Christian A. Wurm

Fluorescence nanoscopy by ground-state depletion and single-molecule return.

We introduce far-field fluorescence nanoscopy with ordinary fluorophores based on switching the majority of them to a metastable dark state, such as the triplet, and calculating the position of those left or those that spontaneously returned to the ground state. Continuous widefield illumination by a single laser and a continuously operating camera yielded dual-color images of rhodamine- and fluorescent protein–labeled (living) samples, proving a simple yet powerful super-resolution approach.

Spherical nanosized focal spot unravels the interior of cells

The resolution of any linear imaging system is given by its point spread function (PSF) that quantifies the blur of an object point in the image. The sharper the PSF, the better the resolution is. In standard fluorescence microscopy, however, diffraction dictates a PSF with a cigar-shaped main maximum, called the focal spot, which extends over at least half the wavelength of light (λ = 400–700 nm) in the focal plane and >λ along the optical axis (z). Although concepts have been developed to sharpen the focal spot both laterally and axially, none of them has reached their ultimate goal: a spherical spot that can be arbitrarily downscaled in size. Here we introduce a fluorescence microscope that creates nearly spherical focal spots of 40–45 nm (λ/16) in diameter. Fully relying on focused light, this lens-based fluorescence nanoscope unravels the interior of cells noninvasively, uniquely dissecting their sub-λ–sized organelles.

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

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.

Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution.

We report on a fiber laser-based stimulated emission-depletion microscope providing down to ∼20 nm resolution in raw data images as well as 15-19 nm diameter probing areas in fluorescence correlation spectroscopy. Stimulated emission depletion pulses of nanosecond duration and 775 nm wavelength are used to silence two fluorophores simultaneously, ensuring offset-free colocalization analysis. The versatility of this superresolution method is exemplified by revealing the octameric arrangement of Xenopus nuclear pore complexes and by quantifying the diffusion of labeled lipid molecules in artificial and living cell membranes.

Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength.

Current far-field fluorescence nanoscopes provide subdiffraction resolution by exploiting a mechanism of fluorescence inhibition. This mechanism is implemented such that features closer than the diffraction limit emit separately when simultaneously exposed to excitation light. A basic mechanism for such transient fluorescence inhibition is the depletion of the fluorophore ground state by transferring it (via a triplet) in a dark state, a mechanism which is workable in most standard dyes. Here we show that microscopy based on ground state depletion followed by individual molecule return (GSDIM) can effectively provide multicolor diffraction-unlimited resolution imaging of immunolabeled fixed and SNAP-tag labeled living cells. Implemented with standard labeling techniques, GSDIM is demonstrated to separate up to four different conventional fluorophores using just two detection channels and a single laser line. The method can be expanded to even more colors by choosing optimized dichroic mirrors and selecting marker molecules with negligible inhomogeneous emission broadening.

Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores.

We demonstrate three-dimensional (3D) super-resolution imaging of stochastically switched fluorophores distributed across whole cells. By evaluating the higher moments of the diffraction spot provided by a 4Pi detection scheme, single markers can be simultaneously localized with <10 nm precision in three dimensions in a layer of 650 nm thickness at an arbitrarily selected depth in the sample. By splitting the fluorescence light into orthogonal polarization states, our 4Pi setup also facilitates the 3D nanoscopy of multiple fluorophores. Offering a combination of multicolor recording, nanoscale resolution and extended axial depth, our method substantially advances the noninvasive 3D imaging of cells and of other transparent materials.

Mitochondrial cristae revealed with focused light

Because of the diffraction resolution barrier, optical microscopes have so far failed in visualizing the mitochondrial cristae, that is, the folds of the inner membrane of this 200 to 400 nm diameter sized tubular organelle. Realizing a approximately 30 nm isotropic subdiffraction resolution in isoSTED fluorescence nanoscopy, we have visualized these essential structures in the mitochondria of intact cells. We find a pronounced heterogeneity in the cristae arrangements even within individual mitochondrial tubules.

Stimulated emission depletion nanoscopy of living cells using SNAP-tag fusion proteins.

We show far-field fluorescence nanoscopy of different structural elements labeled with an organic dye within living mammalian cells. The diffraction barrier limiting far-field light microscopy is outperformed by using stimulated emission depletion. We used the tagging protein hAGT (SNAP-tag), which covalently binds benzylguanine-substituted organic dyes, for labeling. Tetramethylrhodamine was used to image the cytoskeleton (vimentin and microtubule-associated protein 2) as well as structures located at the cell membrane (caveolin and connexin-43) with a resolution down to 40 nm. Comparison with structures labeled with the yellow fluorescent protein Citrine validates this labeling approach. Nanoscopic movies showing the movement of connexin-43 clusters across the cell membrane evidence the capability of this technique to observe structural changes on the nanoscale over time. Pulsed or continuous-wave lasers for excitation and stimulated emission depletion yield images of similar resolution in living cells. Hence fusion proteins that bind modified organic dyes expand widely the application range of far-field fluorescence nanoscopy of living cells.

Rhodamines NN: A Novel Class of Caged Fluorescent Dyes**

Caged (that is, masked) fluorescent dyes are maintained in their nonfluorescent state by the incorporation of a photochemical labile group. The photosensitive masking group or “molecular cage” can be cleaved-off by irradiation with nearUV light, thereby rendering the dye fluorescent. Caged fluorescent dyes are of enormous interest for biological imaging because they may be used, for example, for the analysis of protein dynamics, multicolor fluorescence microscopy, and far-field optical nanoscopy. o-Nitrobenzyl groups are often used as masking groups; however, the use of these dyes is limited because of their rather complex synthesis and the unwanted by-products liberated by photolysis. Herein we report on the synthesis and characterization of a novel class of caged compounds—rhodamine NN dyes, which have a 2-diazoketone (COCNN) caging group incorporated into a spiro-9H-xanthene fragment (compounds 3 and 9-R in Schemes 1 and 3, respectively). This very simple and small caging group is the core element of a new class of masked rhodamines that have remarkable properties. The rhodamine NN dyes can be easily prepared and conjugated with biomolecules, they undergo rapid uncaging under standard irradiation conditions (with wavelengths 420 nm) with formation of highly fluorescent rhodamine derivatives, and they can be used in aqueous buffers, as well as in various embedding media utilized in imaging applications. In microscopy, these novel rhodamines may be used as labels alone or in combination with conventional fluorescent dyes and switchable rhodamine spiroamides. In the latter case, they enable new imaging protocols based on the stepwise activation and detection of several fluorescent markers. The combination of the new rhodamine NN derivative (9-R) with the photochromic spiroamide of rhodamine S and a normal (uncaged) N,N,N’,N’-tetramethylrhodamine resulted in a monochoromatic multilabel imaging scheme with low cross-talk, despite using three fluorophores with very similar absorption and emission spectra. Rhodamines are very photostable and bright fluorescent dyes which can readily be chemically modified and caged. Coumarines and fluorescein have also been used as caged fluorescent dyes. As a photocleavable unit, most of these caged compounds contain a 2-nitrobenzyl group or a derivative with an alkyl or a carboxy group in the a position to the phenyl ring (at the CH2 group) and/or one or two methoxy groups in the aromatic ring. Compounds with a free carboxy group are required for bioconjugation. However, the synthesis of caged rhodamines with a free (“second”) carboxy group is difficult and their yield is low. The 2-nitrobenzyl group and its substitutes are bulky and generate toxic, colored, and highly reactive 2-nitrosobenzaldehyde or 2-nitrosobenzophenone derivatives upon photolysis. These compounds or their oligomers are expected to be poisonous to living cells, and they are also colored and interfere with optical measurements. Other modern caging groups with the required absorption in the near-UV region are also bulky, rather lipophilic, and the procedures for their synthesis and introduction are often complex. For example, 2-(N,N-dimethylamino)-5-nitrophenol was reported to give photocleavable phenyl esters. 7-Diethylamino-4-(hydroxymethyl)-2H-chromen-2-one is known to form esters which can be cleaved easily by irradiation at 412 nm. Derivatives of 8-bromo-7-hydroxyquinoline and 6-bromo-7-hydroxycoumarines have also been proposed as light-sensitive protecting groups. The photolysis of these caged compounds generates light-absorbing by-products. We set out to prepare masked fluorescent dyes without bulky caging groups. A very small 2-diazoketone fragment would be an ideal caging group, provided that it is still possible to integrate this group into the colorless form of a fluorescent dye and then restore the fluorescent state by photolysis. Rhodamines are ideal for this purpose, because they contain a carboxy group, which is known to form colorless and nonfluorescent lactones or lactams with the spiro-9H-xanthene fragment. Furthermore, this carboxy group may be transformed into a 2-diazoketone residue. For the practical realization of this caging strategy, we used rhodamine B as a model compound and performed the reaction of diazomethane with its acid chloride 1. The yellow crystalline diazoketone 3 was obtained in high yield (Scheme 1). In the course of the facile caging reaction, the positively charged C9 atom of the xanthene fragment attacks the negatively charged carbon atom of the diazomethane residue in the intermediate 2. The simultaneous abstraction of a proton furnishes the stable five-membered ring. [*] Dr. V. N. Belov, Dr. C. A. Wurm, Dr. V. P. Boyarskiy, Dr. S. Jakobs, Prof. Dr. S. W. Hell Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11, 37077 G ttingen (Germany) Fax: (+49)551-201-2506 E-mail: vbelov@gwdg.de cwurm@gwdg.de shell@gwdg.de Homepage: http://www.mpibpc.gwdg.de/abteilungen/200/

STED super-resolution microscopy reveals an array of MINOS clusters along human mitochondria

The mitochondrial inner membrane organizing system (MINOS) is a conserved large hetero-oligomeric protein complex in the mitochondrial inner membrane, crucial for the maintenance of cristae morphology. MINOS has been suggested to represent the core of an extended protein network that controls mitochondrial function and structure, and has been linked to several human diseases. The spatial arrangement of MINOS within mitochondria is ill-defined, however. Using super-resolution stimulated emission depletion (STED) microscopy and immunogold electron microscopy, we determined the distribution of three known human MINOS subunits (mitofilin, MINOS1, and CHCHD3) in mammalian cells. Super-resolution microscopy revealed that all three subunits form similar clusters within mitochondria, and that MINOS is more abundant in mitochondria around the nucleus than in peripheral mitochondria. At the submitochondrial level, mitofilin, a core MINOS subunit, is preferentially localized at cristae junctions. In primary human fibroblasts, mitofilin labeling uncovered a regularly spaced pattern of clusters arranged in parallel to the cell growth surfaces. We suggest that this array of MINOS complexes might explain the observed phenomenon of largely horizontally arranged cristae junctions that connect the inner boundary membrane to lamellar cristae. The super-resolution images demonstrate an unexpectedly high level of regularity in the nanoscale distribution of the MINOS complex in human mitochondria, supporting an integrating role of MINOS in the structural organization of the organelle.