Zero-Overlap Fluorophores for Fluorescent Studies at Any Concentration

Robust visualization of membrane protein by aptamer mediated proximity ligation assay and Förster resonance energy transfer

In situ cell imaging plays a crucial role in studying physiological and pathological processes of cells. Proximity ligation assay (PLA) and rolling circle amplification (RCA) are commonly used to study the abundance and interactions of biological macromolecules. The most frequently applied strategy to visualize the RCA products is with single-fluorophore probe, however, cellular auto-fluorescence and unbound fluorescent probes could interfere with RCA products, leading to non-specific signals. Here, we present a novel approach combining aptamer mediated PLA, RCA, and Förster Resonance Energy Transfer (FRET), namely Apt-PLA-RCA-FRET, for sensitive in situ imaging and analysis of the abundances and interactions of membrane proteins such as tetraspanin CD63 and human epidermal growth factor receptor 2 (HER2). Apt-RCA-FRET was initially designed to show its ability to assess the abundance of target proteins on different cells. Dual functional oligonucleotides served as both the aptamer for recognizing specific membrane proteins and the primer of circular DNA for following RCA process, and the resulting RCA products were subsequently imaged by FRET signals from Cy3 to Cy5 probes which hybridized sequentially on them. FRET was demonstrated to show its great potential to resist the interferences of nonspecific fluorescence compared to single-fluorophore strategies. PLA was then introduced to Apt-RCA-FRET to investigate the spatial localization of different proteins on cell membrane and their interactions. Our approach utilizing aptamer as membrane proteins recognition element simply converted the abundance of proteins into nucleic acid signals and facilitated the following signal amplification, thus it serves as an important alternative to methods typically based on antibody and presents a more robust and sensitive method for analyzing the abundances of different cell membrane proteins and their spatial localization, which offers valuable insights into physiological and pathological processes of cells.

Multicomponent synthesis of stereogenic-at-boron fluorophores (BOSPYR) from boronic acids, salicylaldehydes, and 2-formylpyrrole hydrazones

This work describes one-step syntheses of various stereogenic-at-boron fluorochromes (BOSPYR) via multicomponent reactions involving readily accessible boronic acids, salicylaldehydes, and 2-formylpyrrole hydrazones. The dyes absorb and emit in the visible region of the electromagnetic radiation, and are characterized by large Stokes shifts (2850-4930 cm-1) with weak fluorescence emissions (Φfl: 1.5-9.1%). Notably, the dimmed fluorescence of BOSPYRs recovers upon transition to viscous media (21-fold for 1a). The representative compound 1a exhibits clear Cotton effects with dissymmetry factors of ca. |gabs| ∼ 1.9 × 10-3 in the visible region, indicating efficient asymmetry induction to the chromophore. The X-ray molecular structure of 1a shows that the chromophore deviates from planarity by 17.2°, which may contribute significantly to the inherent chirality of the fluorophore. A computational examination of excited states by time-dependent density functional theory (TD-DFT) identifies the emission mechanism as arising from a locally-excited (LE) state.

Macrocyclic Bridgehead Fluorophores, Pyrrolyl-diazabicyclo[8.3.1]tetradecadienones, with Giant Stokes Shifts

A previously unknown class of fluorophores was discovered, which represents 14-membered bridgehead heterocycles, pyrrolyl-diazabicyclo[8.3.1]tetradecadienones, herein referred to as PY-14-ONEs. The new fluorophores are characterized by giant Stokes shifts of ∼8000-10,250 cm-1 and virtually zero overlap of the absorption and emission bands. They exhibit fluorescence maxima in the blue-green region (454 ≤ λem ≤ 513 nm, MeCN), which shift to the red side when converted to their water-soluble salts by alkylation with MeI (478 ≤ λem ≤ 516 nm, water). PY-14-ONEs were obtained by an original synthesis from DBU, 1,8-diazabicyclo[5.4.0]undec-7-ene, which reacts with acylethynylpyrroles without catalysts under mild conditions to afford PY-14-ONEs in a 34-58% yield. The reaction represents a ring expansion of DBU. Since acylethynylpyrroles are readily available, the discovered reaction opens promising possibilities for the development of new fluorophores. The results of our time-dependent DFT calculations indicate that the pyrrole ring in PY-14-ONEs plays an important role in the formation of the Stokes shifts, which can be further enhanced by attaching appropriate substituents to it, capable of creating in S1 an extended conjugated system and causing a substantial alternation of the molecular structure via its planarization.

