Amino(oligo)thiophene-based environmentally sensitive biomembrane chromophores

There is a growing need for cellular imaging with fluorescent probes that emit at longer wavelengths to minimize the effects of absorption, autofluorescence, and scattering from biological tissue. In this paper a series of new environmentally sensitive hemicyanine dyes featuring amino(oligo)thiophene donors have been synthesized via aldol condensation between a 4-methylpyridinium salt and various amino(oligo)thiophene carboxaldehydes, which were, in turn, obtained from amination of bromo(oligo)thiophene carboxaldehyde. Side chains on these fluorophores impart a strong affinity for biological membranes. Compared with benzene analogues, these thiophene fluorophores show significant red shift in the absorption and emission spectra, offering compact red and near-infrared emitting fluorophores. More importantly, both the fluorescence quantum yields and the emission peaks are very sensitive to various environmental factors such as solvent polarity or viscosity, membrane potential, and membrane composition. These chromophores also exhibit strong nonlinear optical properties, including two-photon fluorescence and second harmonic generation, which are themselves environmentally sensitive. The combination of long wavelength fluorescence and nonlinear optical properties make these chromophores very suitable for applications that require sensing or imaging deep inside tissues.     

Live-cell-permeant thiophene fluorophores and cell-mediated formation of fluorescent fibrils

In our search for thiophene fluorophores that can overcome the limits of currently available organic dyes in live-cell staining, we synthesized biocompatible dithienothiophene-S,S-dioxide derivatives (DTTOs) that were spontaneously taken up by live mouse embryonic fibroblasts and HeLa cells. Upon treatment with DTTOs, the cells secreted nanostructured fluorescent fibrils, while cell viability remained unaltered. Comparison with the behavior of other cell-permeant, newly synthesized thiophene fluorophores showed that the formation of fluorescent fibrils was peculiar to DTTO dyes. Laser scanning confocal microscopy of the fluorescent fibrils showed that most of them were characterized by helical supramolecular organization. Electrophoretic analysis and theoretical calculations suggested that the DTTOs were selectively recognized by the HyPro component of procollagen polypeptide chains and incorporated through the formation of multiple H-bondings.     

Novel fluorophores: efficient synthesis and photophysical study

[structure: see text] We have synthesized novel fluorophores by using Sonogashira reactions of 1,4-bis(dibromovinyl)benzene and 2,5-bis(dibromovinyl)thiophene with various aromatic bromides. The emission maxima of these fluorophores vary from the indigo blue to the reddish-orange region, depending on the structures of aromatic nuclei and peripheral moieties.     

Excited-State Intramolecular Proton Transfer Dyes with Dual-State Emission Properties: Concept,Examples and Applications

Dual-state emissive (DSE) fluorophores are organic dyes displaying fluorescence emission both in dilute and concentrated solution and in the solid-state, as amorphous, single crystal, polycrystalline samples or thin films. This comes in contrast to the vast majority of organic fluorescent dyes which typically show intense fluorescence in solution but are quenched in concentrated media and in the solid-state owing to π-stacking interactions; a well-known phenomenon called aggregation-caused quenching (ACQ). On the contrary, molecular rotors with a significant number of free rotations have been engineered to show quenched emission in solution but strong fluorescence in the aggregated-state thanks to restriction of the intramolecular motions. This is the concept of aggregation-induced emission (AIE). DSE fluorophores have been far less explored despite the fact that they are at the crossroad of ACQ and AIE phenomena and allow targeting applications both in solution (bio-conjugation, sensing, imaging) and solid-state (organic electronics, data encryption, lasing, luminescent displays). Excited-State Intramolecular Proton Transfer (ESIPT) fluorescence is particularly suitable to engineer DSE dyes. Indeed, ESIPT fluorescence, which relies on a phototautomerism between normal and tautomeric species, is characterized by a strong emission in the solid-state along with a large Stokes’ shift, an enhanced photostability and a strong sensitivity to the close environment, a feature prone to be used in bio-sensing. A drawback that needs to be overcome is their weak emission intensity in solution, owing to detrimental molecular motions in the excited-state. Several strategies have been proposed in that regard. In the past few years, a growing number of examples of DSE-ESIPT dyes have indeed emerged in the literature, enriching the database of such attractive dyes. This review aims at a brief but concise overview on the exploitation of ESIPT luminescence for the optimization of DSE dyes properties. In that perspective, a synergistic approach between organic synthesis, fluorescence spectroscopy and ab initio calculations has proven to be an efficient tool for the construction and optimization of DSE-ESIPT fluorophores.     

Hybrid Rhodamine Fluorophores in the Visible/NIR Region for Biological Imaging

Fluorophores and probes are invaluable for the visualization of the location and dynamics of gene expression, protein expression, and molecular interactions in complex living systems. Rhodamine dyes are often used as scaffolds in biological labeling and turn‐on fluorescence imaging. To date, their absorption and emission spectra have been expanded to cover the entire near‐infrared region (650–950 nm), which provides a more suitable optical window for monitoring biomolecular production, trafficking, and localization in real time. This review summarizes the development of rhodamine fluorophores since their discovery and provides strategies for modulating their absorption and emission spectra to generate specific bathochromic‐shifts. We also explain how larger Stokes shifts and dual‐emissions can be obtained from hybrid rhodamine dyes. These hybrid fluorophores can be classified into various categories based on structural features including the alkylation of amidogens, the substitution of the O atom of xanthene, and hybridization with other fluorophores.     

A General Strategy Toward pH-Resistant Phenolic Fluorophores for High-Fidelity Sensing and Bioimaging Applications

Aryl alcohol-type or phenolic fluorophores offer diverse opportunities for developing bioimaging agents and fluorescence probes. Due to the inherently acidic hydroxyl functionality, phenolic fluorophores provide pH-dependent emission signals. Therefore, except for developing pH probes, the pH-dependent nature of phenolic fluorophores should be considered in bioimaging applications but has been neglected. Here we show that a simple structural remedy converts conventional phenolic fluorophores into pH-resistant derivatives, which also offer “medium-resistant” emission properties. The structural modification involves a single-step introduction of a hydrogen-bonding acceptor such as morpholine nearby the phenolic hydroxyl group, which also leads to emission bathochromic shift, increased Stokes shift, enhanced photo-stability and stronger emission for several dyes. The strategy greatly expands the current fluorophores’ repertoire for reliable bioimaging applications, as demonstrated here with ratiometric imaging of cells and tissues.     

Impact of Heteroatom Substitution on Dual-State Emissive Rigidified 2-(2’-hydroxyphenyl)benzazole Dyes: Towards Ultra-Bright ESIPT Fluorophores**

2-(2’-Hydroxyphenyl)benzazole (HBX) fluorophores are well-known excited-state intramolecular proton transfer (ESIPT) emitters largely studied for their synthetic versatility, photostability, strong solid-state fluorescence and ability to engineer dual emission, thus paving the way to applications as white emitters, ratiometric sensors, and cryptographic dyes. However, they are heavily quenched in solution, due to efficient non-radiative pathways taking place as a consequence of the proton transfer in the excited-state. In this contribution, the nature of the heteroring constitutive of these rigidified HBX dyes was modified and we demonstrate that this simple structural modification triggers major optical changes in terms of emission color, dual emission engineering, and importantly, fluorescent quantum yield. Investigation of the photophysical properties in solution and in the solid state of a series of ethynyl-TIPS extended HBX fluorophores, along with ab initio calculations demonstrate the very promising abilities of these dyes to act as bright dual-state emitters, in both solution (even in protic environments) and solid state.     

Oligonucleotide-stabilized Ag nanocluster fluorophores

Single-stranded oligonucleotides stabilize highly fluorescent Ag nanoclusters, with emission colors tunable via DNA sequence. We utilized DNA microarrays to optimize these scaffold sequences for creating nearly spectrally pure Ag nanocluster fluorophores that are highly photostable and exhibit great buffer stability. Five different nanocluster emitters have been created with tunable emission from the blue to the near-IR and excellent photophysical properties. Ensemble and single molecule fluorescence studies show that oligonucleotide encapsulated Ag nanoclusters exhibit significantly greater photostability and higher emission rates than commonly used cyanine dyes.     

Preparation of Fluorescence Tunable Polymer Nanoparticles by One-step Mini-emulsion

Fluorescence tunable polymer nanoparticles were prepared by incorporating two hydrophobic fluorescent dyes (9, 10-diphenylanthracene: DPA and nitrobenzoxadiazolyl: NBD) into polymethylmethacrylate (PMMA) nanoparticles via one-step mini-emulsion polymerization method. The prepared fluorescent nanoparticles exhibit the spectral properties of both DPA and NBD dye, indicating that the two fluorophores have been incorporated into the nanoparticles. The nanoparticles greatly enhance the fluorescence emission of the two hydrophobic dyes in aqueous media probably by providing good protection of the dye molecules in the polymer nanoparticles matrix. Moreover, by varying the doping ratio of the two hydrophobic dyes, the polymer nanoparticles exhibit tunable and distinguishable emission characteristics under a single wavelength excitation via occuring fluorescence resonance energy transfer (FRET).     

Synthesis of fluorescent rhodamine dyes using an extension of the Heck reaction

Both benzo[b]thiophene and indole containing rhodamine dyes were synthesized according to a new pathway requiring a Heck-type coupling and a Pictet-Spengler reaction. The electron-rich indolic dye was shown to have noteworthy absorption and emission maximum.     

Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates

Fluorescence detection and imaging are vital technologies in the life sciences and clinical diagnostics. The key to obtaining high-resolution images and sensitive detection is to use fluorescent molecules or particles that absorb and emit visible light with high efficiency. We have synthesized supramolecular complexes consisting of a branched DNA template and fluorogenic intercalating dyes. Because dyes can intercalate up to every other base pair, high densities of fluorophores are assembled yet the DNA template keeps them far enough away from each other to prevent self-quenching. The efficiency with which these noncovalent assemblies absorb light is more than 10-fold greater than that of the individual dye molecules. F?rster resonance energy transfer from the intercalated dyes to covalently attached acceptor dyes is very efficient, allowing for wavelength shifting of the emission spectrum. Simple biotinylation of the DNA template allows for labeling of streptavidin-coated synthetic microspheres and mouse T-cells.     

Bright,Color-Tunable Fluorescent Dyes in the Vis/NIR Region: Establishment of New “Tailor-Made” Multicolor Fluorophores Based on Borondipyrromethene

A new series of high-performance fluorophores named Keio Fluors (KFL), which are based on borondipyrromethene (BODIPY), are reported. The KFL dyes cover a wide spectral range from the yellow (547 nm) to the near-infrared (NIR, 738 nm) region, and their emission wavelength could be easily and subtly controlled based on simple molecular modifications only, without losing their optical properties. This “tailor-made” synthetic strategy for tuning the emission wavelength enabled the creation of fourteen KFL dyes with well-controlled emission colors (yellow, orange, red, far-red, and NIR). Moreover, these KFL dyes also retain their excellent optical properties, such as spectral bands sharper than quantum dots, high extinction coefficients (140 000–316 000 M ⁻¹ cm⁻¹), and high quantum yields (0.56–0.98), without any critical solvent polarity dependent decrease of their brightness. These advantageous characteristics make the KFL dyes potentially useful as new candidates of fluorescent standard dyes to substitute or to complement existing long-wavelength fluorescent dyes, such as cyanines, oxazines, rhodamines, or other BODIPY dyes.     

Coumarin-based two-photon AIE fluorophores: Photophysical properties and biological application

Based on the coumarin skeleton, we deliberately designed two groups of fluorophores, termed as Coum-R and Naph-Coum-R, using the diphenylamino group as the electron donor, which displayed long-wavelength emissions (red spectral region), large Stokes shift (up to 204 nm), superior AIE performance, and large two-photon absorbance cross-sections (as high as 365 GM). The electron-withdrawing substituents at the 3-position of these dyes could induce a significant red-shift in their emission spectra. Preliminary imaging experiments demonstrated the capability of these dyes as two-photon fluorophores for specifically staining lipid droplets in living cells.     

Large Stokes shift fluorescent dyes based on a highly substituted terephthalic acid core

The synthesis of dyes based on a highly substituted terephthalic acid core is described, starting from readily available 2,5-dihydroxy-terephthalic acid diethyl ester. The dyes are highly colored, soluble in organic solvents and reasonably fluorescent in solution and in the solid state. The maxima for absorption and emission are around 402 and 502 nm, respectively. The fluorophores are readily cyclized to generate compounds which comprise the basic 6,13-dihydroxy-chromeno[2,3-b]xanthene-7,14-dione unit. These new derivatives are nonfluorescent.     

A structural remedy toward bright dipolar fluorophores in aqueous media

The donor–acceptor (D–A) type dipolar fluorophores, an important class of luminescent dyes with two-photon absorption behaviour, generally emit strongly in organic solvents but poorly in aqueous media. To understand and enhance the poor emission behaviour of dipolar dyes in aqueous media, we undertake a rational approach that includes a systematic structure variation of the donor, amino substituent of acedan, an important two-photon dye. We identify several factors that influence the emission behaviour of the dipolar dyes in aqueous media through computational and photophysical studies on new acedan derivatives. As a result, we can make acedan dyes emit bright fluorescence under one- and two-photon excitation in aqueous media by suppressing the liable factors for poor emission: 1,3-allylic strain, rotational freedom, and hydrogen bonding with water. We also validate that these findings can be generally extended to other dipolar fluorophores, as demonstrated for naphthalimide, coumarin and (4-nitro-2,1,3-benzoxadiazol-7-yl)amine (NBD) dyes. The new acedan and naphthalimide dyes thus allow us to obtain much brighter two-photon fluorescent images in cells and tissues than in their conventional forms. As an application of these findings, a thiol probe is synthesized based on a new naphthalimide dye, which shows greatly enhanced fluorescence from the widely used N,N-dimethyl analogue. The results disclosed here provide essential guidelines for the development of efficient dipolar dyes and fluorescence probes for studying biological systems, particularly by two-photon microscopy.     

Distyryl-boradiazaindacenes: facile synthesis of novel near IR emitting fluorophores

Boradiazaindacenes with methyl substituents at 3 and 5 positions were for the first time shown to undergo efficient double condensation reactions with an aromatic aldehyde yielding a series of extended conjugation dyes. These new fluorophores have absorption maxima in the range of 650-660 nm. The dyes reported here have large quantum yields with 20 nm Stokes' shifted emission peaks. The straightforward synthesis of such red shifted BODIPY derivatives is important in relation to the synthesis of novel and useful fluorescent chemosensors. In addition, this facile transformation may make these new fluorophores' building blocks in the construction of large functional supramolecular systems.     

Synthesis and evaluation of self-calibrating ratiometric viscosity sensors

We describe the design, synthesis and fluorescent profile of a family of self-calibrating dyes that provide ratiometric measurements of fluid viscosity. The design is based on covalently linking a primary fluorophore (reference) that displays a viscosity-independent fluorescence emission with a secondary fluorophore (sensor) that exhibits a viscosity-sensitive fluorescence emission. Characterization of fluorescent properties was made with separate excitation of the units and through Resonance Energy Transfer from the reference to the sensor dye. The chemical structures of both fluorophores and the linker length have been evaluated in order to optimize the overall brightness and sensitivity of the viscosity measurements. We also present an application of such ratiometric dyes for the detection of membrane viscosity changes in a liposome model.     

Synthesis and spectroscopic properties of ring-fused thiophene bridged push–pull dyes and their application in dye-sensitized solar cells

Bisdimethylfluorenylamino-based push–pull dyes bearing one or two benzo[c]thiophene and its precursor bicyclo[2.2.2]octadiene (BCOD) fused thiophene as π bridge have been synthesized. The effect of fused-ring on thiophene bridge for the spectroscopic and electrochemical properties of these dyes has been investigated. Dye-sensitized solar cells fabricated with these dyes show moderate photovoltaic properties.     

Photophysical properties of acene DCDHF fluorophores: long-wavelength single-molecule emitters designed for cellular imaging

We report the solvatochromic, viscosity-sensitive, and single-molecule photophysics of the fluorophores DCDHF-N-6 and DCDHF-A-6. These molecules are members of the dicyanomethylenedihydrofuran (DCDHF) class of single-molecule emitters that contain an amine electron donor and a DCDHF acceptor linked by a conjugated unit; DCDHF-N-6 and DCDHF-A-6 have naphthalene- and anthracene-conjugated linkers, respectively. These molecules maintain the beneficial photophysics of the phenylene-linked DCDHF (i.e., photostability, emission wavelength dependence on solvent polarity, and quantum yield sensitivity to solvent viscosity), yet offer absorption and emission at longer wavelengths that are more appropriate for cellular imaging. We demonstrate that these new fluorophores are less photolabile in an aqueous environment than several other commonly used dyes (rhodamine 6G, Texas Red, and fluorescein). Finally, we image single copies of the acene DCDHFs diffusing in the plasma membrane of living cells.     

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.