Imaging of conformational changes of proteins with a new environment-sensitive fluorescent probe designed for site-specific labeling of recombinant proteins in live cells

Hybrid Small-Molecule/Protein Fluorescent Probes

Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.

Turn-on fluorogenic sensors based on an anthraquinone signaling unit for the detection of Zn(II) and Cd(II) ions

Turn-on fluorescent chemosensors based on an anthraquinone moiety, N,N'-(9,10-dioxo-9,10-dihydroanthracene-1,8-diyl)bis(2-(bis(pyridin-2-ylmethyl)amino)acetamide) (1) and N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,6-diyl)bis(2-(bis(pyridin-2-ylmethyl)amino)acetamide) (2), have been successfully synthesized with the overall yields of 61% and 90%, respectively. The structures of both chemosensors 1 and 2 were elucidated using several spectroscopic techniques such as 1H NMR, 13C NMR, 2D-NMR, FTIR and HRMS. The target chemosensor 1 is a promising tool for the detection of trace levels of d10 metal ions, such as Zn(II) and Cd(II) ions, by exhibiting a significant fluorescence enhancement via a turn-on photoinduced electron transfer (PET) mechanism with a rapid and highly reproducible signal, and low detection limit values of 0.408 μM and 0.246 μM, for Zn(II) and Cd(II), respectively.

Phosphorogenic Iridium(III) bis-Tetrazine Complexes for Bioorthogonal Peptide Stapling, Bioimaging, Photocytotoxic Applications, and the Construction of Nanosized Hydrogels

The dual functionality of 1,2,4,5-tetrazine as a bioorthogonal reactive unit and a luminescence quencher has shaped tetrazine-based probes as attractive candidates for luminogenic labeling of biomolecules in living systems. In this work, three cyclometalated iridium(III) complexes featuring two tetrazine units were synthesized and characterized. Upon photoexcitation, the complexes were non-emissive but displayed up to 3900-fold emission enhancement upon the inverse electron-demand Diels-Alder (IEDDA) [4+2] cycloaddition with (1R,8S,9s)-bicyclo[6.1.0]non-4-yne (BCN) substrates. The rapid reaction kinetics (k₂ up to 1.47×10⁴  M^-1  s^-1 ) of the complexes toward BCN substrates allowed effective peptide labeling. The complexes were also applied as live cell bioimaging reagents and photocytotoxic agents. One of the complexes was utilized in the preparation of luminescent nanosized hydrogels that exhibited interesting cargo delivery properties.

Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook

Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.

Substituted 9-Diethylaminobenzo[a]phenoxazin-5-ones (Nile Red Analogues): Synthesis and Photophysical Properties

Nile Red is a benzo[a]phenoxazone dye containing a diethylamino substituent at the 9-position. In recent years, it has become a popular histological stain for cellular membranes and lipid droplets due to its unrivaled fluorescent properties in lipophilic environments. This makes it an attractive lead for chemical decoration to tweak its attributes and optimize it for more specialized microscopy techniques, e.g., fluorescence lifetime imaging or two-photon excited fluorescence microscopy, to which Nile Red has never been optimized. Herein, we present synthesis approaches to a series of monosubstituted Nile Red derivatives (9-diethylbenzo[a]phenoxazin-5-ones) starting from 1-naphthols or 1,3-naphthalenediols. The solvatochromic responsiveness of these fluorophores is reported with focus on how the substituents affect the absorption and emission spectra, luminosity, fluorescence lifetimes, and two-photon absorptivity. Several of the analogues emerge as strong candidates for reporting the polarity of their local environment. Specifically, the one- and two-photon excited fluorescence of Nile Red turns out to be very responsive to substitution, and the spectroscopic features can be finely tuned by judiciously introducing substituents of distinct electronic character at specific positions. This new toolkit of 9-diethylbenzo[a]phenoxazine-5-ones constitutes a step toward the next generation of optical molecular probes for advancing the understanding of lipid structures and cellular processes.

Effect of the Substitution Position on the Electronic and Solvatochromic Properties of Isocyanoaminonaphthalene (ICAN) Fluorophores

The properties of 1,4-isocyanoaminonaphthalene (1,4-ICAN) and 2,6-isocyanoaminonaphthalene (2,6-ICAN) isomers are discussed in comparison with those of 1,5-isocyanoaminonaphthalene (1,5-ICAN), which exhibits a large positive solvatochromic shift similar to that of Prodan. In these isocyanoaminonaphthalene derivatives, the isocyano and the amine group serve as the donor and acceptor moieties, respectively. It was found that the positions of the donor and the acceptor groups in these naphthalene derivatives greatly influence the Stokes and solvatochromic shifts, which decrease in the following order: 1,5-ICAN > 2,6-ICAN > 1,4-ICAN. According to high-level quantum chemical calculations, this order is well correlated with the charge transfer character of these compounds upon excitation. Furthermore, unlike 1,5-ICAN, the 1,4-ICAN and 2,6-ICAN isomers showed relatively high quantum yields in water, that were determined to be 0.62 and 0.21, respectively. In addition, time-resolved fluorescence experiments revealed that both the radiative and non-radiative decay rates for these three ICAN isomers varied unusually with the solvent polarity parameter E_T(30). The explanations of the influence of the solvent polarity on the resulting steady-state and time-resolved fluorescence emission spectra are also discussed.

Synthesis of fluorescent drug molecules for competitive binding assay based on molecularly imprinted polymers

Fluorescent immunosorbent assay (FIA) is very promising for sensitive and selective analysis in bio-medical applications. Here, we proposed an assay, using fluorescent engineering of analytes and the corresponding molecularly imprinted polymers (MIPs) as a plastic antibody. Three drug molecules (metronidazole, zidovudine and lamivudine) were condensed with 9-aminoacridine, using succinic anhydride as a spacer. The target products were characterized with ¹H-NMR, IR and mass spectrometry. UV-vis absorption and fluorescent properties of the fluorophore-labeled drug molecules were investigated. Feasibility of the fluorescent biomimetic immunosorbent assay based on MIPs was demonstrated in the solution. This work will provide sound foundation for the future application in real sample.

Drug molecules (metronidazole, zidovudine and lamivudine) were successfully labelled with a fluorescent reagent and used to develop fluorescent biomimetic immunosorbent assays using molecularly imprinted polymers in the place of natural antibody.

Organic Arsenicals as Functional Motifs in Polymer and Biomaterials Science

Arsenic (As) exhibits diverse (bio)chemical reactivity and biological activity depending upon its oxidation state. However, this distinctive reactivity has been largely overlooked across many fields owing to concerns regarding the toxicity of arsenic. Recently, a clinical renaissance in the use of arsenicals, including organic arsenicals that are known to be less toxic than inorganic arsenicals, alludes to the possibility of broader acceptance and application in the field of polymer and biomaterials science. Here, current examples of polymeric/macromolecular arsenicals are reported to stimulate interest and highlight their potential as a novel platform for functional, responsive, and bioactive materials.

Green and Red Fluorescent Dyes for Translational Applications in Imaging and Sensing Analytes: A Dual-Color Flag

Red and green are two of the most-preferred colors from the entire chromatic spectrum, and red and green dyes are widely used in biochemistry, immunohistochemistry, immune-staining, and nanochemistry applications. Selective dyes with green and red excitable chromophores can be used in biological environments, such as tissues and cells, and can be irradiated with visible light without cell damage. This critical review, covering a period of five years, provides an overview of the most-relevant results on the use of red and green fluorescent dyes in the fields of bio-, chemo- and nanoscience. The review focuses on fluorescent dyes containing chromophores such as fluorescein, rhodamine, cyanine, boron-dipyrromethene (BODIPY), 7-nitobenz-2-oxa-1,3-diazole-4-yl, naphthalimide, acridine orange, perylene diimides, coumarins, rosamine, Nile red, naphthalene diimide, distyrylpyridinium, benzophosphole P-oxide, benzoresorufins, and tetrapyrrolic macrocycles. Metal complexes and nanomaterials with these dyes are also discussed.

