A Lucifer‐Based Environment‐Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs

Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore ( 1,8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them.     

Rational Design of a Ratiometric Fluorescent Probe Based on Arene–Metal‐Ion Contact for Endogenous Hydrogen Sulfide Detection in Living Cells

We report the design and development of a fluorescent Cd^II ion complex that is capable of the ratiometric detection of H₂S in living cells. This probe exploits the metal‐ion‐induced emission red shift resulting from direct contact between the aromatic ring of a fluorophore and a metal ion (i.e., arene–metal‐ion or “AM” contact). The Cd^II complex displays a large emission blue shift upon interaction with H₂S as the Cd^II‐free ligand is released by the formation of cadmium sulfide. Screening of potential ligands and fluorophores led to the discovery of a pyronine‐type probe, 6? Cd^II, that generated a sensitive and rapid ratio value change upon interaction with H₂S, without interference from the glutathione that is abundant in the cell. The membrane‐impermeable 6? Cd^II was successfully translocated into live cells by using an oligo‐arginine peptide and pyrenebutylate as carriers. As such, 6? Cd^II was successfully applied to the ratiometric detection of both exogenous and endogenous H₂S produced by the enzymes in living cells, thus demonstrating the utility of 6? Cd^II in biological fluorescence analysis.     

Fluorescent Mechanism‐Based Probe for Aerobic Flavin‐Dependent Enzyme Activity

Diversity in non‐ribosomal peptide and polyketide secondary metabolism is facilitated by interactions between biosynthetic domains with discrete monomer loading and their cognate tailoring enzymes, such as oxidation or halogenation enzymes. The cooperation between peptidyl carrier proteins and flavin‐dependent enzymes offers a specialized strategy for monomer selectivity for oxidization of small molecules from within a complex cellular milieu. In an effort to study this process, we have developed fluorescent probes to selectively label aerobic flavin‐dependent enzymes. Here we report the preparation and implementation of these tools to label oxidase, monooxygenase, and halogenase flavin‐dependent enzymes.     

Fast-Response Fluorogenic Probe for Visualizing Hypochlorite in Living Cells and in Zebrafish

A fast-response fluorogenic probe—compound D1 —for monitoring hypochlorite (ClO⁻), based on specific ClO⁻ cleavage of a C=N bond and producing results observable to the naked eye, has been developed. The response of the probe to ClO⁻ increases linearly, and the fluorescence intensity was heightened by a factor of about 25. D1 responses to ClO⁻, with high selectivity and sensitivity, were observable by naked eye within 10 s. D1 can not only detect levels of hypochlorite in vitro, such as in urine, but is also capable of monitoring hypochlorite content under extremely cold conditions, as low as −78 °C. Meanwhile, its good biocompatibility permitted the use of D1 to detect intracellular ClO⁻ by confocal microscopy. Moreover, D1 was successfully applied to monitor exogenous and endogenous ClO⁻ in zebrafish through fluorescence imaging.     

Targeted Delivery of an Activatable Fluorescent Probe for the Detection of Furin Activity in Living Cells

Furin, a protein convertase, plays a crucial role in the progression of tumors. In this work, a new fluorescent probe consisting of a peptide, Arg‐Val‐Arg‐Arg (RVRR), and an aminoluciferin fluorophore was designed and prepared for the responsive and activatable detection of furin activity in vitro and in living cells. We demonstrated that this probe could be responsive toward furin with an “off–on” florescence signal and generated an approximately 3.58‐fold enhancement in the fluorescence intensity in vitro. Fluorescence imaging in MDA‐MB‐468 and LoVo cells showed that the probe could be cleaved by overexpressed furin with fluorescence turn‐on in MDA‐MB‐468 cells, and this probe was also found to be capable of discriminating between furin‐overexpressing and furin‐deficient cell lines. Our research indicates that this probe has great potential for the detection of furin activity in living cells.     

