Photoactivatable Rhodamine Spiroamides and Diazoketones Decorated with “Universal Hydrophilizer” or Hydroxyl Groups

Optimized Properties and Synthesis of Photoactivatable Diazoketorhodamines Facilitate and Enhance High-Throughput Single-Molecule Tracking

Photoactivatable (PA) rhodamine dyes are widely used in single-molecule tracking (SMT) and a variety of other fluorescence-based imaging modalities. One of the most commonly employed scaffolds uses a diazoketone to lock the rhodamine in the nonfluorescent closed form, which can be activated with 405 nm light. However, poor properties of previously reported dyes require significant washing, which can be resource- and cost-intensive, especially when performing microscopy in a large scale and high-throughput fashion. Here, we report improved diazoketorhodamines that perform exceptionally well in single-molecule tracking microscopy. We also report on the optimization of an improved synthetic method for further iteration and tailoring of diazoketorhodamines to the requirements of a specific user.

Photo-uncaging Triggers on Self-Blinking to Control Single-Molecule Fluorescence Kinetics for Super-resolution Imaging

Super-resolution imaging, especially a single-molecule localization approach, has raised a fluorophore engineering revolution chasing sparse single-molecule dark-bright blinking transforms. Yet, it is a challenge to structurally devise fluorophores manipulating the single-molecule blinking kinetics. In this pursuit, we have developed a triggering strategy by innovatively integrating the photoactivatable nitroso-caging strategy into self-blinking sulfonamide to form a nitroso-caged sulfonamide rhodamine (NOSR). Our fluorophore demonstrated controllable self-blinking events upon phototriggered caging unit release. This exceptional blink kinetics improved the super-resolution imaging integrity on microtubules compared to self-blinking analogues. With the aid of paramount single-molecule fluorescence kinetics, we successfully reconstructed the ring structure of nuclear pores and the axial morphology of mitochondrial outer membranes. We foresee that our synthetic approach of photoactivation and self-blinking would facilitate rhodamine devising for super-resolution imaging.

Super-resolution imaging of linearized chromatin in tunable nanochannels

Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Furthermore, through careful selection of self-blinking fluorescent dyes and the design of the nanochannel system, we achieve direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging of the linearized chromatin. As an initial demonstration, rDNA chromatin extracted from Tetrahymena is analyzed by multi-color imaging of total DNA, newly synthesized DNA, and newly synthesized histone H3. Our analysis reveals a relatively even distribution of newly synthesized H3 across two halves of the rDNA chromatin with palindromic symmetry, supporting dispersive nucleosome segregation. As a proof-of-concept study, our work achieves super-resolution imaging of native chromatin fibers linearized and immobilized in tunable nanochannels. It opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.

Accelerated MINFLUX Nanoscopy, through Spontaneously Fast-Blinking Fluorophores

The introduction of MINFLUX nanoscopy allows single molecules to be localized with one nanometer precision in as little as one millisecond. However, current applications have so far focused on increasing this precision by optimizing photon collection, rather than minimizing the localization time. Concurrently, commonly used fluorescent switches are specifically designed for stochastic methods (e.g., STORM), optimized for a high photon yield and rather long on-times (tens of milliseconds). Here, accelerated MINFLUX nanoscopy with up to a 30-fold gain in localization speed is presented. The improvement is attained by designing spontaneously blinking fluorescent markers with remarkably fast on-times, down to 1-3 ms, matching the iterative localization process used in a MINFLUX microscope. This design utilizes a silicon rhodamine amide core, shifting the spirocyclization equilibrium toward an uncharged closed form at physiological conditions and imparting intact live cell permeability, modified with a fused (benzo)thiophene spirolactam fragment. The best candidate for MINFLUX microscopy (also suitable for STORM imaging) is selected through detailed characterization of the blinking behavior of single fluorophores, bound to different protein tags. Finally, optimization of the localization routines, customized to the fast blinking times, renders a significant speed improvement on a commercial MINFLUX microscope.

