Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons

A new class of molecular beacons were developed in which pyrene fluorophores were connected both at 3' and 5' ends of a single-stranded oligonucleotide. The two pyrene-based fluorophores were synthesized from the same starting material, so that the preparation of the beacons was simplified. The detection strategy of the beacons for target DNAs is based on "excimer-monomer emission switching" of the pyrene fluorophores: excimer emission of the pyrene moieties changed to monomer one when the beacons hybridized with the targets. This type of two-state mode of fluorescence allows unambiguous detection of the target DNAs because strict 1:1 correlation between the nonhybridized and the hybridized beacons can be monitored by the presence of isoemissive points of the fluorescence changes. The beacons can detect target 19-mer DNAs and can discriminate the targets from their single-nucleotide mismatches at 1 nM concentration. Advantages of the excimer-monomer switching molecular beacons were discussed in comparison with conventional ones.     

Pyrene: a probe to study protein conformation and conformational changes

The review focuses on the unique spectral features of pyrene that can be utilized to investigate protein structure and conformation. Pyrene is a fluorescent probe that can be attached covalently to protein side chains, such as sulfhydryl groups. The spectral features of pyrene are exquisitely sensitive to the microenvironment of the probe: it exhibits an ensemble of monomer fluorescence emission peaks that report on the polarity of the probe microenvironment, and an additional band at longer wavelengths, the appearance of which reflects the presence of another pyrene molecule in spatial proximity (~10 ?). Its high extinction coefficient allows us to study labeled proteins in solution at physiologically relevant concentrations. The environmentally- and spatially-sensitive features of pyrene allow monitoring protein conformation, conformational changes, protein folding and unfolding, protein-protein, protein-lipid and protein-membrane interactions.     

Fluorescence-labelled DNA probes to detect complementary sequences in homogeneous media

Sensitive, safe and easy-to-use probes for the detection of nucleic acids are urgently called for. To this end we are in the process of developing a fluorescence-based technique to work in homogeneous assay media. We have examined pyrene and fluorescein as fluorescent labels for natural DNA probes. A fraction of the cytosine residues of a single-stranded cDNA was randomly labelled with either pyrene or fluorescein using the bisulfite-catalyzed diamine reaction. Both fluorophores showed fluorescence quenching when the labelled probe was hybridized with its complementary strand and we describe the changes in steady-state fluorescence intensity that occurred upon hybridization. Our results demonstrate that pyrene quenching is more efficient than fluorescein quenching and thus pyrene-labelled probes are more sensitive for detecting and quantifying DNA from natural sources.     

Installation/modulation of the emission response via click reaction

We have demonstrated the installation of a fluorescence property into a nonfluorescent precursor and modulation of an emission response of a pyrene fluorophore via click reaction. The synthesized fluorophores show different solvatochromicity and/or intramolecular charge transfer (ICT) feature as is revealed from the UV-visible, fluorescence photophysical properties of these fluorophores, and DFT/TDDFT calculation. We observed that some of the synthesized fluorophores showed purely ICT character while emission from some of them arose from the LE state. A structureless and solvent polarity-sensitive dual emission behavior was observed for one of the triazolylpyrene fluorophores that contains an electron-donating -NMe(2) substituent (fluorophore, 7a). Conversely, triazolylpyrene with an electron-withdrawing -CN group (fluorophore, 7b) showed a solvent polarity-independent vibronic emission. The effect of ICT on the photophysical properties of these fluorophores was studied by fluorescence emission spectra and DFT/TDDFT calculations. Fluorescence lifetimes were also measured in different solvents. All of our findings revealed the delicate interplay of structure and emission properties and thus having broader general utility. As the CT to LE intensity ratio can be employed as a sensing index, the dual emissive fluorophore can be utilized in designing the molecular recognition system too. We envisage that our investigation is of importance for the development of new fluorophores with predetermined photophysical properties that may find a wide range of applications in chemistry, biology, and material sciences.     

