Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.     

A New Dual‐Signalling Electrochemical Sensing Strategy Based on Competitive Host–Guest Interaction of a β‐Cyclodextrin/Poly(N‐acetylaniline)/Graphene‐Modified Electrode: Sensitive Electrochemical Determination of Organic Pollutants

Based on the competitive host–guest interaction between a β‐cyclodextrin/poly(N‐acetylaniline)/electrogenerated‐graphene (β‐CD/PNAANI/EG) film and probe or target molecules, a new dual‐signalling electrochemical sensing method has been developed for the sensitive and selective determination of organic pollutants. As a model system, rhodamine B (RhB) and 1‐aminopyrene (1‐AP) were adopted as the probe and target molecules, respectively. Due to the host–guest interaction, RhB molecules can enter into the hydrophobic inner cavity of β‐CD, and the β‐CD/PNAANI/EG‐modified glassy carbon electrode displays a remarkable oxidation peak due to RhB. In the presence of 1‐AP, competitive association to β‐CD occurs and the RhB molecules are displaced by 1‐AP. This results in a decreased oxidation peak current of RhB and the appearance of an oxidation peak current for 1‐AP, and the changes of these signals correlate linearly with the concentration of 1‐AP. When the value ΔI_1‐AP+∣ΔI_RhB∣ (ΔI_1‐AP and ΔI_RhB are the change values of the oxidation peak currents of 1‐AP and RhB, respectively) is used as the response signal to quantitatively determine the concentration of 1‐AP, the detection limit is much lower than that given by using ΔI_1‐AP or ΔI_RhB as the response signal. This dual‐signalling sensor can provide more sensitive target recognition and will have important applications in the sensitive and selective electrochemical determination of electroactive organic pollutants.     

A Lysosome‐Compatible Near‐Infrared Fluorescent Probe for Targeted Monitoring of Nitric Oxide

The requirement for nitric oxide (NO) of lysosomes has motivated the development of a sophisticated fluorescent probe to monitor the distribution of this important biomolecule at the subcellular level in living cells. A near‐infrared (NIR) fluorescent Si‐rhodamine (SiRB)‐NO probe was designed based on the NO‐induced ring‐opening process of Si‐rhodamine. The probe exhibits fast chromogenic and fluorogenic responses, and high sensitivity and selectivity toward trace amounts of NO. Significantly, the spirolactam in Si‐rhodamine exhibits very good tolerance to H⁺, which in turn brings extremely low background fluorescence not only in the physiological environment but also under acidic conditions. The stability of the highly fluorescent product in acidic solution provides persistent fluorescence emission for long‐term imaging experiments. To achieve targeted imaging with improved spatial resolution and sensitivity, an efficient lysosome‐targeting moiety was conjugated to a SiRB‐NO probe, affording a tailored lysosome‐targeting NIR fluorescent Lyso‐SiRB‐NO probe. Inheriting the key advantages of its parent SiRB‐NO probe, Lyso‐SiRB‐NO is a functional probe that is suited for monitoring lysosomal NO with excellent lysosome compatibility. Imaging experiments demonstrated the monitoring of both exogenous and endogenous NO in real time by using the Lyso‐SiRB‐NO probe.     

Counterion‐Controlled Self‐Sorting in an Amphiphilic Calixarene Micellar System

Molecular recognition of small molecules and ions by artificial receptors in microheterogeneous media such as micelles and vesicles can, in principle, provide better models of biological systems in comparison with bulk solutions. In this work we have investigated the complexation of an organic fluorescent probe with amphiphilic calixarene receptor below and above the critical micelle concentration (CMC). For concentrations below the CMC, the probe forms a host–guest complex with the calixarene behaving like a traditional host–guest system operating in bulk solution. Above the CMC, multiple equilibrium processes are established and the probe can exchange between the recognition site of the calixarene in the monomeric state, micellized state and/or the micellar hydrophobic core. Careful analysis of the results obtained from NMR spectroscopy and fluorescence experiments allowed us to propose a quantitative model to describe the system. The increment of the local concentration of Na⁺ counterions at the Stern layer displace the dye to the micelle core through competitive binding of Na⁺ in the cavity of the receptor and is decisive for the observed self‐sorting behavior.     

Quinolinium‐Based Fluorescent Probes for the Detection of Thiophenols in Environmental Samples and Living Cells

A new type of fluorescent probes for thiophenols, 6HQM‐DNP and 7HQM‐DNP, containing 6‐ or 7‐hydroxy quinonlinium as fluorophore and 2,4‐dinitrophenoxy (DNP) as nucleophilic recognition unit were constructed. As ethers, these non‐fluorescent probe molecules can release the corresponding fluorescent quinolinium (6HQM and 7HQM) through aromatic nucleophilic substitution (S_NAr) by thiolate anions from thiophenols. The sensing reaction is highly sensitive (detection limit of 8 nM for 7HQM‐DNP) and highly selective to thiophenols over aliphatic thiols and other nucleophiles under neutral conditions (pH 7.3). The probes respond rapidly to thiophenols, with second‐order rate constants k=45 M ^?1 s^?1 for 7HQM‐DNP and 24 M ^?1 s^?1 for 6HQM‐DNP. Furthermore, the selective detection of thiophenols in living cells by 7HQM‐DNP was demonstrated by confocal fluorescence imaging. In addition, these quinolinium salts show excellent chemical and thermal stability. In conclusion, this type of probes may find use in the detection of thiophenols in environmental samples and biosystems.     

An Aurone‐derived Low‐molecular‐weight Fluorescence Probe for the Detection of Hg2+ in Aqueous Solution and Living Cells

A low‐molecular‐weight fluorescent probe 1 (M.W. = 238.24) based on aurone was synthesized, and its application in fluorescent detection of Hg²⁺ in aqueous solution and living cells was reported. It exhibited an “on–off” fluorescent response toward Hg²⁺ in aqueous solution. Both the color and fluorescence changes of the probe were remarkably specific for Hg²⁺ in the presence of other common metal ions, satisfying the selective requirements for biomedical and environmental monitoring application. The probe has been applied in direct measurement of Hg²⁺ content in river water samples and imaging of Hg²⁺ in living cells, which further indicates the potential application values in environmental and biological systems.     

FRET‐based Fluorescent and Colorimetric Probe for Selective Detection of Hg(II) and Cu(II) with Dual‐mode

A dual‐function fluorescence resonance energy transfer (FRET)‐based fluorescent and colorimetric probe was rationally fabricated from an energy donor coumarin moiety and an energy acceptor rhodamine moiety linked by a thiohydrazide arm for selective detection of Hg²⁺ and Cu²⁺. Two distinct mechanisms were used for the selective detection. Results revealed that probe 1 showed high fluorescent selectivity towards Hg²⁺ and evident colorimetric selectivity for Cu²⁺, which was suitable for ‘naked‐eye’ detection.     

A Rapid and Sensitive Aptamer‐Based Electrochemical Biosensor for Direct Detection of Escherichia Coli O111

A sensitive and specific electrochemical biosensor based on target‐induced aptamer displacement was developed for direct detection of Escherichia coli O111. The aptamer for Escherichia coli O111 was immobilized on a gold electrode by hybridization with the capture probe anchored on the electrode surface through Au‐thiol binding. In the presence of Escherichia coli O111, the aptamer was dissociated from the capture probe‐aptamer duplex due to the stronger interaction between the aptamer and the Escherichia coli O111. The consequent single‐strand capture probe could be hybridized with biotinylated detection probe and tagged with streptavidin‐alkaline phosphatase, producing sensitive enzyme‐catalyzed electrochemical response to Escherichia coli O111. The designed biosensor showed weak electrochemical signal to Salmonella typhimurium, Staphylococcus aureus and common non‐pathogenic Escherichia coli, indicating high specificity for Escherichia coli O111. Under the optimal conditions, the proposed strategy could directly detect Escherichia coli O111 with the detection limit of 112 CFU mL^?1 in phosphate buffer saline and 305 CFU mL^?1 in milk within 3.5 h, demonstrated the sensitive and accurate quantification of target pathogenic bacteria. The designed biosensor could become a powerful tool for pathogenic microorganisms screening in clinical diagnostics, food safety, biothreat detection and environmental monitoring.     

In‐Situ Spin Labeling of His‐Tagged Proteins: Distance Measurements under In‐Cell Conditions

New spin labeling strategies have immense potential in studying protein structure and dynamics under physiological conditions with electron paramagnetic resonance (EPR) spectroscopy. Here, a new spin‐labeled chemical recognition unit for switchable and concomitantly high affinity binding to His‐tagged proteins was synthesized. In combination with an orthogonal site‐directed spin label, this novel spin probe, Proxyl‐trisNTA (P‐trisNTA) allows the extraction of structural constraints within proteins and macromolecular complexes by EPR. By using the multisubunit maltose import system of E. coli: 1) the topology of the substrate‐binding protein, 2) its substrate‐dependent conformational change, and 3) the formation of the membrane multiprotein complex can be extracted. Notably, the same distance information was retrieved both in vitro and in situ allowing for site‐specific spin labeling in cell lysates under in‐cell conditions. This approach will open new avenues towards in‐cell EPR.     

Zn2+‐Regulated Self‐Sorting and Mixing of Phosphates and Carboxylates on the Surface of Functionalized Gold Nanoparticles

Herein, we describe the self‐sorting of phosphate‐ and carboxylate‐containing molecules on the surface of monolayer‐protected gold nanoparticles. Self‐sorting is driven by selective interactions between the phosphate probe and Zn²⁺ complexes in one monolayer; these interactions force the carboxylate probe to move to a second type of nanoparticle. This process effectively separates the probes and causes their localization in well‐defined spaces surrounding the nanoparticles. The removal/addition of Zn²⁺ metal ions from the system is used to convert the system from an ordered to a disordered state and vice versa. The possibility to control the location and transport of populations of molecules in a complex mixture creates new perspectives for the development of innovative complex catalytic systems that mimic nature.     

Development of Imidazoline‐2‐Thiones Based Two‐Photon Fluorescence Probes for Imaging Hypochlorite Generation in a Co‐Culture System

We designed and prepared the imidazoline‐2‐thione containing OCl^? probes, PIS and NIS , which operate through specific reactions with OCl^? that yield corresponding fluorescent imidazolium ions. Importantly, we demonstrated that PIS can be employed to image OCl^? generation in macrophages in a co‐culture system. We have also employed two‐photon microscopy and PIS to image OCl^? in live cells and tissues, indicating that this probe could have wide biological applications.     

Rolling‐Circle Amplification Detection of Thrombin Using Surface‐Enhanced Raman Spectroscopy with Core‐Shell Nanoparticle Probe

An ultrasensitive surface‐enhanced Raman spectroscopy (SERS) sensor based on rolling‐circle amplification (RCA)‐increased “hot‐spot” was developed for the detection of thrombin. The sensor contains a SERS gold nanoparticle@Raman label@SiO₂ core‐shell nanoparticle probe in which the Raman reporter molecules are sandwiched between a gold nanoparticle core and a thin silica shell by a layer‐by‐layer method. Thrombin aptamer sequences were immobilized onto the magnetic beads (MBs) through hybridization with their complementary strand. In the presence of thrombin, the aptamer sequence was released; this allowed the remaining single‐stranded DNA (ssDNA) to act as primer and initiate in situ RCA reaction to produce long ssDNAs. Then, a large number of SERS probes were attached on the long ssDNA templates, causing thousands of SERS probes to be involved in each biomolecular recognition event. This SERS method achieved the detection of thrombin in the range from 1.0×10^?12 to 1.0×10^?8 M and a detection limit of 4.2×10^?13 M , and showed good performance in real serum samples.     

A Stimuli‐Responsive Nanogel‐Based Sensitive and Selective Fluorescent Sensor for Cr3+ with Thermo‐Induced Tunable Detection Sensitivity

Stimuli‐responsive poly(N‐isopropylacrylamide) nanogel with covalently labeled rhodamine B urea derivatives (P(NIPAM‐co‐RhBUA)) is utilized as a sensitive fluorescent probe for Cr³⁺ in aqueous solution, and its thermo‐induced tunable detection capacity is investigated. At 20 °C, non‐fluorescent nanogel can selectively bind with Cr³⁺ over some other metal ions, leading to prominent fluorescence OFF–ON switching due to the recognition of RhBUA with Cr³⁺. Upon heating above the phase transition temperature, enhanced fluorescence intensity is observed (≈61‐fold increase at 45 °C) for the nanogel in the presence of Cr³⁺, accompanied with an improved detection sensitivity, which suggest that hydrophobic microenvironment generated in the collapsed nanogel plays an active role for their detection performance.

     

A Post‐Synthetically Modified MOF for Selective and Sensitive Aqueous‐Phase Detection of Highly Toxic Cyanide Ions

Selective and sensitive detection of toxic cyanide (CN^?) by a post‐synthetically altered metal–organic framework (MOF) has been achieved. A post‐synthetic modification was employed in the MOF to incorporate the specific recognition site with the CN^? ion over all other anions, such as Cl^?, Br^?, and SCN^?. The aqueous‐phase sensing and very low detection limit, the essential prerequisites for an effective sensory material, have been fulfilled by the MOF. Moreover, the present detection level meets the standard set by the World Health Organization (WHO) for the permissible limit of cyanide concentration in drinking water. The utilization of MOF‐based materials as the fluorometric probes for selective and sensitive detection of CN^? ions has not been explored till now.     

A Covalent Approach for Site‐Specific RNA Labeling in Mammalian Cells

Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported for the site‐ and sequence‐specific covalent labeling of RNAs in mammalian cells by using tRNA^Ile2‐agmatidine synthetase (Tias) and click chemistry. The crystal structure of Tias in complex with an azide‐bearing agmatine analogue was solved to unravel the structural basis for Tias/substrate recognition. The unique RNA sequence specificity and plastic Tias/substrate recognition enable the site‐specific transfer of azide/alkyne groups to an RNA molecule of interest in vitro and in mammalian cells. Subsequent click chemistry reactions facilitate the versatile labeling, functionalization, and visualization of target RNA.     

The Uncommon Channel‐Based Ln‐MOFs for Highly Selective Fe3+ Detection and Superior Rhodamine B Adsorption

Two new isostructural 3D lanthanide–organic frameworks [H₂N(Me)₂] [Ln₃(OH)(bpt)₃(H₂O)₃] (DMF)₂?(H₂O)₄ ( 1‐Ln ; Ln=Sm and Eu) with a 1D channel (25 Å) have been successfully assembled from the rare trinuclear [Ln₃(OH)(COO)₉] clusters and biphenyl‐3,4′,5‐tricarboxylic acid (H₃bpt) and exhibit high stability towards water in the pH range 3–10. MOF 1‐Eu is a promising luminescent probe for sensing Fe³⁺ in aqueous solution and is also selective towards rhodamine B (RhB) with a superior adsorption capacity of 735 mg g^?1, which is the highest among the reported Ln‐MOFs for RhB removal so far. Periodic DFT calculations further confirmed the selective adsorption of rhodamine B over other dyes.     

Development of a 18F‐Labeled Tetrazine with Favorable Pharmacokinetics for Bioorthogonal PET Imaging

A low‐molecular‐weight ¹⁸F‐labeled tetrazine derivative was developed as a highly versatile tool for bioorthogonal PET imaging. Prosthetic groups and undesired carrying of ¹⁸F through additional steps were evaded by direct ¹⁸F‐fluorination of an appropriate tetrazine precursor. Reaction kinetics of the cycloaddition with trans‐cyclooctenes were investigated by applying quantum chemical calculations and stopped‐flow measurements in human plasma; the results indicated that the labeled tetrazine is suitable as a bioorthogonal probe for the imaging of dienophile‐tagged (bio)molecules. In vitro and in vivo investigations revealed high stability and PET/MRI in mice showed fast homogeneous biodistribution of the ¹⁸F‐labeled tetrazine that also passes the blood–brain barrier. An in vivo click experiment confirmed the bioorthogonal behavior of this novel tetrazine probe. Due to favorable chemical and pharmacokinetic properties this bioorthogonal agent should find application in bioimaging and biomedical research.     

Rhodamine Spiroamides for Multicolor Single‐Molecule Switching Fluorescent Nanoscopy

The design, synthesis, and evaluation of new rhodamine spiroamides are described. These molecules have applications in optical nanoscopy based on random switching of the fluorescent single molecules. The new markers may be used in (co)localization studies of various objects and their (mutual) positions and shape can be determined with a precision of a few tens of nanometers. Multicolor staining, good photoactivation, a large number of emitted photons, and selective chemical binding with amino or thiol groups were achieved due to the presence of various functional groups on the rhodamine spiroamides. Rigidized sulfonated xanthene fragment fused with six‐membered rings, N,N′‐bis(2,2,2‐trifluoroethyl) groups, and a combination of additional double bonds and sulfonic acid groups with simple aliphatic spiroamide residue provide multicolor properties and improve performance of the rhodamine spiroamides in photoactivation and bioconjugation reactions. Having both essential parts of the photoswitchable assembly—the switching and the fluorescent (reporter) groups—combined in one chemical entity make this approach attractive for further development. A series of rhodamine spiroamides is presented along with characterizations of their most relevant properties for application as fluorescent probes in single‐molecule switching and localization microscopy. Optical images with resolutions on the nanometer scale illustrate the potential of the labels in the colocalization of biological objects and the two‐photon activation technique with optical sectioning.     

The Substituent Effect of 1‐Arylazonaphthen‐2‐ols on Azo‐hydrazone Tautomerization According to NMR Analysis

The substituent effect on azo‐hydrazone tautomerization of 1‐arylazonaphthen‐ols is studied by means of NMR analysis. Among the ¹³C chemical shifts, the C(2) of this series compound is the most sensitive to the variation in the nature of substituent on the phenyl ring. Therefore, the variation in the chemical shifts of C(2) is used to probe the substituent effect by using the substituent chemical shifts and free energy vs. Hammett’s constant (χρ⁺). Both methods give a negative correlation slope, indicating the electron‐with‐ drawing groups favor the hydrazone tautomer form. The effect on the chemical shifts of C(2) of compound 8 in ten solvents can be classified as the solvent with a proton‐donor, proton‐acceptor and arenes system. The substituent with electron‐donating character is more sensitive to the nature of solvent and it favors the hydrazone form. Free energy obtained from the dynamic NMR technique indicates the tautomerization favors the hydrazone‐form for the substituent with electron‐withdrawing character.     

Investigating the interaction of sunset yellow aggregates and 6‐fluoro‐2‐naphthoic acid: increasing probe molecule complexity

The interaction of small molecules with non‐covalent assemblies is of wide interest. The use of a magnetically active reporter nucleus allows information to be obtained in the presence of spectral overlap or in cases of high dynamic range. In this paper, we explore the interaction of a larger probe molecule, 6‐fluoro‐2‐naphthoic acid with assemblies of sunset yellow using ¹⁹F chemical shifts and diffusion NMR methods. Comparing the observations with previous studies using fluorophenols, 6‐fluoro‐2‐naphthoic acid prefers to associate as clusters at the ends of the sunset yellow stacks. Copyright © 2014 John Wiley & Sons, Ltd.