New Red-Emitting Tetrazine-Phenoxazine Fluorogenic Labels for Live-Cell Intracellular Bioorthogonal Labeling Schemes

The synthesis of a set of tetrazine-bearing fluorogenic dyes suitable for intracellular labeling of proteins in live cells is presented. The red excitability and emission properties ensure minimal autofluorescence, while through-bond energy-transfer-based fluorogenicity reduces nonspecific background fluorescence of unreacted dyes. The tetrazine motif efficiently quenches fluorescence of the phenoxazine core, which can be selectively turned on chemically upon bioorthogonal inverse-electron-demand Diels-Alder reaction with proteins modified genetically with strained trans-cyclooctenes.

The molecular mechanism of heme loss from oxidized soluble guanylate cyclase induced by conformational change

Heme oxidation and loss of soluble guanylate cyclase (sGC) is thought to be an important contributor to the development of cardiovascular diseases. Nevertheless, it remains unknown why the heme loses readily in oxidized sGC. In the current study, the conformational change of sGC upon heme oxidation by ODQ was studied based on the fluorescence resonance energy transfer (FRET) between the heme and a fluorophore fluorescein arsenical helix binder (FlAsH-EDT2) labeled at different domains of sGC β1. This study provides an opportunity to monitor the domain movement of sGC relative to the heme. The results indicated that heme oxidation by ODQ in truncated sCC induced the heme-associated αF helix moving away from the heme, the Per/Arnt/Sim domain (PAS) domain moving closer to the heme, but led the helical domain going further from the heme. We proposed that the synergistic effect of these conformational changes of the discrete region upon heme oxidation forces the heme pocket open, and subsequent heme loss readily. Furthermore, the kinetic studies suggested that the heme oxidation was a fast process and the conformational change was a relatively slow process. The kinetics of heme loss from oxidized sGC was monitored by a new method based on the heme group de-quenching the fluorescence of FlAsH-EDT2.

A Nile Red/BODIPY-based bimodal probe sensitive to changes in the micropolarity and microviscosity of the endoplasmic reticulum

We herein report a fluorescent bimodal probe (1) capable of determining ER viscosity and polarity changes using FLIM and fluorescence ratiometry, respectively; during ER stress caused by tunicamycin, the viscosity was increased from ca. 129.5 to 182.0 cP and the polarity of the ER (dielectric constant, ε) enhanced from 18.5 to 21.1.

Solvent effects on the photophysical properties of poly[1,4-dihydroxyanthraquinoneimine-1,3-bis(phenylene-ester-methylene)tetramethyldisiloxane]

Absorption and fluorescence spectra of a polyquinoneimine, PQI, built on 1,4-dihydroxyanthraquinone and a siloxane diamine, 1,3-bis(amino-phenylene-ester-methylene)tetramethyldisiloxane, have been investigated in solvents of different polarities. The effect of solvents on the spectral properties was investigated using Lippert-Mataga and Bakhshiev polarity functions and Catalán's multiple linear regression approach. Absorption and fluorescence spectra in studied solvents exhibit hypsochromic and bathochromic shifts, respectively. The polarity of the solvent was the main parameter which changes the spectral properties of PQI. Also, the binary mixtures of chloroform with methanol and dimethyl sulfoxide were used to analyze the intermolecular interactions and preferential solvation. The preferential solvation parameters (local mole fraction (X₂(L)), excess function (δs₂) and preferential solvation constant (KPS)) were calculated from spectral data and discussed as a function of cosolvent content. The values of quantum yield, decreased linearly with increasing solvent polarity (for non-polar and polar solvents).

Ultrasound promoted synthesis of Nile Blue derivatives

Ultrasound irradiation was used for the first time towards the synthesis of new Nile Blue related benzo[a]phenoxazinium chlorides possessing isopentylamino, (2-cyclohexylethyl)amino and phenethylamino groups at 5-position of the heterocyclic system. The efficacy of sonochemistry was investigated with some of our earlier reported synthesis of benzo[a]phenoxazinium chlorides. This newer protocol proved competent in terms of reaction times and enhanced yields. Photophysical studies carried out in ethanol, water and simulated physiological conditions, revealed that emission maxima occurred in the range 644-656 nm, with high fluorescent quantum yields. Other attractive feature exhibited by these materials includes good thermal stability. These properties might be useful in the development of fluorescent probes for biotechnology.

Macro-/micro-environment-sensitive chemosensing and biological imaging

We have summarized the research progress on fluorescent sensors responsive to environmental factors, including local viscosity, polarity, temperature, hypoxia and pH.

Exploration of biarsenical chemistry--challenges in protein research

The fluorescent modification of proteins (with genetically encoded low-molecular-mass fluorophores, affinity probes, or other chemically active species) is extraordinarily useful for monitoring and controlling protein functions in vitro, as well as in cell cultures and tissues. The large sizes of some fluorescent tags, such as fluorescent proteins, often perturb normal activity and localization of the protein of interest, as well as other effects. Of the many fluorescent-labeling strategies applied to in vitro and in vivo studies, one is very promising. This requires a very short (6- to 12-residue), appropriately spaced, tetracysteine sequence (-CCXXCC-); this is either placed at a protein terminus, within flexible loops, or incorporated into secondary structure elements. Proteins that contain the tetracysteine motif become highly fluorescent upon labeling with a nonluminescent biarsenical probe, and form very stable covalent complexes. We focus on the development, growth, and multiple applications of this protein research methodology, both in vitro and in vivo. Its application is not limited to intact-cell protein visualization; it has tremendous potential in other protein research disciplines, such as protein purification and activity control, electron microscopy imaging of cells or tissue, protein-protein interaction studies, protein stability, and aggregation studies.

Detection of CXCR4 receptors on cell surface using a fluorescent metal nanoshell

Fluorescence cell imaging can be used for disease diagnosis and cellular signal transduction. Using a metal nanoshell as molecular imaging agent, we develop a cellular model system to detect CXCR4 chemokine receptor on T-lymphatic cell surface. These metal nanoshells are observed to express enhanced emission intensity and shortened lifetimes due to the near-field interactions. They are covalently bound with anti-CXCR4 monoclonal antibodies for immunoreactions with the target sites of the CXCR4 receptors on the CEM-SS cells. The fluorescence intensity and lifetime cell images are recorded with a time-resolved confocal microscopy. As expected, the emission signals from the metal nanoshells are clearly isolated from the cellular autofluorescence due to strong intensities and distinctive lifetimes. The number of emission spots on the single cell image is estimated by direct count to the emission signals. Analyzing a pool of cell images, a maximal count number is obtained in a range of 200±50. Because there is an average of ̃approximately 6000 binding sites on the cell surface, we estimate that one emission spot from the metal nanoshell may represent ̃approximately 30 CXCR5 receptors. In addition, the CXCR4 receptors are estimated to distribute on ̃approximately 70% area of the cell surface.

Tetracysteine-tagged prion protein allows discrimination between the native and converted forms

The conformational conversion of prion protein (PrP) from a native conformation to the amyloid form is a hallmark of transmissible spongiform encephalopathies. Conversion is usually monitored by fluorescent dyes, which bind generic amyloids and are less suited for living cell imaging. We report a new method for the synthesis of membrane-permeable and membrane-impermeable biarsenical reagents, which are then used to monitor murine PrP (mPrP) misfolding. We introduced tetracysteine (TC) tags into three different positions of mPrP, which folded into a native-like structure. Whereas mPrPs with a TC tag inserted at the N-terminus or C-terminus supported fibril formation, insertion into the helix 2-helix 3 loop inhibited conversion. We devised a quantitative protease-free method to determine the fraction of converted PrP, based on the ability of the fluorescein arsenical helix binder reagent to differentiate between the monomeric and fibrilized form of TC-tagged PrP, and showed that TC-tagged mPrP could be detected on transfected cells, thereby expanding the potential use of this method for the detection and study of conformational diseases.

Monitoring protein interactions and dynamics with solvatochromic fluorophores

Solvatochromic fluorophores possess emission properties that are sensitive to the nature of the local microenvironment. These dyes have been exploited in applications ranging from the study of protein structural dynamics to the detection of protein-binding interactions. Although the solvatochromic indole fluorophore of tryptophan has been utilized extensively for in vitro studies to advance our understanding of basic protein biochemistry, the emergence of new extrinsic synthetic dyes with improved properties, in conjunction with recent developments in site-selective methods to incorporate these chemical tools into proteins, now open the way for studies in more complex systems. Herein, we discuss recent technological advancements and their application in the design of powerful reporters, which serve critical roles in modern cell biology and assay development.

Thiol-reactive derivatives of the solvatochromic 4-N,N-dimethylamino-1,8-naphthalimide fluorophore: a highly sensitive toolset for the detection of biomolecular interactions

The solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide (4-DMN) possesses extremely sensitive emission properties due largely to the low intrinsic fluorescence it exhibits in polar protic solvents such as water. This makes it well suited as a probe for the detection of a wide range of biomolecular interactions. Herein we report the development and evaluation of a new series of thiol-reactive agents derived from this fluorophore. The members of this series vary according to linker type and the electrophilic group required for the labeling of proteins and other biologically relevant molecules. Using the calcium-binding protein calmodulin as a model system, we compare the performance of the 4-DMN derivatives to that of several commercially available solvatochromic fluorophores identifying many key factors important to the successful application of such tools. This study also demonstrates the power of this new series of labeling agents by yielding a fluorescent calmodulin construct capable of producing a greater than 100-fold increase in emission intensity upon binding to calcium.

Fluorescence proteins, live-cell imaging, and mechanobiology: seeing is believing

Fluorescence proteins (FPs) have been widely used for live-cell imaging in the past decade. This review summarizes the recent advances in FP development and imaging technologies using FPs to monitor molecular localization and activities and gene expressions in live cells. We also discuss the utilization of FPs to develop molecular biosensors and the principles and application of advanced technologies such as fluorescence resonance energy transfer (FRET), fluorescence recovery after photobleaching (FRAP), fluorescence lifetime imaging microscopy (FLIM), and chromophore-assisted light inactivation (CALI). We present examples of the application of FPs and biosensors to visualize mechanotransduction events with high spatiotemporal resolutions in live cells. These live-cell imaging technologies, which represent a frontier area in biomedical engineering, can shed new light on the mechanisms regulating mechanobiology at cellular and molecular levels in normal and pathophysiological conditions.

Selective Chemical Labeling of Proteins with Small Fluorescent Molecules Based on Metal-Chelation Methodology

Site-specific chemical labeling utilizing small fluorescent molecules is a powerful and attractive technique for in vivo and in vitro analysis of cellular proteins, which can circumvent some problems in genetic encoding labeling by large fluorescent proteins. In particular, affinity labeling based on metal-chelation, advantageous due to the high selectivity/simplicity and the small tag-size, is promising, as well as enzymatic covalent labeling, thereby a variety of novel methods have been studied in recent years. This review describes the advances in chemical labeling of proteins, especially highlighting the metal-chelation methodology.

Probing the sequence of conformationally induced polarity changes in the molecular chaperonin GroEL with fluorescence spectroscopy

Hydrophobic interactions play a major role in binding non-native substrate proteins in the central cavity of the bacterial chaperonin GroEL. The sequence of local conformational changes by which GroEL and its cofactor GroES assist protein folding can be explored using the polarity-sensitive fluorescence probe Nile Red. A specific single-cysteine mutant of GroEL (Cys261), whose cysteine is located inside the central cavity at the apical region of the protein, was covalently labeled with synthetically prepared Nile Red maleimide (NR). Bulk fluorescence spectra of Cys261-NR were measured to examine the effects of binding of the stringent substrate, malate dehydrogenase (MDH), GroES, and nucleotide on the local environment of the probe. After binding denatured substrate, the fluorescence intensity increased by 32 +/- 7%, suggesting enhanced hydrophobicity at the position of the label. On the other hand, in the presence of ATP, the fluorescence intensity decreased by 13 +/- 3%, implying increased local polarity. To explore the sequence of local polarity changes, substrate, GroES, and various nucleotides were added in different orders; the resulting changes in emission intensity provide insight into the sequence of conformational changes occurring during GroEL-mediated protein folding.

Flash labeling of a nuclear receptor domain (D domain of ultraspiracle) fused to tetracysteine tag

Biarsenical fluorescein compounds feature unique fluorescence characteristics and special binding mechanism to tetracysteine tags with certain structures and these dyes offer a feasible method for site specific labeling of heterologously expressed proteins. We aimed FlAsH fluorescent labeling of tetracysteine fused hinge region of the ultraspiracle from Drosophila melanogaster (DmUSP-D domain) to facilitate functional studies of this receptor domain. A CCPGCC tetracysteine motif was integrated between His6, Gateway attB1, and Flag tags and attached to the N-terminus of the DmUSP-D. The fusion protein was expressed in Esherichia coli and the FlAsH labeling was performed in bacterial extracts, under conditions which are compatible with receptor function. The dye was bound to the tetracysteine tag with high affinity and complex stability and the labeling proved to be specific for the target fusion protein. Results indicate that FlAsH labeling of the internal CCPGCC motif can be a valuable tool for the functional characterisation of any nuclear receptor domains.

FRET-based monitoring of conformational change of the β2 adrenergic receptor in living cells

The beta(2) adrenergic receptor (beta(2)AR) is a G protein-coupled receptor that is selective to epinephrine. We demonstrate herein monitoring of an agonist-induced conformational change of beta(2)AR in living cells. The monitoring method is based on fluorescence resonance energy transfer from a cyan fluorescent protein (CFP) to a biarsenical fluorophore, FlAsH, attached to the C-terminus, and the third intracellular loop (ICL3), respectively. Recombinant beta(2)ARs exhibited agonist-induced increases in the FlAsH/CFP emission ratio, indicating that the ICL3 approached the C-terminus upon activation. Since the emission ratio changes were on a time scale of seconds, the conformational change of beta(2)AR in living cells was more rapid than that of purified beta(2)AR measured in vitro. Interestingly, the direction of the emission ratio change of beta(2)AR was opposite to that of the norepinephrine-responsive alpha(2A) adrenergic receptor reported recently. It was suggested that this discrepancy corresponds directly to the diametric biological functions, i.e., the activation or inactivation of adenylyl cyclase.

Painting protein misfolding in the cell in real time with an atomic-scale brush

The direct observation of specific biochemical events in living cells is now possible as a result of combined advances in molecular biology and fluorescence microscopy. By genetically encoding the source of a unique spectroscopic signal, target proteins can be selectively detected within the complex cellular environment, with limited interference from background signals. A recent study takes advantage of arsenical reagent-based methodologies to monitor in vivo protein misfolding and inclusion body formation in real time. This approach promises to yield important information on the kinetics of aggregate formation in living cells and its relation to the time-course of protein expression and post-translational processing. The ability to follow protein self-association in real time accurately from its early stages is unique to this method, and has far-reaching implications for both biotechnology and misfolding-based disease.

A new protein conformation indicator based on biarsenical fluorescein with an extended benzoic acid moiety

We demonstrate herein a new protein conformation indicator based on biarsenical fluorescein with an extended benzoic acid moiety. The present indicator is reactive to a genetically introduced tetracysteine motif (Cys-Cys-Xaa-Xaa-Cys-Cys, where Xaa is a noncysteine amino acid) of proteins. Compared to the original biarsenical fluorescein (FlAsH) and the biarsenical Nile red analogue (BArNile), the present indicator exhibited larger fluorescence intensity changes in response to Ca(2+)-induced conformational rearrangements of calmodulin. A calculation of the highest occupied molecular orbital (HOMO) level of the benzoic acid moiety of the indicator molecule supports possible involvement of a photoinduced electron transfer (PET) process. These results indicate that the present indicator is useful for sensitive detection of protein conformational changes.

Selective chemical labeling of proteins in living cells

Labeling proteins with fluorophores, affinity labels or other chemically or optically active species is immensely useful for studying protein function in living cells or tissue. The use of genetically encoded green fluorescent protein and its variants has been particularly valuable in this regard. In an effort to increase the diversity of available protein labels, various efforts to append small molecules to selected proteins in vivo have been reported. This review discusses recent advances in selective, in vivo protein labeling based on small molecule ligand-receptor interactions, intein-mediated processes, and enzyme-catalyzed protein modifications.

Labeling of fusion proteins of O6-alkylguanine-DNA alkyltransferase with small molecules in vivo and in vitro

The in vivo and in vitro labeling of fusion proteins with synthetic molecules capable of probing and controlling protein function has the potential to become an important method in functional genomics and proteomics. We have recently introduced an approach for the specific labeling of fusion proteins, which is based on the generation of fusion proteins with the human DNA repair protein O6-alkylguanine-DNA alkyltransferase (hAGT) and the irreversible reaction of hAGT with O6-benzylguanine derivatives. Here, we report optimized protocols for the synthesis of O6-benzylguanine derivatives and the use of such derivatives for the labeling of different hAGT fusion proteins in vivo and in vitro.

Interaction of 2-Hydroxy-substituted Nile Red Fluorescent Probe with Organic Nitrogen Compounds

The fluorescent properties of 2-hydroxy Nile red dye (HONR) proved to be highly sensitive to the basicity of hydrogen bond acceptors. Fluorescence quantum yields and fluorescence decay profiles were measured as the function of the concentration of organic nitrogen compounds in solvents of various polarities. The detailed mechanism and the kinetics of the fluorescence quenching were revealed with the combined analysis of the steady-state and time-resolved spectroscopic data. The relative contribution of the competing reaction steps was found to be very sensitive to the basicity of the additive and to solvent polarity. The most profound change appeared in the unimolecular deactivation pathways of the excited hydrogen-bonded HONR, whereas the formation rate of this species varied to a lesser extent. The dissociation into excited HONR and ground-state base was able to compete with the energy dissipation only when 2,4,6-trimethylpyridine was used as hydrogen bond acceptor in toluene. The bimolecular quenching of the excited hydrogen-bonded complex played significant role in apolar solvents. Proton displacement along the hydrogen bond in the excited complex led to excited ion pairs in polar media.

Novel stable fluorophore, 6-methoxy-4-quinolone, with strong fluorescence in wide pH range of aqueous media, and its application as a fluorescent labeling reagent

6-Methoxy-4-quinolone (6-MOQ, 1), an oxidation product derived from 5-methoxyindole-3-acetic acid, is a novel fluorophore, which has several useful characteristics for biomedical analysis. Compound 1 has strong fluorescence with a large Stokes' shift in aqueous media, and the maximum fluorescence excitation and emission wavelengths are 243 nm and 374 nm, respectively. The molar absorptivity at the maximum excitation wavelength and fluorescence quantum yield in aqueous 10% (v/v) methanol are 32 600 L mol(-1) cm(-1) and 0.38, respectively. The fluorescence intensity of 1 is scarcely affected by changing the medium pH, showing strong fluorescence from pH 2.0 to 11.0. In addition, 1 is highly stable against light and heat, and no degradation was observed at 60 degrees C for 3 days with exposure to daylight. As a fluorescent labeling reagent, [(6-methoxy-4-oxo-1,4-dihydroquinolin-3-yl)methyl]amine (6-MOQ-NH2, 2) was synthesized, and determination of carboxylic acids was demonstrated; 50 pmol of standard propionic acid and isobutyric acid were derivatized, and the obtained S/N ratios for 10 fmol (injection amount) of these two acids were 206 and 164, respectively.