Highly fluorescent polycaprolactones decorated with di(thiophene‐2‐yl)‐diketopyrrolopyrrole: A covalent strategy of tuning fluorescence properties in solid states

Well‐defined 1,4‐diketo‐3,6‐di(thiophen‐2‐yl)pyrrolo[3,4‐c]pyrrole (DTDPP) labeled polycaprolactones (PCL) with different chain lengths were synthesized and characterized. The effect of polymer chain lengths on the optical properties of DTDPP in solid states was studied by UV‐Vis absorption spectroscopy as well as steady‐state and dynamic fluorescence spectroscopies. Our results indicate that when the PCL side chain is extended to a certain length, the intermolecular aggregation of DTDPP units can be reduced significantly due to segregation effect of PCL. This approach offers a new facile strategy to address the common problem of aggregation‐caused quenching existing in organic fluorophores. These highly fluorescent biodegradable PCL polymers may find broad biomedical applications such as fluorescence‐based bioimaging and tissue engineering. © 2015 Wiley Periodicals, Inc. J. Polym. Sci. Part A: Polym. Chem. 2015 , 53, 1032–1042     

Helix triangle: unique peptide-based molecular architecture

We here report a unique cyclic peptide structure, "helix triangle", as a unique example of peptide-based molecular architecture. The cyclic peptide is designed to have a triangular shape in which three 9mer helical peptide units make the sides and three pyrene derivatives make the apexes. The helical peptide units are ideally linear, and the pyrene units are ideal 60 degrees angular components. The yield of the cyclic peptide was relatively high despite its large cycle size. Absorption and fluorescence spectroscopy revealed that the three pyrene units do not interact with each other electronically, and circular dichroism spectroscopy indicated that the helical peptide units take 3(10)-helical conformation. Geometry optimization by the semi-empirical molecular orbital method gave a triangular structure with 3(10)-helices as the plausible molecular structure. To gain more information on the geometry and demonstrate one example of its self-assemblies, the monolayer of the cyclic peptide was prepared at the air/water interface, and its surface pressure-molecular area isotherm was studied. The isotherm indicated formation of a stable monolayer and suggested that the cyclic peptide actually takes the triangular structure predicted by the geometry optimization. The monolayer was then transferred onto a substrate and characterized by various methods. Ellipsometry and infrared reflection-absorption spectroscopy confirmed that the cyclic peptide has horizontal orientation to the surface in the monolayer. Furthermore, absorption and fluorescence spectroscopy showed that the isolated electronic properties of the pyrene units are intact even in a condensed state in the monolayer.     

Suppression of aggregation-induced fluorescence quenching in pyrene derivatives: photophysical properties and crystal structures

Two new pyrene-based fluorophores, namely 1-[4-(2,2-diphenylvinyl)phenyl]pyrene (PVPP) and 1,3,6,8-tetrakis[4-(2,2-diphenylvinyl)phenyl]pyrene (TPVPP), were synthesized through Suzuki coupling reaction and well characterized. PVPP successfully suppresses the fluorescence quenching of pyrene units in the solid state, displaying aggregation-induced enhanced emission. Despite the same substituent, TPVPP shows a different fluorescent behavior. On the basis of the crystal structures, the distinct optical behavior is discussed and clarified. The intermolecular C-H?π interaction has a dramatic effect on their photophysical properties in the solid state.     

Strong π-π stacking interactions led to the mis-assignment of dimer emissions to the monomers of 1-acetylpyrene

Both experimental and computational studies showed owing to strong π-π stacking interactions, 1-acetylpyrene mainly exists in dimers and molecular aggregates even at low concentrations, which led to the mis-assignment of its monomer emission peaks.     

FLUORESCENCE SPECTROSCOPY OF BENZO[a]PYRENE DIOL EPOXIDE-DNA ADDUCTS. CONFORMATION-SPECIFIC EMISSION SPECTRA

The fluorescence characteristics of adducts derived from the covalent binding of the highly tumorigenic (+) and the non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) to native calf thymus DNA are significantly different from one another both at room temperature and at 77 K. The ratio R of fluorescence intensities of the (0,0) band I (situated near 380 nm) and vibronic band V (near 400 nm) of the pyrene ring system in the BPDE-DNA adducts and of the tetraol (BPT) hydrolysis product of BPDE is very sensitive to the polarity of the solvent, thus mimicking the well known behavior of pyrene itself (A. Nakajima, 1971, Bull. Chem. Soc. Jpn. 44, 3272). The fluorescence excitation and emission spectra of the (+)-BPDE-DNA adducts are relatively sharp and only slightly red-shifted (2-3 nm) with respect to those of BPT in aqueous buffer solution, and R = 1.07 when the fluorescence is excited at the maximum of the absorption spectrum; this compares with R = 1.17 for BPT in water, R = 0.75 in ether, and R = 0.84 for noncovalently intercalated BPT. These results suggest that the pyrene ring system in the covalent (+)-BPDE-DNA adducts is located in an environment which is relatively exposed to the aqueous environment, while physically intercalated BPT molecules are located at hydrophobic binding sites. The fluorescence characteristics of the (-)-BPDE-DNA adducts are more heterogeneous and thus more complex than those of the (+)-adducts. The R ratio depends rather strongly on the wavelength of excitation; a minor, more highly fluorescent and relatively solvent-accessible form of adducts exhibits an R ratio of 1.01. The major, less solvent accessible form is characterized by a larger red shift in the absorption spectrum (approximately 10 nm) and emission spectrum (approximately 6 nm for the (0,0) band) relative to BPT, and an R ratio of 1.07. These characteristics suggest that the local environments of the pyrenyl residues in the (-)-BPDE-DNA adducts are significantly different from those of BPT bound noncovalently to DNA by the intercalation mechanism. Fluorescence methods, particularly at low temperatures where the bands are better resolved and the fluorescence yields are significantly greater than at room temperature, can also be used to distinguish covalent DNA adducts derived from the binding of (+)-BPDE and (-)-BPDE to native double-stranded DNA.     

Oligodeoxyfluorosides: Strong Sequence Dependence of Fluorescence Emission

We describe the properties of a series of oligomeric polyfluorophores assembled on the DNA backbone. The 11 oligomers (oligodeoxyfluorosides, ODFs), 4-7 monomers in length, were composed of only two fluorescent monomers and a spacer in varied sequences, and were designed to test how fluorescent nucleobases can interact electronically to yield complexity in fluorescence emission. The monomer fluorophores were deoxyribosides of pyrene and perylene, which emit light in violet and blue wavelengths, respectively. The experiments show that simple variation in sequence and spacing can dramatically change fluorescence, yielding emission maxima ranging from 380 to 557 nm and visible colors from violet to orange-red. Fluorescence lifetime data, excitation spectra, and absorption data point to a number of multi-fluorophore electronic interactions, including pyrene-pyrene and perylene-perylene excimers, pyrene-perylene exciplexes, as well as monomer dye emissions, contributing to the final spectral outcomes. Thus, two simple fluorophores can be readily combined to give emissions over much of the visible spectrum, all requiring only a single excitation. The results demonstrate that fluorescent nucleobases in oligomeric form can act cooperatively as electronic units, and that fluorophore sequence in such oligomers is as important as fluorophore composition in determining fluorescence properties.     

ACRYLAMIDE AND MOLECULAR OXYGEN FLUORESCENCE QUENCHING AS A PROBE OF SOLVENT-ACCESSIBILITY OF AROMATIC FLUOROPHORES COMPLEXED WITH DNA IN RELATION TO THEIR CONFORMATIONS: CORONENE-DNA AND OTHER COMPLEXES

Abstract— The relationships between the accessibilities to fluorescence quenchers (O2 and acrylamide) of three different aromatic molecules and their modes of binding to double-stranded DNA were investigated. Proflavin was selected for this study because it is a known intercalator, while Hoechst 33258 is known to bind externally in the minor groove of DNA; it is shown here that the relatively bulky polycyclic aromatic hydrocarbon coronene forms partial intercalation complexes, and thus represents a third class of fluorophore-DNA binding. Fluorescence quenching results suggest that Hoechst 33258 bound to DNA is fully accessible to 02, that the accessibility of partially intercalated coronene is reduced to 20% of the free-solution value, while the accessibility of intercalated proflavin to molecular oxygen is at least ten times smaller than for free polycyclic aromatic molecules in fluid solutions. In contrast, the fluorescence of all these three fluorophores bound to DNA is insensitive to acrylamide (the effective accessibilities appear to be reduced by factors greater than 50 upon binding to DNA). It is concluded that O, is useful as a qualitative probe of the type of binding and solvent exposure of fluorophore-DNA complexes, while acrylamide appears to be of limited utility. However, acrylamide fluorescence quenching may be useful for studies of other types of fluorophore-DNA complexes since the fluorescence of the pyrene residues in covalent adducts derived from the binding of benzo(a)pyrene diol expoxide to DNA was found to be at least partially sensitive to acrylamide.     

Further Insight into the Photostability of the Pyrene Fluorophore in Halogenated Solvents

Pyrene fluorophores of pyrene‐functionalized CdSe quantum dots (QD@Py), as well as alkylpyrene and pyrene itself (Py), undergo fast degradation in aerated chloroform under ultraviolet‐A (UV‐A, 316<λ<400 nm) illumination. Steady‐state fluorescence studies of irradiated chloroform solutions of QD@Py show formation of new bands, red‐shifted compared to that of the pyrene moiety. Similar behaviour is observed for pyrene and the alkylpyrene system. Column chromatography of the pyrene photolysate in chloroform allowed us to isolate photoproducts arising from pyrene degradation, and to obtain information on the structure of the photoproducts responsible for the emission bands. The most predominant photoproducts were those originating from the reaction of pyrene with dichloromethyl radicals. The phototransformation of QD@Py and the alkylpyrene involves mainly detachment of the alkyl chain from the aromatic ring, induced also by dichloromethyl radicals, and oxidation of the alkyl chain at the benzylic position was detected as well. By contrast, these pyrene systems show a high photostability in aerated dichloromethane. Transient absorption measurements showed formation of both pyrene triplet and pyrene radical cation for all pyrene systems in these halogenated solvents. The yield of pyrene radical cations for Py is higher than for QD@Py and the alkylpyrene. In addition, pyrene radical cations were longer‐lived in dichloromethane than in chloroform. The reason for the pyrene photostability in dichloromethane is the different reactivity of chloromethyl and dichloromethyl radicals towards pyrene and oxygen. These studies show that the use of dichloromethane can be a suitable alternative to chloroform when the good solubility properties of these halogenated solvents are needed to dissolve pyrene when this chromophore is used as a fluorescent probe.     

Single Benzene Green Fluorophore: Solid‐State Emissive,Water‐Soluble,and Solvent‐ and pH‐Independent Fluorescence with Large Stokes Shifts

Benzene is the simplest aromatic hydrocarbon with a six‐membered ring. It is one of the most basic structural units for the construction of π conjugated systems, which are widely used as fluorescent dyes and other luminescent materials for imaging applications and displays because of their enhanced spectroscopic signal. Presented herein is 2,5‐bis(methylsulfonyl)‐1,4‐diaminobenzene as a novel architecture for green fluorophores, established based on an effective push–pull system supported by intramolecular hydrogen bonding. This compound demonstrates high fluorescence emission and photostability and is solid‐state emissive, water‐soluble, and solvent‐ and pH‐independent with quantum yields of Φ=0.67 and Stokes shift of 140 nm (in water). This architecture is a significant departure from conventional extended π‐conjugated systems based on a flat and rigid molecular design and provides a minimum requirement for green fluorophores comprising a single benzene ring.     

Single Benzene Green Fluorophore: Solid‐State Emissive,Water‐Soluble,and Solvent‐ and pH‐Independent Fluorescence with Large Stokes Shifts

Benzene is the simplest aromatic hydrocarbon with a six‐membered ring. It is one of the most basic structural units for the construction of π conjugated systems, which are widely used as fluorescent dyes and other luminescent materials for imaging applications and displays because of their enhanced spectroscopic signal. Presented herein is 2,5‐bis(methylsulfonyl)‐1,4‐diaminobenzene as a novel architecture for green fluorophores, established based on an effective push–pull system supported by intramolecular hydrogen bonding. This compound demonstrates high fluorescence emission and photostability and is solid‐state emissive, water‐soluble, and solvent‐ and pH‐independent with quantum yields of Φ=0.67 and Stokes shift of 140 nm (in water). This architecture is a significant departure from conventional extended π‐conjugated systems based on a flat and rigid molecular design and provides a minimum requirement for green fluorophores comprising a single benzene ring.     

Pyrene excimer-based calix[4]arene FRET chemosensor for mercury(II)

A novel calix[4]arene derivative locked in the 1,3-alternate conformation (2) bearing two pyrene and rhodamine fluorophores was synthesized as a selective sensor for the Hg(2+) ion. The sensoring is based on FRET from pyrene excimer emissions to ring-opened rhodamine absorption upon complexation of the Hg(2+) ion. Addition of Hg(2+) to a mixed solution of 2 gave significantly enhanced fluorescence at ～576 nm via FRET with excitation at 343 nm. We also found that the pyrene excimer emissions formed by the intramolecular π-π interactions are more effective in obtaining strong FRET bands than those by intermolecular π-π interactions.     

