Molecular engineering of torsional potentials in fluorogenic dyes via electronic substituent effects

Fluorogenic dyes such as thiazole orange (TO) and malachite green have been used in live cellular imaging due to their low quantum yield in solution but large fluorescence enhancements when bound to cellular nucleic acids or to a specific surface-expressed protein partner. Better understanding of the structure-property relationships that establish this fluorogenic behavior could benefit the design of improved dyes. In TO the fluorogenic properties are related to twisting of the dye, following electronic excitation in solution, from an emissive planar structure to a nonemissive twisted structure. Herein we develop a computational approach to identify electron acceptor/donor substitution patterns that impart desirable properties to the dye, such as inducing spectral shifts while maintaining an excited-state torsional surface that will lead to fluorogenic behavior. Additivity of substituent effects, on properties such as spectral shifts and excited-state torsional barriers, is tested and found to be sufficiently accurate that it can be used to identify promising dye candidates. Although additivity suggests an underlying linearity in the substituent effects, additional simplifications stemming from linearity could not be identified. The approach is tested on TO, considering seven different substituents at seven substitution positions, to identify fluorogenic dyes that will span a range of wavelengths. Additivity allows quantum chemical calculations on singly substituted molecules (49 molecules) to be used to make estimates for all substitution patterns (nearly 10(6) molecules).     

Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments

Fluoromodules are complexes formed upon the noncovalent binding of a fluorogenic dye to its cognate biomolecular partner, which significantly enhances the fluorescence quantum yield of the dye. Previously, several single-chain, variable fragment (scFv) antibodies were selected from a yeast cell surface-displayed library that activated fluorescence from a family of unsymmetrical cyanine dyes covering much of the visible and near-IR spectrum. The current work expands our repertoire of genetically encodable scFv-dye pairs by selecting and characterizing a group of scFvs that activate fluorogenic violet-absorbing, blue-fluorescing cyanine dyes, based on oxazole and thiazole heterocycles. The dye binds to both yeast cell surface-displayed and soluble scFvs with low nanomolar K(d) values. These dye-protein fluoromodules exhibit high quantum yields, approaching unity for the brightest system. The promiscuity of these scFvs with other fluorogenic cyanine dyes was also examined. Fluorescence microscopy demonstrates that the yeast cell surface-displayed scFvs can be used for multicolor imaging. The prevalence of 405 nm lasers on confocal imaging and flow cytometry systems make these new reagents potentially valuable for cell biological studies.     

Benzothiadiazole-based dyes that emit red light in solution,solid, and liquid state

In this paper, we report the preparation and red-light-emitting behavior of benzothiadiazole–tris(alkyloxy)phenylethene dyes. In solution, we observed an efficient red light emission with high fluorescence quantum yields (up to 0.78). With increase in solvent polarity, the emission bands shifted to longer wavelengths accompanied by a large Stokes shift of up to 152 nm. A moderate fluorescence quantum yield of 0.52 could be achieved even in the polar solvent dimethylformamide. Red light emission with good fluorescence quantum yields (up to 0.50) was also observed in the bulk solid, liquid, and film state.     

Azole-linked coumarin dyes as fluorescence probes of domain-forming polymers.

The binding of 7-aminocoumarins, substituted in the 3-position with heterocyclic benzimidazole or benzothiazole groups by domain-forming polymers in water has been studied. The acrylic polyelectrolyte, poly(methacrylic) acid (PMAA) was used as a solubilizing agent for coumarin dyes 6, 7, and 30 in water. The acid-base properties of these bound coumarin dyes were monitored spectroscopically on titration of aqueous solutions. Alterations in the fluorescence wavelength and intensity, quantum yields, lifetimes, and polarization are consistent with the preferential binding of the dyes in compact hydrophobic domains that form at a pH regime in which the polymer is in its protonated (uncharged) state. In this pH range (<4.0), coumarins 7 and 30 are bound as monocations, whereas coumarin 6 remains in its neutral form. Reduced quantum yields and lifetimes of fluorescence for cationic coumarins can be understood in terms of the imposition of a low-lying electron transfer state, an example of a twisted intramolecular charge transfer (TICT) intermediate. Effects of polymer microenvironment on the rate of TICT state decay (a reverse electron transfer) are observed. Coumarins of the azole type may find use as fluoroprobes of the microenvironments of proteins and other biological macromolecules and as agents for pH sensing.     

Dipolar 3-methoxychromones as bright and highly solvatochromic fluorescent dyes

Herein, three environment-sensitive (solvatochromic) fluorescent dyes presenting a strong electron acceptor 3-methoxychromone unit and varied electron donor 2-aryl were developed. All three dyes showed remarkable polarity-dependent shifts of the emission maximum, which increase with extension of the dye conjugation. For the 3-methoxychromone bearing a 7-(diethylamino)-9,9-dimethylfluoren-2-yl donor group the difference between the excited and the ground state dipole moments, estimated from the Lippert-Mataga expression, reached 20 D, which is among the largest reported for neutral dipolar fluorophores. Moreover, the new dyes are characterized by significant two-photon absorption cross-section (up to 450 GM) and large fluorescence quantum yields. The strong decrease in the fluorescence quantum yields of the dyes in polar protic solvents was observed together with the increase in the non-radiative deactivation rates, which can originate from twisted intramolecular charge transfer and intermolecular proton transfer phenomena. In comparison to the parent 3-hydroxychromone derivatives, the new dyes presented significantly improved photostability, which confirms that photodegradation of 3-hydroxychromones occurs from a product of the excited-state intramolecular proton transfer (phototautomer). Finally, an application of the new dyes for probing local binding site polarity of serum albumin was shown. This new class of fluorescent dyes may serve as attractive building blocks for future molecular sensors utilizing environment-sensitive fluorophores.     

Effect of viscosity on the singlet-excited state dynamics of some hemicyanine dyes

Photophysical properties of hemicyanine dyes (1 - 3) were investigated in solvents of varying polarity and viscosity. Hemicyanines possess relatively low fluorescence quantum yields (1%) in polar solvents. A significant increase in fluorescence quantum yield and lifetimes was observed with increase in viscosity of the solvent medium. The radiative, as well as nonradiative decay channels from the singlet-excited state were investigated by varying the viscosity of the medium. The viscosity-dependent radiationless relaxation observed in hemicyanine dyes is suggestive of a restricted rotor motion in the singlet excited state.     

Emission characteristics of laser dyes C1 and Rh6G in cross-linked polyvinyl alcohol solutions

The lifetimes and the relative quantum yields for fluorescence of two laser dyes Coumarin 1 and Rhodamine 6G have been determined in cross-linked polyvinyl alcohol matrix. The cross-linking has been achieved using gamma radiation. The relative fluorescence quantum yields of the dyes increased with increasing cross-linking of the polymer, but the fluorescence lifetimes remained unchanged within experimental error. The results have been attributed to a reduction in the loss of the excitation energy via the internal conversion of the excited singlet state due to increase in the viscosity of the medium brought about by the increased cross-linking of the polymer.     

Fluorescent properties of cationic-anionic polymethine dyes

The fluorescence spectra were studied and the quantum yields of the fluorescence of a number of cationic-anionic polymethine dyes were measured in polar, low-polarity, and nonpolar solvents. It was shown that the fluorescence spectra of cationic-anionic dyes in polar solvents, like the absorption spectra, represent the sum of the fluorescence spectra of the corresponding cationic and anionic dyes. For dyes in which the absorption bands of the anion and cation are close and a new short-wave band arises in the ion pairs, excitation into this band virtually does not lead to fluorescence, which is a consequence of the forbidden nature of the long-wave transition that arises as a result of the interaction of the chromophores. For a number of cationic-anionic dyes in ion pairs an energy transfer is observed: When an ion possessing short-wave absorption is excited, an ion with long-wave absorption fluoresces.N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 117977 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 11, pp. 2532–2539, November, 1992.     

Novel fluorescent dyes with fused perylene tetracarboxlic diimide and BODIPY analogue structures

Two novel fluorescent dyes based on perylene tetracarboxylic diimides and BODIPY were designed and synthesized. Significant features, such as longer wavelength absorption and emission, high fluorescence quantum yields, and strong electron accepting abilities, are observed for these compounds.     

Experimental and DFT studies: novel structural modifications greatly enhance the solvent sensitivity of live cell imaging dyes

Structural modifications of previously reported merocyanine dyes (Toutchkine, A.; Kraynov, V.; Hahn, K. J. Am. Chem. Soc. 2003, 125, 4132-4145) were found to greatly enhance the solvent dependence of their absorbance and fluorescence emission maxima. Density functional theory (DFT) calculations have been performed to understand the differences in optical properties between the new and previously synthesized dyes. Absorption and emission energies were calculated for several new dyes using DFT vertical self-consistent reaction field (VSCRF) methods. Geometries of ground and excited states were optimized with a conductor-like screening model (COSMO) and self-consistent field (SCF) methods. The new dyes have enhanced zwitterionic character in the ground state and much lower polarity in the excited state, as shown by the DFT-VSCRF calculations. Consistently, the position of the absorption bands are strongly blue-shifted in more polar solvent (methanol compared to benzene), as predicted by the DFT spectral calculations. Inclusion of explicit H-bonding solvent molecules within the quantum model further enhances the predicted shifts and is consistent with the observed spectral broadening. Smaller but significant spectral shifts in polar versus nonpolar solvent are predicted and observed for emission bands. The new dyes show large fluorescence quantum yields in polar hydrogen-bonding solvents; qualitatively, the longest bonds along the conjugated chain at the excited S1 state minimum are shorter in the more polar solvent, inhibiting photoisomerization. The loss of photostability of the dyes is a consequence of the reaction with and electron transfer to singlet oxygen, starting oxidative dye cleavage. The calculated vertical ionization potentials of three dyes I-SO, AI-SO(4), and AI-BA(4) in benzene and methanol are consistent with their relative photobleaching rates; the charge distributions along the conjugated chains for the three dyes are similarly predictive of higher reaction rates for AI-SO(4) and AI-BA(4) than for I-SO. Time-dependent DFT calculations were also performed on AI-BA(4); these were less accurate than the VSCRF method in predicting the absorption energy shift from benzene to methanol.     

Near-infrared fluorescent probes: synthesis and spectroscopic investigations of a few amphiphilic squaraine dyes

With the objective of developing near-infrared fluorescence probes for biological applications, a few squaraine dyes 3a-d, containing amphiphilic substituents, were synthesized and their photophysical properties have been investigated in the presence and absence of the organized media. These dyes exhibited absorption in the range 630-650 nm, with significant absorption coefficients (epsilon = 1-3 x 10(5) M(-1) cm(-1)) in the aqueous medium. The fluorescence spectra of these dyes showed emission maximum from 660 to 675 nm, depending on the nature of substituents. The fluorescence quantum yields were in the range from 0.15 to 0.21 in ethanol, but 10 times lower values were observed (phi(f) = 0.01-0.02) in the aqueous medium. In the presence of micelles such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, and Triton X-100, these dyes showed negligible changes in their absorption properties, whereas a significant enhancement (5-10-folds) in their fluorescence yields was observed. Picosecond time-resolved studies indicated that these dyes show single-exponential decay in ethanol and ethanol-water mixtures; however, they exhibit biexponential decay with longer lifetimes in the presence of the micellar media. The results indicate that these novel amphiphilic squaraine dyes 3a-d, which exhibit favorable photophysical properties, good solubility in the aqueous medium, and interact efficiently with micelles, can have potential biological applications as near-infrared fluorescence sensors.     

Synthesis of water-soluble, ring-substituted squaraine dyes and their evaluation as fluorescent probes and labels

A series of ring-substituted squaraines absorbing and emitting in the red and NIR spectral region was synthesized and their spectral and photophysical properties (quantum yields, fluorescence lifetimes) and photostabilities were measured and compared to Cy5, a commonly used fluorescent label. The absorption maxima in aqueous media were found to be between 628 and 667 nm and the emission maxima are between 642 and 685 nm. Squaraine dyes exhibit high extinction coefficients (163,000–265,000 M⁻¹ cm⁻¹) and lower quantum yields (2–7%) in aqueous buffer but high quantum yields (up to 45%) and long fluorescence lifetimes (up to 3.3 ns) in presence of BSA. Dicyanomethylene- and thio-substituted squaraines exhibit an additional absorption around 400 nm with extinction coefficients between 21,500 and 44,500 M⁻¹ cm⁻¹. These dyes are excitable not only with red but also with blue diode lasers or light emitting diodes. Due to the favourable spectral and photophysical properties these dyes can be used as fluorescent probes and labels for intensity- and fluorescence lifetime-based biomedical applications.     

Photophysics of Xanthene Dyes at High Concentrations in Solid Environments: Charge Transfer Assisted Triplet Formation

The photophysical behavior of two xanthene dyes, Eosin Y and Phloxine B, included in microcrystalline cellulose particles is studied in a wide concentration range, with emphasis on the effect of dye concentration on fluorescence and triplet quantum yields. Absolute fluorescence quantum yields in the solid‐state were determined by means of diffuse reflectance and steady‐state fluorescence measurements, whereas absolute triplet quantum yields were obtained by laser‐induced optoacoustic spectroscopy and their dependence on dye concentration was confirmed by diffuse reflectance laser flash photolysis and time‐resolved phosphorescence measurements. When both quantum yields are corrected for reabsorption and reemission of radiation, Φ _F values decrease strongly on increasing dye concentration, while a less pronounced decay is observed for Φ _T. Fluorescence concentration quenching is attributed to the formation of dye aggregates or virtual traps resulting from molecular crowding. Dimeric traps are however able to generate triplet states. A mechanism based on the intermediacy of charge‐transfer states is proposed and discussed. Calculation of parameters for photoinduced electron transfer between dye molecules within the traps evidences the feasibility of the proposed mechanism. Results demonstrate that photoactive energy traps, capable of yielding dye triplet states, can be formed even in highly‐concentrated systems with random dye distributions.     

The excited-state interaction of resazurin and resorufin with amines in aqueous solutions. Photophysics and photochemical reactions

The photophysics and photochemical behavior of the phenoxazin-3-one dyes, resazurin and resorufin, have been studied in aqueous solutions. The irradiation of resazurin in the presence of amines leads to deoxygenation of the N-oxide group, giving resorufin. This photoreaction is highly dependent on the amine structure and is efficient only in the presence of tertiary aliphatic amines. The absorption and fluorescence properties of these dyes are dependent on pH. At pH above 7.5 both dyes are in their anionic form. For resorufin this form is highly fluorescent (phiF = 0.75). At lower pH the fluorescence is strongly reduced. The N-oxide dye presents a very weak fluorescence quantum yield (0.11), which also is reduced at low pH. Flash photolysis experiments allowed characterization of the triplet state and the transients formed after irradiation of these dyes in the absence and presence of amines. The triplet quantum yields are 0.08 for resazurin and 0.04 for resorufin. The photodeoxygenation of N-oxide in the presence of amines occurs from the triplet state.     

Aptamers switch on fluorescence of triphenylmethane dyes

MG and SRB aptamers, which are short RNA sequences originally selected only for binding to malachite green or sulforhodamine B, can greatly enhance the fluorescence of normally nonfluorescent triphenylmethane dyes. MG aptamer enhances the quantum yields of malachite green (MG) and a novel rigidized derivative, indolinyl malachite green (IMG) by >2000-fold. SRB aptamer brightens patent blue V and VF by >90-fold. These enhancements are specific because MG aptamer has no effect on patent blue dyes and SRB aptamer has little or no effect on MG and IMG. Such sequence-specific fluorescence labeling of short RNA motifs is a first step toward genetically encodable fusion tags for imaging selected RNAs in vitro and in cells.     

Spectral Properties of Fluorogenic Thiophene‐derived Triarylmethane Dyes

Spectral properties and fluorogenic behaviors of five novel thiophene variants of malachite green (MG), termed MGTs, were determined. Appreciable changes as a function of homologation and substitution pattern, including absorption band positions and intensities and fluorescence quantum yields were observed. In particular, the shorter wavelength y‐band absorption was found to shift over a nearly 200 nm range based on aryl group variation, allowing fine‐tuning of the excitation wavelength for these dyes. In addition, the fluorescence intensity of some MGTs increased significantly (up to 4600‐fold) when the dye was bound to a cognate protein partner, which is potentially useful for cell imaging studies.     

