Current Progress in Expansion Microscopy: Chemical Strategies and Applications.

Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre- and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development.

Improved Dye Survival in Expansion Microscopy through Stabilizer-Conjugated Linkers.

Expansion microscopy (ExM) has been widely used to detect biomolecules in cultured cells and tissue samples due to its enablement of super resolution imaging with conventional microscopes, via physical expansion of samples. However, reaction conditions inherent to the process bring about strong fluorescent signal loss during polymerization and digestion and thus limit the brightness of the signal obtained post expansion. Here, we explore the impact of stabilizer-containing organic fluorophores in ExM, as a mitigation strategy for this radical-induced dye degradation. Through direct conjugation of 4-nitrophenylalanine (NPA) to our previously developed trifunctional reagents, we validate and demonstrate that these multifunctional linkers enable visualization of different organelles with improved fluorescent intensity, owning to protection of the dyes to radical induced degradation as well as to photoprotection upon imaging. At this point, we cannot disentangle the relative contribution of both mechanisms. Furthermore, we report anchoring linkers that allow straightforward application of NPA or Trolox to commercially available fluorophore-conjugated antibodies. We show that these anchoring linkers enable complete retention of biological targets while increasing fluorophore photostability. Our results provide guidance in exploring these stabilizer-modified agents in ExM and methods for increased signal survival through the polymerization steps of the ExM protocols.

A Universal Labeling Strategy for Nucleic Acids in Expansion Microscopy.

Expansion microscopy (ExM) enables the nanoscale imaging of ribonucleic acids (RNAs) on a conventional fluorescence microscope, providing information on the intricate patterns of gene expression at (sub)cellular resolution and within spatial context. To extend the use of such strategies, we examined a series of multivalent reagents that allow the labeling and grafting of deoxyribonucleic acid (DNA) oligonucleotide probes in a unified approach. We show that the reagents are directly compatible with third-generation in situ hybridization chain reaction RNA FISH (fluorescence in situ hybridization) techniques while displaying complete retention of the targeted transcripts. Furthermore, we validate and demonstrate that our labeling method is compatible with multicolor staining. Through oligonucleotide-conjugated antibodies, we demonstrate excellent performance in ×4 ExM and ×10 ExM, achieving a resolution of ∼50 nm in ×10 ExM for both pre- and postexpansion labeling strategies. Our results indicate that our multivalent molecules enable the rapid functionalization of DNA oligonucleotides for ExM.

A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA.

The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.

Impact of the Keto-Enol Tautomeric Equilibrium on the BODIPY Chromophore.

An intramolecular tautomeric fluorescent BODIPY sensor has been designed and synthesized. The obtained BODIPY dye is a combination of the 4-bora- 3a, 4a-diaza- s-indacene core and a diketone fragment. The study of conformational equilibria in the ground and excited states has been completed for a broad range of solvent polarity by steady state and NMR methods as well as by DFT and TD-DFT calculations. The interpretation of the unique emission observed in hydrogen bond accepting solvents upon the excitation of the fluorescent dye in the S0-S2 transition has been accomplished. The Jablonski diagram has been analyzed for the observed processes in the BODIPY dye studied on the basis of DFT and TD-DFT calculations.

Methyltransferase-Directed Labeling of Biomolecules and its Applications.

Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.

A Blue-Light-Emitting BODIPY Probe for Lipid Membranes.

Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C18, that can be excited in the blue spectral region. Compound 1 has unbranched octadecyl chains at the 3,5-positions and a meso-amino function. In organic solvents, the absorption and emission maxima of 1 are determined mainly by solvent acidity and dipolarity. The fluorescence quantum yield is high and reaches 0.93 in 2-propanol. The fluorescence decays are well fitted with a single-exponential in pure solvents and in small and giant unilamellar vesicles (GUV) with a lifetime of ca. 4 ns. Probe 1 partitions in the same lipid phase as DiI-C18(5) for lipid mixtures containing sphingomyelin and for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC). The lipid phase has no effect on the fluorescence lifetime but influences the fluorescence anisotropy. The translational diffusion coefficients of 1 in GUVs and OLN-93 cells are of the same order as those reported for DiI-C18. The directions of the absorption and emission transition dipole moments of 1 are calculated to be parallel. This is reflected in the high steady-state fluorescence anisotropy of 1 in high ordered lipid phases. Molecular dynamic simulations of 1 in a model of the DOPC bilayer indicate that the average angle of the transition moments with respect to membrane normal is ca. 70°, which is comparable with the value reported for DiI-C18.

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry.

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).

8-HaloBODIPYs and their 8-(C, N, O, S) substituted analogues: solvent dependent UV-vis spectroscopy, variable temperature NMR, crystal structure determination, and quantum chemical calculations.

The UV-vis electronic absorption and fluorescence emission properties of 8-halogenated (Cl, Br, I) difluoroboron dipyrrin (or 8-haloBODIPY) dyes and their 8-(C, N, O, S) substituted analogues are reported. The nature of the meso-substituent has a significant influence on the spectral band positions, the fluorescence quantum yields, and lifetimes. As a function of the solvent, the spectral maxima of all the investigated dyes are located within a limited wavelength range. The spectra of 8-haloBODIPYs display the narrow absorption and fluorescence emission bands and the generally quite small Stokes shifts characteristic of classic difluoroboron dipyrrins. Conversely, fluorophores with 8-phenylamino (7), 8-benzylamino (8), 8-methoxy (9), and 8-phenoxy (10) groups emit in the blue range of the visible spectrum and generally have larger Stokes shifts than common BODIPYs, whereas 8-(2-phenylethynyl)BODIPY (6) has red-shifted spectra compared to ordinary BODIPY dyes. Fluorescence lifetimes for 6, 8, and 10 have been measured for a large set of solvents and the solvent effect on their absorption and emission maxima has been analyzed using the generalized Catalán solvent scales. Restricted rotation about the C8-N bond in 7 and 8 has been observed via temperature dependent (1)H NMR spectroscopy, whereas for 10 the rotation about the C8-O bond is not hindered. The crystal structure of 8 demonstrates that the short C8-N bond has a significant double character and that this N atom exhibits a trigonal planar geometry. The crystal structure of 10 shows a short C8-O bond and an intramolecular C-H···π interaction. Quantum-chemical calculations have been performed to assess the effect of the meso-substituent on the spectroscopic properties.

Optical Mapping: Detecting Genomic Resistance Cassettes in MRSA.

Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant bacterium with a global presence in healthcare facilities as well as community settings. The resistance of MRSA to beta-lactam antibiotics can be attributed to a mobile genetic element called the staphylococcal cassette chromosome mec (SCCmec), ranging from 23 to 68 kilobase pairs in length. The mec gene complex contained in SCCmec allows MRSA to survive in the presence of penicillin and other beta-lactam antibiotics. We demonstrate that optical mapping (OM) is able to identify the bacterium as S. aureus, followed by an investigation of the presence of kilobase pair range SCCmec elements by examining the associated OM-generated barcode patterns. By employing OM as an alternative to traditional DNA sequencing, we showcase its potential for the detection of complex genetic elements such as SCCmec in MRSA. This approach holds promise for enhancing our understanding of antibiotic resistance mechanisms and facilitating the development of targeted interventions against MRSA infections.

UV-vis spectroscopy of the coupling products of the palladium-catalyzed C-H arylation of the BODIPY core.

The steady-state, UV-vis electronic absorption and fluorescence emission properties of a large set of 3-aryl and 3,5-diaryl substituted difluoroboron dipyrromethene dyes obtained via direct, palladium-catalyzed C-H (het)arylation of the BODIPY core are reported. The spectra display the narrow absorption and fluorescence emission bands and the generally quite small Stokes shifts characteristic of classic difluoroboron dipyrrins. As a function of the solvent, the spectral maxima are located within a very narrow wavelength range and are slightly red-shifted with increasing solvent polarizability, which is shown to be the crucial parameter influencing the wavelength position of the maxima. The extended π-conjugation in the 3,5-diaryl products always leads to bathochromically shifted absorption and emission spectra compared to those of the 3-aryl analogues. The derivative with a 3-mesityl substituent has blue-shifted spectra in comparison to its 3-phenyl substituted analogue, reflecting the diminished π-conjugation in the former due to steric strain. The nature of the meso-aryl has only a small effect on the spectral positions but affects the fluorescence quantum yield Φ. The majority of the dyes have high Φ (>0.85), except the compounds with meso-phenyl and meso-(p-nitrophenyl) substituents. Quantum-chemical calculations were performed to evaluate the differences in spectroscopic properties upon substitution of the BODIPY core and to compare them with the corresponding experimental results.