A One‐Step Staining Probe for Phosphatidylethanolamine

Phosphatidylethanolamine (PE) is an abundant phospholipid in cellular membranes, but relatively little is known about the kinetics of PE in biological membrane systems. Characterizing PE on a cellular level has been challenging owing to a lack of proper molecular tools. The lantibiotic duramycin and its structural analogue, cinnamycin, are currently the only known polypeptides that have an established stereospecific structure for binding membrane PE with high affinity and high specificity. These lantibiotics are recognized for their potential as molecular probes for studying PE kinetics in various membranes. However, owing to their antibiotic nature, duramycin and cinnamycin exhibit appreciable levels of cytotoxicity at low micromolar concentrations in cultured mammalian cells by inducing membrane distortion and possible PE redistribution. These issues can potentially complicate study design and data interpretation. Here, we report the construction of a molecular probe consisting of duramycin attached to the C terminus of green fluorescent protein (GFP) by a PEG linker at a stoichiometry of 1. The construct retained specific binding toward PE and essentially no cytotoxicity compared to native duramycin. The biological utilities of this probe were demonstrated in a number of cellular staining studies involving PE dynamics. The availability of a one‐step, nontoxic molecular probe for PE will enable characterization of the biology of this important phospholipid.     

Red Fluorescent Turn‐On Ligands for Imaging and Quantifying G Protein‐Coupled Receptors in Living Cells

Classical fluorescence‐based approaches to monitor ligand–protein interactions are generally hampered by the background signal of unbound ligand, which must be removed by tedious washing steps. To overcome this major limitation, we report here the first red fluorescent turn‐on probes for a G protein‐coupled receptor (oxytocin receptor) at the surface of living cells. The peptide ligand carbetocin was conjugated to one of the best solvatochromic (fluorogenic) dyes, Nile Red, which turns on emission when reaching the hydrophobic environment of the receptor. We showed that the incorporation of hydrophilic octa(ethylene glycol) linker between the pharmacophore and the dye minimized nonspecific interaction of the probe with serum proteins and lipid membranes, thus ensuring receptor‐specific turn‐on response. The new ligand was successfully applied for background‐free imaging and quantification of oxytocin receptors in living cells.     

Two‐Photon Fluorescent Imaging of Myelination in the Spinal Cord

Myelination is a fundamental biological process in the vertebrate nervous system. Damage to or malformation of myelin can lead to various neurological diseases; for example, demyelination in the spinal cord is a major cause of paralysis of patients suffering from multiple sclerosis and related diseases. The ability to directly track myelin levels in the spinal cord is needed in order to assess the efficacy of therapeutics in promoting myelin repair. To address this unmet need, 4‐((E)‐4‐((E)‐4‐aminostyryl)‐2,5‐dimethoxystyryl)‐N‐methylaniline, known as Case Imaging Compound (CIC), has been developed as a myelin‐targeted fluorescent imaging agent that selectively binds to myelin. CIC was synthesized via an improved route and evaluated as a fluorescent probe for two‐photon fluorescent imaging of myelin in the spinal cord in both demyelinated and dysmyelinated models. In vitro and ex vivo tissue staining both suggest that CIC selectively binds to in animal models. Further evaluation in animal models indicated that CIC is sensitive to differences in myelin content in healthy versus pathological myelin. CIC could potentially be useful in the development and evaluation of novel therapies for multiple sclerosis and other demyelinating diseases.     

Activity-Based Near-Infrared Fluorescent Probe for LMP7: A Chemical Proteomics Tool for the Immunoproteasome in Living Cells

Probing the unknown: The immunoproteasome, an alternative form of the constitutive proteasome, has been implicated in a number of pathological states such as cancer and autoimmune diseases. In an effort to understand the role of the immunoproteasome in cells, the first immunoproteasome-specific near-infrared fluorescent probe has been developed.     

Carbonate-Based Fluorescent Chemical Tool for Uncovering Carboxylesterase 1 (CES1) Activity Variations in Live Cells

Carboxylesterase 1 (CES1) plays a key role in the metabolism of endogenous biomolecules and xenobiotics including a variety of pharmaceuticals. