The review covers the knowledge on photoremovable protecting
groups and includes all relevant chromophores studied in the
time period of 2000–2012; the most relevant earlier works are
also discussed.

/pdf/photoremovable-protecting-groups-in-chemistry-and-biology-2n33qs6p7b.pdf

Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy

This review focuses on classifying different types of long wavelength absorbing BODIPY dyes based on the wide range of structural modification methods that have been adopted, and on tabulating their spectral and photophysical properties. The structure–property relationships are analyzed in depth with reference to molecular modeling calculations, so that the effectiveness of the different structural modification strategies for shifting the main BODIPY spectral bands to longer wavelengths can be readily compared, along with their effects on the fluorescence quantum yield (ΦF) values. This should facilitate the future rational design of red/NIR region BODIPY dyes for a wide range of different applications.

Structural modification strategies for the rational design of red/NIR region BODIPYs

The ideal fluorescent probe for bioimaging is bright, absorbs at long wavelengths and can be implemented flexibly in living cells and in vivo. However, the design of synthetic fluorophores that combine all of these properties has proved to be extremely difficult. Here, we introduce a biocompatible near-infrared silicon-rhodamine probe that can be coupled specifically to proteins using different labelling techniques. Importantly, its high permeability and fluorogenic character permit the imaging of proteins in living cells and tissues, and its brightness and photostability make it ideally suited for live-cell super-resolution microscopy. The excellent spectroscopic properties of the probe combined with its ease of use in live-cell applications make it a powerful new tool for bioimaging.

/pdf/a-near-infrared-fluorophore-for-live-cell-super-resolution-343a5b9hs7.pdf

A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins.

Mammalian mtDNA is packaged in DNA-protein complexes denoted mitochondrial nucleoids. The organization of the nucleoid is a very fundamental question in mitochondrial biology and will determine tissue segregation and transmission of mtDNA. We have used a combination of stimulated emission depletion microscopy, enabling a resolution well below the diffraction barrier, and molecular biology to study nucleoids in a panel of mammalian tissue culture cells. We report that the nucleoids labeled with antibodies against DNA, mitochondrial transcription factor A (TFAM), or incorporated BrdU, have a defined, uniform mean size of ∼100 nm in mammals. Interestingly, the nucleoid frequently contains only a single copy of mtDNA (average ∼1.4 mtDNA molecules per nucleoid). Furthermore, we show by molecular modeling and volume calculations that TFAM is a main constituent of the nucleoid, besides mtDNA. These fundamental insights into the organization of mtDNA have broad implications for understanding mitochondrial dysfunction in disease and aging.

/pdf/super-resolution-microscopy-reveals-that-mammalian-u6e46n0ud8.pdf

Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA

Stimulated emission depletion (STED) microscopy provides subdiffraction resolution while preserving useful aspects of fluorescence microscopy, such as optical sectioning, and molecular specificity and sensitivity However, sophisticated microscopy architectures and high illumination intensities have limited STED microscopy's widespread use in the past Here we summarize the progress that is mitigating these problems and giving substantial momentum to STED microscopy applications We discuss the future of this method in regard to spatiotemporal limits, live-cell imaging and combination with spectroscopy Advances in these areas may elevate STED microscopy to a standard method for imaging in the life sciences

STED super-resolved microscopy.

https://chemistry-europe.onlinelibrary.wiley.com/doi/pdf/10.1002/chem.201290178

Inside Cover: Red‐Emitting Rhodamines with Hydroxylated, Sulfonated, and Phosphorylated Dye Residues and Their Use in Fluorescence Nanoscopy (Chem. Eur. J. 41/2012)

Sulfonated 2(7)-aminoacridone and 1-aminopyrene dyes and their use as fluorescent tags, in particular for carbohydrate analysis The invention relates to fluorescent dyes with multiple negatively charged groups in their ionized form which are aminoacridone sulfonamides or 1-aminopyrenes having of one of the following general formulae A-D: Formula (A), Formula (B), Formula (C), Formula (D), wherein the ionizable groups X are typically selected from the following: SH, COOH, SO3H, OSO3H, OP(O)(OH)2, OP(O)(OH)Ra, P(O)(OH)2, P(O)(OH)Ra, where Ra= C1-C4alkyl or substituted C1-C4alkyl. The invention further relates to the use of these dyes as fluorescent tags, in particular for reducing sugars and glycans.

Sulfonated 2(7)-aminoacridone and 1-aminopyrene dyes and their use as fluorescent tags, in particular for carbohydrate analysis

L'invention concerne de nouveaux colorants fluorescents comportant des groupes hydroxymethyle phosphoryles; un procede de preparation des colorants et leur utilisation dans des techniques d'imagerie. Ces colorants fluorescents sont des colorants a base de coumarine, de rhodamine ou de BODIPY presentant une des formules generales suivantes (I-III) dans lesquelles W = OP(0)Y 1 Y 2 ou P(0)Υ 1 Υ 2 , Y 1 et Y 2 representant independamment l'un quelconque des residus suivants: OH, O(-), OR a et OR b , NHR a et NHR b , NR a R b et NR c R d , OR a et NHR b , OR a et NR b R c , NHR a et NR b R c ; et un sel quelconque de ceux-ci.

Colorants fluorescents comportant des groupes hydroxyméthyle phosphorylés et leur utilisation en microscopie photonique et dans des techniques d'imagerie

The invention relates to novel cell-penetrating fluorescent dyes with with secondary alcohol functionalities having one of the following general formulae I-III and 4: The invention also relates to the use of these compounds for optical microscopy and imaging techniques.

Kirill Kolmakov

Papers

Inside Cover: Red‐Emitting Rhodamines with Hydroxylated, Sulfonated, and Phosphorylated Dye Residues and Their Use in Fluorescence Nanoscopy (Chem. Eur. J. 41/2012)

Sulfonated 2(7)-aminoacridone and 1-aminopyrene dyes and their use as fluorescent tags, in particular for carbohydrate analysis

Colorants fluorescents comportant des groupes hydroxyméthyle phosphorylés et leur utilisation en microscopie photonique et dans des techniques d'imagerie

Cell-penetrating fluorescent dyes with secondary alcohol functionalities