Synthesis and in vitro evaluation of a PDT active BODIPY-NLS conjugate.

Two new photosensitizers based on the BODIPY scaffold have been synthesized, of which one bears an NLS peptide, which is linked to the BODIPY's core using the copper catalysed azide-alkyne click reaction. The phototoxicities of these BODIPY based photosensitizers have been determined, as well as their dark toxicities. Although the conjugation of a single NLS peptide to the BODIPY did not lead to any observable nuclear localization, the photosensitizer did exhibit a superior photoxicity. Cellular co-localization experiments revealed a localization of both dyes in the lysosomes, as well as a partial localization within the ER (for the peptide-bearing BODIPY).

Fluorescent indicators based on BODIPY.

This critical review covers the advances made using the 4-bora-3a,4a-diaza-s-indacene (BODIPY) scaffold as a fluorophore in the design, synthesis and application of fluorescent indicators for pH, metal ions, anions, biomolecules, reactive oxygen species, reactive nitrogen species, redox potential, chemical reactions and various physical phenomena. The sections of the review describing the criteria for rational design of fluorescent indicators and the mathematical expressions for analyzing spectrophotometric and fluorometric titrations are applicable to all fluorescent probes (206 references).

Trifunctional Linkers Enable Improved Visualization of Actin by Expansion Microscopy.

Expansion microscopy (ExM) revolutionized the field of super-resolution microscopy by allowing for subdiffraction resolution fluorescence imaging on standard fluorescence microscopes. However, it has been found that it is hard to visualize actin filaments efficiently using ExM. To improve actin imaging, multifunctional molecules have been designed with moderate success. Here, we present optimized methods for phalloidin conjugate grafting that have a high efficiency for both cellular and tissue samples. Our optimized strategy improves anchoring and signal retention by ∼10 times. We demonstrate the potential of optimized trifunctional linkers (TRITON) for actin imaging in combination with immunolabeling using different ExM protocols. 10X ExM of actin labeled with optimized TRITON enabled us to visualize the periodicity of actin rings in cultured hippocampal neurons and brain slices by Airyscan confocal microscopy. Thus, TRITON linkers provide an efficient grafting method, especially in cases in which the concentration of target-bound monomers is insufficient for high-quality ExM.

Visible absorption and fluorescence spectroscopy of conformationally constrained, annulated BODIPY dyes.

Six conformationally restricted BODIPY dyes with fused carbocycles were synthesized to study the effect of conformational mobility on their visible electronic absorption and fluorescence properties. The symmetrically disubstituted compounds (2, 6) have bathochromically shifted absorption and fluorescence spectral maxima compared to those of the respective asymmetrically monosubstituted dyes (1, 5). Fusion of conjugation extending rings to the α,ß-positions of the BODIPY core is an especially effective method for the construction of boron dipyrromethene dyes absorbing and emitting at longer wavelengths. The fluorescence quantum yields Φ of dyes 1-6 are high (0.7 ≤ Φ ≤ 1.0). The experimental results are backed up by quantum chemical calculations of the lowest electronic excitations in 1, 2, 5, 6, and corresponding dyes of related chemical structure but without conformational restriction. The effect of the molecular structure on the visible absorption and fluorescence emission properties of 1-6 has been examined as a function of solvent by means of the recent, generalized treatment of the solvent effect, proposed by Catalán (J. Phys. Chem. B 2009, 113, 5951-5960). Solvent polarizability is the primary factor responsible for the small solvent-dependent shifts of the visible absorption and fluorescence emission bands of these dyes.

Oligo(p-phenylene ethynylene)-BODIPY derivatives: synthesis, energy transfer, and quantum-chemical calculations.