Combining aminocyanine dyes with polyamide dendrons: a promising strategy for imaging in the near-infrared region

Cyanine dyes are known for their fluorescence in the near-IR (NIR) region, which is desirable for biological applications. We report the synthesis of a series of aminocyanine dyes containing terminal functional groups such as acid, azide, and cyclooctyne groups for further functionalization through, for example, click chemistry. These aminocyanine dyes can be attached to polyfunctional dendrons by copper-catalyzed azide alkyne cycloaddition (CuAAC), strain-promoted azide alkyne cycloaddition (SPAAC), peptide coupling, or direct S(NR)1 reactions. The resulting dendron-dye conjugates were obtained in high yields and displayed high chemical stability and photostability. The optical properties of the new compounds were studied by UV/Vis and fluorescence spectroscopy. All compounds show large Stokes shifts and strong fluorescence in the NIR region with high quantum yields, which are optimal properties for in vivo optical imaging.     

A fluorogenic ‘click’ reaction of azidoanthracene derivatives

Fluorogenic reactions have broad applications in biolabeling, combinatorial synthesis of fluorescent dyes, and materials development. It was recently reported that the highly selective and efficient Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction can be employed in designing new types of fluorogenic reactions. In this study, we report a fluorogenic reaction using anthracene azides as starting materials. The fluorescence of the anthryl core can be greatly inhibited upon introducing electron-donating azido groups in the proximity. Such weakly fluorescent anthracene azides demonstrate high reactivity with a variety of alkynes under the CuAAC conditions producing a strongly fluorescent triazole product with high quantum yields. This reaction can be used in the synthesis and screening of fluorescent dyes combinatorially. Compared with most existing methods, the fluorogenic CuAAC reaction is a much milder and simpler technique to prepare large libraries of fluorescent dyes without further purification. In order to demonstrate the efficiency of using anthracene azides for biolabeling applications, both small molecules and biomolecules including the multialkyne-derivatized cowpea mosaic virus and tobacco mosaic virus had been studied.     

Local viscosity analysis of triblock copolymer micelle with cyanine dyes as a fluorescent probe

The local viscosity of Pluronic F127 triblock copolymer micelles in water was determined with cyanine dyes as fluorescent probes. These dyes show very weak fluorescence at a low temperature, but show enhanced fluorescence at a temperature higher than the critical micellization temperature (T(cm)). This is because a viscous environment within the micelle suppresses the formation of a nonradiative twisted intramolecular charge transfer (TICT) excited state of the dyes. The good correlation between the fluorescence quantum yields of the dyes and the viscosity and the temperature of the media allows a determination of local viscosity of micelle based on the fluorescence quantum yields. The local viscosity of both core and corona regions of micelles increases at >T(cm) and shows a maximum at a temperature 7-9 °C higher than T(cm), and decreases at higher temperature due to the increased fluidity. The core viscosity is larger than that of the corona, and the corona viscosity increases toward the micelle center. The polymer concentration has different effects on the core and corona viscosity: the corona viscosity increases with a polymer concentration increase at the entire temperature range, whereas the core viscosity increases only at a low temperature. The corona viscosity increase is due to the condensation of a large number of polyethylene oxide (PEO) blocks. In contrast, the dehydration degree of polypropylene oxide (PPO) blocks in the core scarcely changes, and the core has a similar composition regardless of polymer concentration. The larger polymer concentration promotes a micelle formation at lower temperature where the fluidity increase is very weak, resulting in larger core viscosity.     

Conformationally restricted dipyrromethene boron difluoride (BODIPY) dyes: highly fluorescent, multicolored probes for cellular imaging

Novel fluorescent, conformationally restricted dipyrromethene boron difluoride (BODIPY) dyes have been prepared by introducing a naphthalenyl group at the meso position of the BODIPY core. These BODIPY dyes exhibit increased fluorescence quantum yields compared with dyes that have a meso-position phenyl group with internal rotation. The absorption and emission wavelengths of such conformationally restricted BODIPY dyes can be easily tuned to the near-IR range by derivatization through a condensation reaction with benzaldehyde derivatives. The two-photon absorption properties of these BODIPY dyes were also investigated and the results show that they exhibit increased two-photon excited fluorescence compared to analogue dyes that contain a phenyl group. The one- and two-photon fluorescence imaging of living cells by using selected BODIPY dyes has been successfully demonstrated.