Indium(III)-induced fluorescent excimer formation and extinction in calix[4]arene-fluoroionophores

New fluorogenic or/and chromogenic calix[4]arenes 1-3 with two facing amide groups linked to fluorescent pyrene units are synthesized. Orientations of the pyrene units are remote from each other in 1 and face-to-face pi-stacked in 2, which produces different photophysical properties. In the excited state, the two pyrene units of 2 form a strong intramolecular excimer displaying an emission at 472 nm with a relatively weak monomer emission at 395 nm. In contrast, 1 exhibits only a monomer emission at 398 nm because intramolecular hydrogen bonding between the phenolic OH oxygens and the amide hydrogens prevents pi-stacking of the two pyrene groups. Fluorescence changes upon addition of various metal ions show that 1 has a remarkably high selectivity for In(3+) over the other metal ions tested. Compound 1 forms 2:1 (metal:ligand), as well as 1:1 complexes, with In(3+), with fluorescence varying uniquely with the complex stoichiometry. Compound 3, which possess two pyrene units and two chromogenic azo groups, shows almost the same binding behavior toward metal ions as does 1, together with additional bathochromic shifts of the absorption maximum. Compared with 1, compound 3 emits a considerably weaker fluorescence, which is attributed to electron transfer from the pyrene units to the nitro groups of the phenylazo moieties.     

Pyrene solubilization capacity in octaethylene glycol monododecyl ether (C12E8) micelles

We used fluorescence quenching, vibronic band ratios and excimer fluorescence techniques to quantify the statistics of pyrene solubilization in nonionic octaethylene glycol monododecyl ether (C₁₂E₈) micelles. Using a two-phase model (aqueous and micellar pseudophases) to interpret fluorescence results, we found that all three of these experimental methods provide consistent information about pyrene partitioning between aqueous and micellar pseudophases. From dynamic quenching experiments we determined the pyrene partition coefficient and the average number of pyrene molecules solubilized per micelle over a range of surfactant concentrations. The pyrene partition coefficient increases with increasing surfactant concentration. We confirmed the partitioning results by excimer fluorescence measurements. Quenching results indicate that pyrene is accessible to Cu²⁺ quenchers even in the limit of high surfactant concentration where solubilized pyrene is in the infinite dilution limit in the micellar pseudophase. This suggests that solubilized pyrene resides in the micellar palisade layer. We determined the maximum number of pyrene solubilizates allowed per micelle (micellar solubilization capacity) by applying a three-phase model to fluorescence experiments conducted in the presence of solid phase pyrene. The estimated maximum capacity is 6 pyrene molecules per micelle. The three phase partitioning model successfully predicted the excimer fluorescence in the presence of solid pyrene.     

Delayed Fluorescent Emission from Pyrene Doped Phenanthrene Nanoparticles Based on Triplet-triplet Energy Transfer

Doped nanoparticles were prepared from pyrene and phenanthrene using a facile reprecipitation method. The doped nanoparticles presented unique delayed fluorescent emissions of pyrene under the unprotected condition. The ratio of the intensity of delayed fluorescence (I_DF) to that of phosphorescence (I_P) is about 4:1, which almost keeps unchanged with the decrease of pyrene content at room temperature. The intensity of the delayed fluorescence emissions is dependent on the relative content of pyrene, as well as the aggregation degree of nanoparticles. The delayed emissions are contributed to efficient triplet‐triplet energy transfer from phenanthrene (donor) to pyrene (acceptor). Steady fluorescence measurement have proved that the singlet‐singlet energy transfer process was also existent dominated by the radiation energy transfer mechanism.     

Highly selective fluorescent recognition of phenyl amino alcohol based on ferrocenyl macrocyclic derivatives

Four ferrocenyl macrocyclic derivatives 3 and 4 containing anthracene fluorophores have been synthesized. The fluorescent properties of these receptors have been studied in three organic solvents, both in the absence and presence of phenyl amino alcohols. All receptors exhibit sensitive fluorescence response to l- or d-phenylglycinol, a strong emission band is produced due to the intermolecular exciplex between host and guest. These special phenomena were not observed when other species were used as the guests; such highly selective fluorescent response indicates that these receptors can easily discriminate phenylglycinol from other similar species. Solvent comparative experiments also indicate that acetonitrile is the most appropriate solvent to detect this fluorescent change. The intramolecular energy transfer between excited anthracene and ferrocene, and π–π stacking interaction between the aromatic rings play critical roles in this special fluorescence enhancement. Model calculations at DFT level further suggest the possible interaction modes, structures and relatively steric position between the host and guest also influence the optical response.     

A fluoride-selective PCT chemosensor based on formation of a static pyrene excimer

[reaction: see text] Calixarene-based fluorescent chemosensor 1 with two fluorogenic pyrene units conjugated to amide groups as guest recognition sites is synthesized. Complexation of F(-) by 1 causes a red shift of its absorption band to 400 nm (Deltalambda = 54 nm) and a blue shift of the excimer emission to 470 nm (Deltalambda = 12 nm) together with enhanced fluorescence intensity. The blue-shifted excimer emission is attributed to a pyrene dimer formed in the ground state, a so-called static excimer.