The synthesis and energy-transfer properties of a series of oligo(p-phenylene ethynylene)-BODIPY (OPEB) cassettes are reported. A series of oligo(p-phenylene ethynylene)s (OPEs) with different conjugated chain lengths as energy donor subunit in the energy-transfer system were capped at both ends with BODIPY chromophores as energy-acceptor subunits. The effect of the conjugated chain of OPEs on energy transfer in the OPEB cassettes was investigated by UV/Vis and fluorescence spectroscopy and modeling. With increasing number n of phenyl acetylene units (n=1-7), the absorption and emission maxima of OPEn are bathochromically shifted. In the OPEBn analogues, the absorption maximum assigned to the BODIPY moieties is independent of the length of the OPE spacer. However, the relative absorption intensity of the BODIPY band decreases when the number of phenyl acetylene units is increased. The emission spectra of OPEBn are dominated by a band peaking at 613 nm, corresponding to emission of the BODIPY moieties, regardless of whether excitation is at 420 or 550 nm. Furthermore, a very small band is observed with a maximum between 450 and 500 nm, and its intensity relative to that of the BODIPY emission increases with increasing n, that is, the excited state of OPE subunits is efficiently quenched in OPEBn by energy transfer to the BODIPY moieties. Energy transfer (ET) from OPEn to BODIPY in OPEBn is very efficient (all Φ(ET) values are greater than 98 %) and only slightly decreases with increasing length of the OPE units. These results are supported by theoretical studies that show very high energy transfer efficiency (Φ(ET) >75 %) from the OPE spacer to the BODIPY end-groups for chains with up to 15-20 units.

1,7-Disubstituted boron dipyrromethene (BODIPY) dyes: synthesis and spectroscopic properties.

1,7-Dihalogenated boron dipyrromethene dyes were successfully synthesized and substituted, thus providing an entry to the final, elusive reactivity pattern. The spectroscopic properties of 1,7-disubstituted BODIPY dyes were studied and are discussed as a function of their structure.

Evaluation of Direct Grafting Strategies via Trivalent Anchoring for Enabling Lipid Membrane and Cytoskeleton Staining in Expansion Microscopy.

Super-resolution fluorescence microscopy is a key tool in the elucidation of biological fine structures, providing insights into the distribution and interactions of biomolecular complexes down to the nanometer scale. Expansion microscopy is a recently developed approach for achieving nanoscale resolution on a conventional microscope. Here, biological samples are embedded in an isotropically swollen hydrogel. This physical expansion of the sample allows imaging with resolutions down to the tens-of-nanometers. However, because of the requirement that fluorescent labels are covalently bound to the hydrogel, standard, small-molecule targeting of fluorophores has proven incompatible with expansion microscopy. Here, we show a chemical linking approach that enables direct, covalent grafting of a targeting molecule and fluorophore to the hydrogel in expansion microscopy. We show application of this series of molecules in the antibody-free targeting of the cell cytoskeleton and in an example of lipid membrane staining for expansion microscopy. Furthermore, using this trivalent linker strategy, we demonstrate the benefit of introducing fluorescent labels post-expansion by visualizing an immunostaining through fluorescent oligonucleotide hybridization after expanding the polymer. Our probes allow different labeling approaches that are compatible with expansion microscopy.

Fluorescent SAM analogues for methyltransferase based DNA labeling.

In this work, the preparation of new S-adenosyl-l-methionine (SAM) analogues for sequence specific DNA labeling is evaluated. These non-natural analogues, comprising cysteine rather than the natural homolog, were obtained in near quantitative conversions from readily available starting materials without relying on using an excess amount of labor intensive molecules. The synthetic strategy was used to generate fluorescent cofactors, with colours spanning the whole visible spectrum, and their applicability in methyltransferase based optical mapping is shown.

Synthesis, spectroscopy, crystal structure, electrochemistry, and quantum chemical and molecular dynamics calculations of a 3-anilino difluoroboron dipyrromethene dye.

An asymmetrically substituted fluorescent difluoroboron dipyrromethene (BODIPY) dye, with a phenylamino group at the 3-position of the BODIPY chromophore, has been synthesized by nucleophilic substitution of 3,5-dichloro-8-(4-tolyl)-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene. The solvent-dependent spectroscopic and photophysical properties have been investigated by means of UV-vis spectrophotometry and steady-state and time-resolved fluorometry and reflect the large effect of the anilino substituent on the fluorescence characteristics. The compound has a low fluorescence quantum yield in all but the apolar solvents cyclohexane, toluene, and chloroform. Its emission maxima in a series of solvents from cyclohexane to methanol are red-shifted by approximately 50 nm in comparison to classic BODIPY derivatives. Its oxidation potential in dichloromethane is at ca. 1.14 V versus Ag/AgCl. The absorption bandwidths and Stokes shifts are much larger than those of typical, symmetric difluoroboron dipyrromethene dyes. The values of the fluorescence rate constant are in the (1.4-1.7) x 10(8) s(-1) range and do not vary much between the solvents studied. X-ray diffraction analysis shows that the BODIPY core is planar. Molecular dynamics simulations show that there is no clear indication for aggregates in solution.