Urea-fused and π-extended single-benzene fluorophores with ultralarge Stokes shifts

The excited-state tautomer equilibrium of the urea-fused single-benzene fluorophore was synthetically modulated to produce exceptionally large Stokes shifts (>12 400 cm-1). The key N-H⋯N hydrogen bonding motif utilizes an endogenous proton for long-wavelength emission or an exogenous proton for acid-base chemistry, the balance of which is exploited for fluorescence switching in the solid state.

Cy5 Dye Cassettes Exhibit Through-Bond Energy Transfer and Enable Ratiometric Fluorescence Sensing

The chemosensor literature contains many reports of fluorescence sensing using polyaromatic hydrocarbon fluorophores such as pyrene, tetraphenylethylene, or polyaryl(ethynylene), where the fluorophore is excited with ultraviolet light (<400 nm) and emits in the visible region of 400-500 nm. There is a need for general methods that convert these "turn-on" hydrocarbon fluorescent sensors into ratiometric sensing paradigms. One simple strategy is to mix the responsive hydrocarbon sensor with a second non-responsive dye that is excited by ultraviolet light but emits at a distinctly longer wavelength and thus acts as a reference signal. Five new cyanine dye cassettes were created by covalently attaching a pyrene, tetraphenylethylene, or biphenyl(ethynylene) component as the ultraviolet-absorbing energy donor directly to the pentamethine chain of a deep-red cyanine (Cy5) energy acceptor. Fluorescence emission studies showed that these Cy5-cassettes exhibited large pseudo-Stokes shifts and high through-bond energy transfer efficiencies upon excitation with ultraviolet light. Practical potential was demonstrated with two examples of ratiometric fluorescence sensing using a single ultraviolet excitation wavelength. One example mixed a Cy5-cassette with a pyrene-based fluorescent indicator that responded to changes in Cu2+ concentration, and the other example mixed a Cy5-cassette with the fluorescent pH sensing dye, pyranine.

Solvent Acts as the Referee in a Match-Up Between Charged and Preorganized Receptors

The prevalence of anion-cation contacts in biomolecular recognition under aqueous conditions suggests that ionic interactions should dominate the binding of anions in solvents across both high and low polarities. Investigations of this idea using titrations in low polarity solvents are impaired by interferences from ion pairing that prevent a clear picture of binding. To address this limitation and test the impact of ion-ion interactions across multiple solvents, we quantified chloride binding to a cationic receptor after accounting for ion pairing. In these studies, we created a chelate receptor using aryl-triazole CH donors and a quinolinium unit that directs its cationic methyl inside the binding pocket. In low-polarity dichloromethane, the 1 : 1 complex (log K1 : 1 ~ 7.3) is more stable than neutral chelates, but fortuitously comparable to a preorganized macrocycle (log K1 : 1 ~ 6.9). Polar acetonitrile and DMSO diminish stabilities of the charged receptor (log K1 : 1 ~ 3.7 and 1.9) but surprisingly 100-fold more than the macrocycle. While both receptors lose stability by dielectric screening of electrostatic stability, the cationic receptor also pays additional costs of organization. Thus even though the charged receptor has stronger binding in apolar solvents, the uncharged receptor has more anion affinity in polar solvents.

Non-adiabatic dynamics simulations of the S1 excited-state relaxation of diacetyl phenylenediamine

The small molecule built around the benzene ring, diacetyl phenylenediamine (DAPA), has attracted much attention due to its synthesis accessibility, large Stokes shift, etc. However, its meta structure m-DAPA does not fluoresce. In a previous investigation, it was found that such a property is due to the fact that it undergoes an energy-reasonable double proton transfer conical intersection during the deactivation of the S₁ excited-state, then returns to the ground state by a nonradiative relaxation process eventually. However, our static electronic structure calculations and non-adiabatic dynamics analysis results indicate that only one reasonable non-adiabatic deactivation channel exists: after being excited to the S₁ state, m-DAPA undergoes an ultrafast and barrierless ESIPT process and reaches the single-proton-transfer conical intersection. Subsequently, the system either returns to the keto-form S₀ state minimum with proton reversion or returns to the single-proton-transfer S₀ minimum after undergoing a slight twist of the acetyl group. The dynamics results show that the S₁ excited-state lifetime of m-DAPA is 139 fs. In other words, we propose an efficient single-proton-transfer non-adiabatic deactivation channel of m-DAPA that is different from previous work, which can provide important mechanistic information of similar fluorescent materials.

Orthogonal, modular anion-cation and cation-anion self-assembly using pre-programmed anion binding sites

Subcomponent self-assembly relies on cation coordination whereas the roles of anions often only emerge during the assembly process. When sites for anions are instead pre-programmed, they have the potential to be used as orthogonal elements to build up structure in a predictable and modular way. We explore this idea by combining cation (M⁺) and anion (X^-) binding sites together and show the orthogonal and modular build up of structure in a multi-ion assembly. Cation binding is based on a ligand (L) made by subcomponent metal-imine chemistry (M⁺ = Cu⁺, Au⁺) while the site for anion binding (X^- = BF₄ ^-, ClO₄ ^-) derives from the inner cavity of cyanostar (CS) macrocycles. The two sites are connected by imine condensation between a pyridyl-aldehyde and an aniline-modified cyanostar. The target assembly [LM-CS-X-CS-ML],⁺ generates two terminal metal complexation sites (LM and ML) with one central anion-bridging site (X) defined by cyanostar dimerization. We showcase modular assembly by isolating intermediates when the primary structure-directing ions are paired with weakly coordinating counter ions. Cation-directed (Cu⁺) or anion-bridged (BF₄ ^-) intermediates can be isolated along either cation-anion or anion-cation pathways. Different products can also be prepared in a modular way using Au⁺ and ClO₄ ^-. This is also the first use of gold(i) in subcomponent self-assembly. Pre-programmed cation and anion binding sites combine with judicious selection of spectator ions to provide modular noncovalent syntheses of multi-component architectures.

Packing-induced selectivity switching in molecular nanoparticle photocatalysts for hydrogen and hydrogen peroxide production

Molecular packing controls optoelectronic properties in organic molecular nanomaterials. Here we report a donor-acceptor organic molecule (2,6-bis(4-cyanophenyl)-4-(9-phenyl-9H-carbazol-3-yl)pyridine-3,5-dicarbonitrile) that exhibits two aggregate states in aqueous dispersions: amorphous nanospheres and ordered nanofibres with π-π molecular stacking. The nanofibres promote sacrificial photocatalytic H₂ production (31.85 mmol g^-1 h^-1) while the nanospheres produce hydrogen peroxide (H₂O₂) (3.20 mmol g^-1 h^-1 in the presence of O₂). This is the first example of an organic photocatalyst that can be directed to produce these two different solar fuels simply by changing the molecular packing. These different packings affect energy band levels, the extent of excited state delocalization, the excited state dynamics, charge transfer to O₂ and the light absorption profile. We use a combination of structural and photophysical measurements to understand how this influences photocatalytic selectivity. This illustrates the potential to achieve multiple photocatalytic functionalities with a single organic molecule by engineering nanomorphology and solid-state packing.

Photoactivatable Large Stokes Shift Fluorophores for Multicolor Nanoscopy

We designed caging-group-free photoactivatable live-cell permeant dyes with red fluorescence emission and ∼100 nm Stokes shifts based on a 1-vinyl-10-silaxanthone imine core structure. The proposed fluorophores undergo byproduct-free one- and two-photon activation, are suitable for multicolor fluorescence microscopy in fixed and living cells, and are compatible with super-resolution techniques such as STED (stimulated emission depletion) and PALM (photoactivated localization microscopy). Use of photoactivatable labels for strain-promoted tetrazine ligation and self-labeling protein tags (HaloTag, SNAP-tag), and duplexing of an imaging channel with another large Stokes shift dye have been demonstrated.

Fluorescent cyclophanes and their applications

With the serendipitous discovery of crown ethers by Pedersen more than half a century ago and the subsequent introduction of host-guest chemistry and supramolecular chemistry by Cram and Lehn, respectively, followed by the design and synthesis of wholly synthetic cyclophanes-in particular, fluorescent cyclophanes, having rich structural characteristics and functions-have been the focus of considerable research activity during the past few decades. Cyclophanes with remarkable emissive properties have been investigated continuously over the years and employed in numerous applications across the field of science and technology. In this Review, we feature the recent developments in the chemistry of fluorescent cyclophanes, along with their design and synthesis. Their host-guest chemistry and applications related to their structure and properties are highlighted.

