Fluorescent properties of oligonucleotide-conjugated thiazole orange probes

The fluorescence properties of thiazole orange, linked via a (1) hydrophobic alkyl or a (2) hydrophilic ethylene glycol chain to the central internucleotidic phosphate group of a pentadeca-2'-deoxyriboadenylate (dA15), are evaluated. Linkage at the phosphate group yields two stereoisomers, S-isomer of the phosphorus chiral center (Sp) and R-isomer of the phosphorus chiral center (Rp); these are studied separately. The character of the linkage chain and the chirality of the internucleotidic phosphate linkage site influence the fluorescent properties of these thiazole orange-oligonucleotide conjugates (TO-probes). Quantum yields of fluorescence (phifl) of between 0.04 and 0.07 were determined for the single-stranded conjugates. The fluorescence yield increased by up to five times upon hybridization with the complementary sequence (d5'[CACT15CAC3']); (phifl values of between 0.06-0.35 were determined for the double-stranded conjugates. The phifl value (0.17) of thiazole orange, 1-(N,N'-trimethylaminopropyl)-4-[3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene]-quinolinium iodide (TO-Pro 1) in the presence of the oligonucleotide duplex (TO-Pro 1: dA15.d5'[CACT15CAC3'] (1:1)) is much less than that for some of the hybrids of the conjugates. Our studies, using steady-state and time-resolved fluorescence experiments, show that a number of discrete fluorescent association species between the thiazole orange and the helix are formed. Time-resolved studies on the four double-stranded TO-probes revealed that the fluorescent oligonucleotide-thiazole orange complexes are common, only the distribution of the species varies with the character of the chain and the chirality at the internucleotidic phosphate site. Those TO-probes in which the isomeric structure of the phosphate-chain linkage is Rp, and therefore such that the fluorophore is directed toward the minor groove, have higher phifl values than the Sp isomer. Of the systems studied, thiazole orange linked by an alkyl chain to the internucleotidic phosphate (Rp isomer) has the highest phifl and the greatest fraction of the longest-lived fluorescent thiazole orange species (in the hybrid form).     

ECHO probes: a concept of fluorescence control for practical nucleic acid sensing

An excitonic interaction caused by the H-aggregation of fluorescent dyes is a new type of useful photophysical process for fluorescence-controlled nucleic acid sensing. This critical review points out the recent advances in exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes, which have a fluorescence-labeled nucleotide in which two molecules of thiazole orange or its derivatives are linked covalently. ECHO probes show absorption shift and emission switching depending on hybridization with the target nucleic acid. The hybridization-sensitive fluorescence emission of ECHO probes and the further modification of probes have made possible a variety of practical applications, such as multicolor RNA imaging in living cells and facile detection of gene polymorphism (144 references).     

Selective turn-on fluorescent probes for imaging hydrogen sulfide in living cells

Hydrogen sulfide (H(2)S) is an important biological messenger but few biologically-compatible methods are available for its detection. Here we report two bright fluorescent probes that are selective for H(2)S over cysteine, glutathione and other reactive sulfur, nitrogen, and oxygen species. Both probes are demonstrated to detect H(2)S in live cells.     

Synthesis of fluorescent probes based on the pyochelin siderophore scaffold

Pyochelin is a siderophore common to several pathogenic bacterial strains. Two conjugates, 1 and 2, between the NBD (4-nitro-benzo[1,2,5]oxadiazole) fluorophore and an N3'-functionalized pyochelin were synthesized. These fluorescent probes unexpectedly increased their fluorescence in an aqueous medium in the presence of iron(III) and were transported into bacterial cells.     

Comparison of N-alkyl acridine orange dyes as fluorescence probes for the determination of cardiolipin

The phospholipid (PL), cardiolipin (CL), is found almost exclusively in the inner membrane of mitochondria and loss of CL is considered as an important indication of cell apoptosis. Previously, 10-N-nonyl acridine orange (NAO) has been used as a fluorescent probe for the visualization of CL in mitochondrial cell membranes and in solution. In this work for the determination of CL, we have synthesized two new fluorescent probes, n-tetradecyl acridine orange (C14-AO), and n-octadecyl acridine orange (C18-AO) by reacting acridine orange with the corresponding n-alkyl bromide. Using excitation and emission wavelengths at about 500 and 525 nm and varying the percentage of methanol in water as the solvent, no interaction between CL and the fluorescent probes at 75% is noted but a proportional quenching of the fluorescence signal by CL is observed at 50% or less for C14-AO and 60% or less for C18-AO. Binding efficiency of these fluorescent probes to CL is compared using dye concentrations of 5, 10, and 20 μM. C18-AO shows a better sensitivity than C14-AO and NAO, respectively, but is less selective. For C14-AO, the detection limit and limit of quantitation are 0.07 and 0.21 μM, respectively, which are better than those previously reported for NAO. One anionic PL, phosphatidic acid, shows some quenching interference to both the C14 and C18 dyes but only at concentrations above the working range for sample analysis. The CL in mitochondrial membrane samples is determined by standard addition using C14-AO. The level of CL in the outer mitochondrial membrane compared to the inner membrane is significantly increased due to the addition of cadmium chloride into the cells causing cell apoptosis.     

香豆素类荧光探针对硫化氢检测的研究进展

硫化氢(H2S)是目前人们发现的第三类生物内源性“气体信使分子”。其及时检测对人类的健康有着非常大的意义。随着荧光探针技术的发展,有机小分子荧光探针受到广大学者的关注。其中,香豆素因其结构简单,荧光量子产率高以及易于功能化而备受青睐。本文根据探针的识别机理综述近三年来报道的香豆素类H2S荧光探针代表性研究成果,并对其进行了展望,为后续设计开发更具实用价值的H2S荧光探针提供一点有益的参考。     

Photocontrollable analyte-responsive fluorescent probes: a photocaged copper-responsive fluorescence turn-on probe

Analyte-responsive fluorescent probes are valuable chemical tools for dissecting complex living systems. However, the major shortcoming of fluorescent probes is that once they enter the cells, control over them is basically lost. It is critical to regulate fluorescent probes in a spatial and temporal manner, as functions of biomolecules are spatiotemporal. On the other hand, light can be manipulated in time and in the application site, so the photocaging technique allows researchers to control the biomolecules of interest in a temporal and spatial fashion. Herein, we propose for the first time the combination of the merits of sensing and photocaging technologies, which may afford the caging version of analyte-responsive fluorescent probes, referred to as photocontrollable analyte-responsive fluorescent probes (PCAFPs). These "smart" fluorescent probes apparently have the intrinsic advantage of spatiotemporal control when compared to traditional fluorescent probes, as the "sensing activity" of PCAFPs is photocontrollable. This should enable biologists to interrogate complex biological systems in a spatial and temporal manner with an innovative chemical tool. In this work, for proof of concept, we report the rational design, synthesis, photocontrollable sensing in solution and in living cells, and mechanistic studies of a molecular prototype of PCAFP for copper as the first paradigm of this new class of smart fluorescent probes. We believe that PCAFPs represent a substantial breakthrough in the sensing and photocaging fields, and that the general concept of PCAFPs should be broadly applicable for a wide variety of biologically relevant species.     

Synthesis and fluorescence properties of dimethylaminonaphthalene-deoxyuridine conjugates as polarity-sensitive probes

The design of probes for monitoring various structures and dynamics of DNA and its surroundings is an important step in understanding biological events accompanying interbiomolecular interaction. We have developed novel fluorescent nucleosides in which the uracil base and the fluorophore are tethered by rigid linkers. They show unique absorption and fluorescence emission spectra. Nucleoside 2 is a fluorophore with high CT character and the fluorescence is very sensitive to solvent polarity. Nucleoside 3 shows absorption and emission maxima with longer wavelength due to extension of the DAN-conjugate system. These fluorophore-deoxyuridine conjugates with unique fluorescence properties would work as reporter probes sensitive to the change in microenvironment around specific sites of DNA.     

"Turn-on" fluorescent sensing with "reactive" probes

Chemical probes are valuable tools for the investigation of biochemical processes, diagnosis of disease markers, detection of hazardous compounds, and other purposes. Therefore, the development of chemical probes continues to grow through various approaches with different disciplines and design strategies. Fluorescent probes have received much attention because they are sensitive and easy-to-operate, in general. To realize desired selectivity toward a given analyte, the recognition site of a fluorescent probe is designed in such a way to maximize the binding interactions, usually through weak molecular forces such as hydrogen bonding, toward the analyte over other competing ones. In addition to such a supramolecular approach, the development of fluorescent probes that sense analytes through chemical reactions has witnessed its usefulness for achieving high selectivity, in many cases, superior to that obtainable by the supramolecular approach. Creative incorporations of the reactive groups to latent fluorophores have provided novel chemical probes for various analytes. In this feature article, we overview the recent progress in the development of turn-on fluorescent probes that are operating through chemical reactions triggered by target analytes. Various chemical reactions have been implemented in the development of many reactive probes with very high selectivity and sensitivity toward target analytes. A major emphasis has been focused on the type of chemical reactions utilized, with the hope that further explorations can be made with new chemical reactions to develop reactive probes useful for various applications.     

Characterization of CdTe/CdSe quantum dots-transferrin fluorescent probes for cellular labeling

In this paper, we prepared three types of transferrin-quantum dots conjugates (QDs-Tf) using three different methods (electrostatic interaction, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) coupling, denatured transferrin (dTf) coating). Fluorescence emission spectra, surface characteristics, zeta potentials of quantum dots (QDs) and QDs-Tf fluorescent probes were characterized by spectrophotometer, capillary electrophoresis, and dynamic light scattering. Fluorescent imaging of HeLa cells was also performed by QDs and QDs-Tf fluorescent probes. It was found that the fluorescence imaging performances of QDs-Tf probes prepared by electrostatic interaction and EDC coupling were better compared with the one prepared by dTf coating. Then a real-time single cell detection system was established to quantitatively evaluate cell labeling effects of QDs-Tf fluorescent probes. It was found that for cell labeling efficiency, the proportion of cells labeled by quantum dot probes to a group of cells, QDs-Tf probe prepared by EDC coupling showed the highest labeling efficiency (85.55 ± 3.88%), followed by electrostatic interaction (78.86 ± 9.57%), and dTf coating showed the lowest (40.09 ± 10.2%). This efficiency order was confirmed by flow cytometry results. This study demonstrated the relationship between conjugation methods and the resultant QDs-Tf probes and provided a foundation for choosing appropriate QDs-Tf probes in cell labeling.     

Rapid, photoactivatable turn-on fluorescent probes based on an intramolecular photoclick reaction

Photoactivatable fluorescent probes are invaluable tools for the study of biological processes with high resolution in space and time. Numerous strategies have been developed in generating photoactivatable fluorescent probes, most of which rely on the photo-"uncaging" and photoisomerization reactions. To broaden photoactivation modalities, here we report a new strategy in which the fluorophore is generated in situ through an intramolecular tetrazole-alkene cycloaddition reaction ("photoclick chemistry"). By conjugating a specific microtubule-binding taxoid core to the tetrazole/alkene prefluorophores, robust photoactivatable fluorescent probes were obtained with fast photoactivation (～1 min) and high fluorescence turn-on ratio (up to 112-fold) in acetonitrile/PBS (1:1). Highly efficient photoactivation of the taxoid-tetrazoles inside the mammalian cells was also observed under a confocal fluorescence microscope when the treated cells were exposed to either a metal halide lamp light passing through a 300/395 filter or a 405 nm laser beam. Furthermore, a spatially controlled fluorescent labeling of microtubules in live CHO cells was demonstrated with a long-wavelength photoactivatable taxoid-tetrazole probe. Because of its modular design and tunability of the photoactivation efficiency and photophysical properties, this intramolecular photoclick reaction based approach should provide a versatile platform for designing photoactivatable fluorescent probes for various biological processes.     

Syntheses and characterizations of novel pyrrolocoumarin probes for SNAP-tag labeling technology

SNAP-tag technology is a revolutionary protein labeling technology employing in various biological studies. Since low signal/noise ratio and severe overlap between the FRET donors/acceptors often occurred in applying present fluorescent probes and thus limited the further applications, development of new fluorescent probes with excellent fluorescent properties is still of request by today’s SNAP-tag technology. In this paper, a number of SNAP-tag protein probes have been developed by incorporating a novel pyrrolocoumarin fluorophore recently developed by our group. Examination of these novel synthetic compounds shows all these materials possess satisfactory fluorescent properties. Among these, probe 7 exhibits the most excellent characters, and its quantum yield, maximum emission wavelength and Stocks shift reach to 0.44, 534 nm and 112 nm, respectively. Further analysis of structure-property relationship indicates that the probes with a longer C3-substituted alkyl (such as pentyl) give stronger fluorescence.     

Activatable imaging probes with amplified fluorescent signals

Current optical imaging probe applications are hampered by poor sensitivity and specificity to the target, but molecular-level fluorescent signal activation strategies can efficiently overcome these limitations. Recent interdisciplinary research that couples the imaging sciences to fluorophore, peptide, polymer, and inorganic-based chemistry has generated novel imaging probes that exhibit high sensitivity and low background noise in both in vitro and in vivo applications. This feature article introduces and discusses the various approaches described by the term "fluorescent signal activation methods" with respect to their unique imaging probe design strategies and applications.     

Design and synthesis of a new class of membrane-permeable triazaborolopyridinium fluorescent probes

A new class of fluorescent triazaborolopyridinium compounds was synthesized from hydrazones of 2-hydrazinylpyridine (HPY) and evaluated as potential dyes for live-cell imaging applications. The HPY dyes are small, their absorption/emission properties are tunable through variation of pyridyl or hydrazone substituents, and they offer favorable photophysical characteristics featuring large Stokes shifts and general insensitivity to solvent or pH. The stability, neutral charge, cell membrane permeability, and favorable relative influences on the water solubility of HPY conjugates are complementary to existing fluorescent dyes and offer advantages for the development of receptor-targeted small-molecule probes. This potential was assessed through the development of a new class of cysteine-derived HPY-conjugate imaging agents for the kinesin spindle protein (KSP) that is expressed in the cytoplasm during mitosis and is a promising chemotherapeutic target. Conjugates possessing the neutral HPY or charged Alexa Fluor dyes that function as potent, selective allosteric inhibitors of the KSP motor were compared using biochemical and cell-based phenotypic assays and live-cell imaging. These results demonstrate the effectiveness of the HPY dye moiety as a component of probes for an intracellular protein target and highlight the importance of dye structure in determining the pathway of cell entry and the overall performance of small-molecule conjugates as imaging agents.     

Dual fluorophore PNA FIT-probes - extremely responsive and bright hybridization probes for the sensitive detection of DNA and RNA

Fluorescently labeled oligonucleotides are commonly employed as probes to detect specific DNA or RNA sequences in homogeneous solution. Useful probes should experience strong increases in fluorescent emission upon hybridization with the target. We developed dual labeled peptide nucleic acid probes, which signal the presence of complementary DNA or RNA by up to 450-fold enhancements of fluorescence intensity. This enabled the very sensitive detection of a DNA target (40 pM LOD), which was detectable at less than 0.1% of the beacon concentration. In contrast to existing DNA-based molecular beacons, this PNA-based method does not require a stem sequence to enforce dye-dye communication. Rather, the method relies on the energy transfer between a "smart" thiazole orange (TO) nucleotide, which requires formation of the probe-target complex in order to become fluorescent, and terminally appended acceptor dyes. To improve upon fluorescence responsiveness the energy pathways were dissected. Hydrophobic, spectrally mismatched dye combinations allowed significant (99.97%) decreases of background emission in the absence of a target. By contrast, spectral overlap between TO donor emission and acceptor excitation enabled extremely bright FRET signals. This and the large apparent Stokes shift (82 nm) suggests potential applications in the detection of specific RNA targets in biogenic matrices without the need of sample pre-processing prior to detection.     

Fluorescent probes for detection of biothiols based on “aromatic nucleophilic substitution-rearrangement” mechanism

“Aromatic nucleophilic substitution-rearrangement (SNAr-rearrangement)” mechanism provided a powerful tool to design fluorescent probes for the discrimination between biothiols.     

Fluorescent probes detecting the phagocytic phase of apoptosis: enzyme-substrate complexes of topoisomerase and DNA

In apoptosis, the initial self-driven suicide phase generates cellular corpses which are digested in the phagolysosomes of professional and amateur phagocytes during the subsequent waste-management phase. This ensures the complete elimination of the genetic material which often contains pathological, viral or cancerous DNA sequences. Although the phagocytic phase is critical for the efficient execution of apoptosis, there are currently few methods specifically adapted for its detailed visualization in the fixed tissue section format. To resolve this we developed new fluorescent probes for in situ research. The probes selectively visualize active phagocytic cells of any lineage (professional, amateur phagocytes or surrounding tissue cells) which engulf and digest apoptotic cell DNA. These fluorescent probes are the covalently-bound enzyme-DNA intermediates produced in a topoisomerase reaction with specific "starting" oligonucleotides. They detect a specific marker of DNase II cleavage activity, which occurs exclusively in phagolysosomes of the cells that engulfed apoptotic nuclei. The probes provide snap-shot images of the digestion process occurring in cellular organelles responsible for the actual execution of phagocytic degradation of apoptotic cell corpses. We applied the probes for visualization of the phagocytic reaction in tissue sections of normal thymus and in several human lymphomas. We also discuss the nature, stability and properties of DNase II-type breaks as a marker of phagocytic activity. This development provides a useful fluorescent tool for studies of pathologies where clearance of dying cells is essential, such as cancers, inflammation, infection and auto-immune disorders.     

Small molecule fluorescent probes of protein vicinal dithiols

The vicinal dithiol motif is widely present in proteins, and is critical for proteins' structures and functions.In recent years, a variety of fluorescent probes with high specificity and outstanding optical properties for sensing protein vicinal dithiols have been developed. In this review, we summarized the fluorescent probes of protein vicinal dithiols in literature. These probes are classified into four types based on their acceptor sites, i.e., biarsenical probes, monoarsenical probes, dimaleimide probes and diacrylate probes.Through analyzing the properties of different probes, we expect that this review would help readers further understand the structural factors of these probes and provide the design strategy for novel fluorescent probes with improved properties.