Bis-Rhodamines Bridged with a Diazoketone Linker: Synthesis, Structure, and Photolysis

Two fluorophores bound with a short photoreactive bridge are fascinating structures and remained unexplored. To investigate the synthesis and photolysis of such dyes, we linked two rhodamine dyes via a diazoketone bridge (−COCN₂−) attached to position 5′ or 6′ of the pendant phenyl rings. For that, the mixture of 5′- or 6′-bromo derivatives of the parent dye was prepared, transformed into 1,2-diarylacetylenes, hydrated to 1,2-diarylethanones, and converted to diazoketones Ar¹COCN₂Ar². The high performance liquid chromatography (HPLC) separation gave four individual regioisomers of Ar¹COCN₂Ar². Photolysis of the model compound—C₆H₅COCN₂C₆H₅—in aqueous acetonitrile at pH 7.3 and under irradiation with 365 nm light provided diphenylacetic acid amide (Wolff rearrangement). However, under the same conditions, Ar¹COCN₂Ar² gave mainly α-diketones Ar¹COCOAr². The migration ability of the very bulky dye residues was low, and the Wolff rearrangement did not occur. We observed only moderate fluorescence increase, which may be explained by the insufficient quenching ability of diazoketone bridge (−COCN₂−) and its transformation into another (weaker) quencher, 1,2-diarylethane-1,2-dione.

A Self-locked β-Cyclodextrin-rhodamine B Spirolactam with Photoswitching Properties

Supramolecular organization and self-assembly are the pillars of functionality of many nanosystems. The covalent conjugate (6-spirolactam rhodamine B-6-monodeoxy)-β-cyclodextrin (Rho-βCD) is assembled as a self-included, rigid nanostructure, identical in the crystal and in aqueous solution, as revealed by detailed X-ray and NMR analyses. Rho-βCD self-assembly is the result of an interesting reaction pathway, which partially de-aggregates Rho and disturbs the zwitterion↔spirolactone equilibrium. Rho-βCD is stable at pH 4.6, but displays controllable photoswitching between the colored, fluorescent, zwitterionic and the colorless, non-fluorescent closed structures, during several iterative cycles. After an initial drop in absorbance, the on-off process continues without further changes under our irradiation conditions, a consequence of the specific self-locked arrangement of Rho in the cavity. Rho-βCD exemplifies a water soluble photoresponsive nanosystem with improved photostability suggesting promising applications in super resolution bioimaging.

BODIPYs with Photoactivatable Fluorescence

The borondipyrromethene (BODIPY) chromophore is a versatile platform for the construction of photoresponsive dyes with unique properties. Specifically, its covalent connection to a photocleavable group can be exploited to engineer compounds with photoswitchable fluorescence. The resulting photoactivatable fluorophores can increase their emission intensity or shift their emission wavelengths in response to switching. Such changes permit the spatiotemporal control of fluorescence with optical stimulations and the implementation of imaging strategies that would be impossible to replicate with conventional fluorophores. Indeed, BODIPYs with photoactivatable fluorescence enable the selective highlighting of intracellular targets, the nanoscaled visualization of sub-cellular components, the real-time monitoring of dynamic events and the photochemical writing of optical barcodes.

GlycoBODIPYs: Sugars Serving as a Natural Stock for Water-soluble Fluorescent Probes of Complex Chiral Morphology

A range of unprocessed, reducing sugar substrates (mono-, di-, and trisaccharides) is shown to take part in a straightforward four-step synthetic route to water-soluble, uncharged BODIPY derivatives with unimpaired chiral integrity and high fluorescence efficiency. A wide compatibility with several postfunctionalizations is demonstrated, thus suggesting a universal utility of the multifunctional glycoconjugates, which we call GlycoBODIPYs. Knoevenagel condensations are able to promote a red-shift in the spectra, thereby furnishing strongly fluorescent red and far-red glycoconjugates of high hydrophilicity. The synthetic outcome was studied by X-ray crystallography and by comprehensive photophysical investigations in several solvent systems. Furthermore, cell experiments illustrate efficient cell uptake and demonstrate differential cell targeting as a function of the integrated chiral information.

Photoactivatable Fluorophore for Stimulated Emission Depletion (STED) Microscopy and Bioconjugation Technique for Hydrophobic Labels

The use of photoactivatable dyes in STED microscopy has so far been limited by two-photon activation through the STED beam and by the fact that photoactivatable dyes are poorly solvable in water. Herein, we report ONB-2SiR, a fluorophore that can be both photoactivated in the UV and specifically de-excited by STED at 775 nm. Likewise, we introduce a conjugation and purification protocol to effectively label primary and secondary antibodies with moderately water-soluble dyes. Greatly reducing dye aggregation, our technique provides a defined and tunable degree of labeling, and improves the imaging performance of dye conjugates in general.

Organocatalytic Synthesis of α-Triphenylmethylamines from Diarylketimines and Phenols

A formal Betti reaction between variously substituted phenols and benzophenone-derived imines to afford α-triphenylmethylamines is reported. The key to the success of this transformation is the in situ generation of the reactive benzophenone iminium species under organocatalytic conditions. Different phenols reacted smoothly, enabling the synthesis of an array of α-triphenylmethylamines, which are highly valued structural motifs in bioactive molecules and chemical sensors.

Tetrazine as a general phototrigger to turn on fluorophores

Light-activated fluorescence affords a powerful tool for monitoring subcellular structures and dynamics with enhanced temporal and spatial control of the fluorescence signal. Here, we demonstrate a general and straightforward strategy for using a tetrazine phototrigger to design photoactivatable fluorophores that emit across the visible spectrum. Tetrazine is known to efficiently quench the fluorescence of various fluorophores via a mechanism referred to as through-bond energy transfer. Upon light irradiation, restricted tetrazine moieties undergo a photolysis reaction that generates two nitriles and molecular nitrogen, thus restoring the fluorescence of fluorophores. Significantly, we find that this strategy can be successfully translated and generalized to a wide range of fluorophore scaffolds. Based on these results, we have used this mechanism to design photoactivatable fluorophores targeting cellular organelles and proteins. Compared to widely used phototriggers (e.g., o-nitrobenzyl and nitrophenethyl groups), this study affords a new photoactivation mechanism, in which the quencher is photodecomposed to restore the fluorescence upon light irradiation. Because of the exclusive use of tetrazine as a photoquencher in the design of fluorogenic probes, we anticipate that our current study will significantly facilitate the development of novel photoactivatable fluorophores.

Live-Cell Imaging at the Nanoscale with Bioconjugatable and Photoactivatable Fluorophores

Optical diffraction fundamentally limits the spatial resolution of conventional fluorescence images to length scales that are, at least, 2 orders of magnitude longer than the dimensions of individual molecules. As a result, the development of innovative probes and imaging schemes to overcome diffraction is very much needed to enable the investigation of the fundamental factors regulating cellular functions at the molecular level. In this context, the chemical synthesis of molecular constructs with photoactivatable fluorescence and the ability to label subcellular components of live cells can have transformative implications. Indeed, the fluorescence of the resulting assemblies can be activated with spatiotemporal control, even in the intracellular environment, to permit the sequential localization of individual emissive labels with precision at the nanometer level and the gradual reconstruction of images with subdiffraction resolution. The implementation of these operating principles for subdiffraction imaging, however, is only possible if demanding photochemical and photophysical requirements to enable photoactivation and localization as well as stringent structural requisites to allow the covalent labeling of intracellular targets in live cells are satisfied. Because of these complications, only a few synthetic photoactivatable fluorophores with appropriate performance for live-cell imaging at the nanoscale have been developed so far. Significant synthetic efforts in conjunction with spectroscopic analyses are still very much needed to advance this promising research area further and turn photoactivatable fluorophores into the imaging probes of choice for the investigation of live cells.

Covalently Tethered Rhodamine Voltage Reporters for High Speed Functional Imaging in Brain Tissue

Voltage-sensitive fluorophores enable the direct visualization of membrane potential changes in living systems. To pair the speed and sensitivity of chemically synthesized fluorescent indicators with cell-type specific genetic methods, we here develop Rhodamine-based Voltage Reporters (RhoVR) that can be covalently tethered to genetically encoded, self-labeling enzymes. These chemical-genetic hybrids feature a photoinduced electron transfer triggered RhoVR voltage-sensitive indicator coupled to a chloroalkane HaloTag ligand through a long, water-soluble polyethylene glycol linker (RhoVR-Halo). When applied to cells, RhoVR-Halo dyes selectively and covalently bind to surface-expressed HaloTag enzyme on genetically modified cells. RhoVR-Halo dyes maintain high voltage sensitivities-up to 34% ΔF/F per 100 mV-and fast response times typical of untargeted RhoVRs, while gaining the selectivity of genetically encodable voltage indicators. We show that RhoVR-Halos can record action potentials in single trials from cultured rat hippocampal neurons and can be used in concert with green-fluorescent Ca2+ indicators like GCaMP to provide simultaneous voltage and Ca2+ imaging. In a brain slice, RhoVR-Halos provide exquisite labeling of defined cells and can be imaged using epifluorescence, confocal, or two-photon microscopy. Using high-speed epifluorescence microscopy, RhoVR-Halos provide a read-out of action potentials from labeled cortical neurons in a rat brain slice, without the need for trial averaging. These results demonstrate the potential of hybrid chemical-genetic voltage indicators to combine the optical performance of small-molecule chromophores with the inherent selectivity of genetically encodable systems, permitting imaging modalities inaccessible to either technique individually.

A H-bond strategy to develop acid-resistant photoswitchable rhodamine spirolactams for super-resolution single-molecule localization microscopy

Rhodamine spirolactam based photoswitches have been extensively applied in super-resolution single-molecule localization microscopy (SMLM). However, the ring-opening reactions of spirolactams are cross-sensitive to acid, limiting their photoswitch use to neutral pH conditions. In addition, the ring-closing reactions of spirolactams are environment-sensitive and slow (up to hours), virtually making rhodamine spirolactams caged fluorescent dyes instead of reversible photoswitches in SMLM. Herein, by introducing hydrogen bonds to stabilize spirolactams, we report a series of acid-resistant rhodamine spirolactams with accelerated ring-closing reactions from fluorescent xanthyliums to non-fluorescent spirolactams, endowing them with good photoswitchable properties even in acidic environments. By further substitution of 6-phenylethynyl naphthalimide on the spirolactam, we shifted the photoactivation wavelength into the visible region (>400 nm). Subsequently, we have successfully applied these dyes in labeling and imaging the cell surface of Bacillus subtilis at pH 4.5 using SMLM.

Strategy to Lengthen the On-Time of Photochromic Rhodamine Spirolactam for Super-resolution Photoactivated Localization Microscopy

Rhodamine derivatives and analogues have been widely used for different super-resolution imaging techniques, including photoactivated localization microscopy (PALM). Among them, rhodamine spirolactams exhibit great superiority for PALM imaging due to a desirable bright-dark contrast during the photochromic switching process. Although considerable attention has been paid to the chemical modifications on rhodamine spirolactams, the on-time of photochromic switching, one of the key characteristics for PALM imaging, has never been optimized in previous developments. In this study, we proposed that simply installing a carboxyl group close to the lactam site could impose an intramolecular acidic environment, stabilize the photoactivated zwitterionic structure, and thus effectively increase the on-time. On the basis of this idea, we have synthesized a new rhodamine spirolactam, Rh-Gly, that demonstrated considerably longer on-time than the other tested analogues, as well as an enhancement of single-molecule brightness, an improvement on signal-to-noise ratio and an enlargement of total collected photons of a single molecule before photobleaching. Finally, super-resolution images of live cell mitochondria stained with Rh-Gly have been obtained with a good temporal resolution of 10 s, as well as a satisfactory localization precision of ∼25 nm. Through self-labeling protein tags, Rh-Gly modified with a HaloTag ligand enabled super-resolution imaging of histone H2B proteins in live HeLa cells; through immunostaining antibodies labeled with an isothiocyanate-substituted Rh-Gly, super-resolution imaging of microtubules was achieved in fixed cells. Therefore, our simple and effective strategy provides novel insight for developing further enhanced rhodamine spirolactams recommendable for PALM imaging.

Fluorogenic probes for super-resolution microscopy

Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.

A Photoactivatable BODIPY Probe for Localization-Based Super-Resolution Cellular Imaging

The synthesis and application of a photoactivatable boron-alkylated BODIPY probe for localization-based super-resolution microscopy is reported. Photoactivation and excitation of the probe is achieved by a previously unknown boron-photodealkylation reaction with a single low-power visible laser and without requiring the addition of reducing agents or oxygen scavengers in the imaging buffer. These features lead to a versatile probe for localization-based microscopy of biological systems. The probe can be easily linked to nucleophile-containing molecules to target specific cellular organelles. By attaching paclitaxel to the photoactivatable BODIPY, in vitro and in vivo super-resolution imaging of microtubules is demonstrated. This is the first example of single-molecule localization-based super-resolution microscopy using a visible-light-activated BODIPY compound as a fluorescent probe.