Protocols.

[29]  S. Hell,et al.  Fluorescence nanoscopy by ground-state depletion and single-molecule return , 2008, Nature Methods.

[30]  David Baddeley,et al.  High-precision structural analysis of subnuclear complexes in fixed and live cells via spatially modulated illumination (SMI) microscopy , 2008, Chromosome Research.

[31]  Thomas Cremer,et al.  Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei. , 2008, Differentiation; research in biological diversity.

[32]  M. Hausmann,et al.  SPDM: light microscopy with single-molecule resolution at the nanoscale , 2008 .

[33]  M. Heilemann,et al.  Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. , 2008, Angewandte Chemie.

[34]  D. Baddeley,et al.  Using conventional fluorescent markers for far‐field fluorescence localization nanoscopy allows resolution in the 10‐nm range , 2009, Journal of microscopy.

[35]  Mark Bates,et al.  Super-resolution fluorescence microscopy. , 2009, Annual review of biochemistry.

[36]  David Baddeley,et al.  SPDM: single molecule superresolution of cellular nanostructures , 2009, BiOS.

[37]  K. Rippe,et al.  Dual color localization microscopy of cellular nanostructures , 2009, Biotechnology journal.

[38]  Christoph Cremer,et al.  Localization microscopy reveals expression-dependent parameters of chromatin nanostructure. , 2010, Biophysical journal.

[39]  Christoph Cremer,et al.  Combining FISH with localisation microscopy: Super-resolution imaging of nuclear genome nanostructures , 2010, Chromosome Research.

[40]  Christoph Cremer,et al.  COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci , 2010, International journal of molecular sciences.

[41]  M. Gunkel.  Lokalisationsmikroskopie mit mehreren Farben und ihre Anwendung in biologischen Präparaten , 2011 .

[42]  P. Müller.  Molekularbiologische Analyse von Her2/neu-Nanostrukturen in unterschiedlichen Brustkrebszelllinien auf Gen- und Proteinebene basierend auf hochaufgelösten fluoreszenzmikroskopischen Darstellungen , 2011 .

[43]  M. Hausmann,et al.  Imaging label-free intracellular structures by localisation microscopy. , 2011, Micron.

[44]  C Cremer,et al.  Analysis of Her2/neu membrane protein clusters in different types of breast cancer cells using localization microscopy , 2011, Journal of microscopy.

[45]  Christoph Cremer,et al.  Superresolution imaging of biological nanostructures by spectral precision distance microscopy , 2011, Biotechnology journal.

[46]  Manfred Kirchgessner,et al.  Visualization and Quantitative Analysis of Reconstituted Tight Junctions Using Localization Microscopy , 2012, PloS one.

[47]  C. Cremer.  Optics Far Beyond the Diffraction Limit , 2012 .