Modeling Non-additive Effects in Neighboring Chemically Identical Fluorophores

Quantitative fluorescence analysis is often used to derive chemical properties, including stoichiometries, of biomolecular complexes. One fundamental underlying assumption in the analysis of fluorescence data─whether it be the determination of protein complex stoichiometry by super-resolution, or step-counting by photobleaching, or the determination of RNA counts in diffraction-limited spots in RNA fluorescence in situ hybridization (RNA-FISH) experiments─is that fluorophores behave identically and do not interact. However, recent experiments on fluorophore-labeled DNA origami structures such as fluorocubes have shed light on the nature of the interactions between identical fluorophores as these are brought closer together, thereby raising questions on the validity of the modeling assumption that fluorophores do not interact. Here, we analyze photon arrival data under pulsed illumination from fluorocubes where distances between dyes range from 2 to 10 nm. We discuss the implications of non-additivity of brightness on quantitative fluorescence analysis.

Acenaphthenoannulation Induced by the Dual Lewis Acidity of Alumina

We have discovered a dual (i. e., soft and hard) Lewis acidity of alumina that enables rapid one-pot π-extension through the activation of terminal alkynes followed by C-F activation. The tandem reaction introduces an acenaphthene fragment - an essential moiety of geodesic polyarenes. This reaction provides quick access to elusive non-alternant polyarenes such as π-extended buckybowls and helicenes through three-point annulation of the 1-(2-ethynyl-6-fluorophenyl)naphthalene moiety. The versatility of the developed method was demonstrated by the synthesis of unprecedented structural fragments of elusive geodesic graphene nanoribbons.

α-Cyanostilbene: A Multifunctional Spectral Engineering Motif

The remarkable photophysical phenomenon of aggregation-induced emission offers excellent strategies to obtain the molecular materials possessing unique spectral signatures such as high fluorescence intensity, excellent quantum yield, large Stokes shift...

Relief of excited-state antiaromaticity enables the smallest red emitter

It is commonly accepted that a large π-conjugated system is necessary to realize low-energy electronic transitions. Contrary to this prevailing notion, we present a new class of light-emitters utilizing a simple benzene core. Among different isomeric forms of diacetylphenylenediamine (DAPA), o- and p-DAPA are fluorescent, whereas m-DAPA is not. Remarkably, p-DAPA is the lightest (FW = 192) molecule displaying red emission. A systematic modification of the DAPA system allows the construction of a library of emitters covering the entire visible color spectrum. Theoretical analysis shows that their large Stokes shifts originate from the relief of excited-state antiaromaticity, rather than the typically assumed intramolecular charge transfer or proton transfer. A delicate interplay of the excited-state antiaromaticity and hydrogen bonding defines the photophysics of this new class of single benzene fluorophores. The formulated molecular design rules suggest that an extended π-conjugation is no longer a prerequisite for a long-wavelength light emission.

Conjugated Molecular Nanotubes

Molecular compounds with permanent tubular architectures displaying radial π-conjugation are exceedingly rare. Their radial and axial delocalization presents them with unique optical and electronic properties, such as remarkable tuning of their Stokes shifts, and redox switching between global and local aromaticity. Although these tubular compounds display large internal void spaces, these attributes have not been extensively explored, thus presenting future opportunities in the development of materials. By using cutting-edge synthetic methodologies to bend aromatic surfaces, large opportunities in synthesis, property discovery, and applications are expected in new members of this family of conjugated molecular nanotubes.

Radially Oriented [n]Cyclo-meta-phenylenes

Molecular compounds with zigzag carbon nanotube geometries are exceedingly rare. Here we report the synthesis and characterization of carbon-based nanotubes with zigzag geometry, best described as radially oriented [n]cyclo-meta-phenylenes, extending the tubularene family of compounds. By the incorporation of edge-sharing benzene rings into the tubularene's radial π-surface, we have uncovered the first step to give rise to the emergence of radial orbital distribution in zigzag nanorings.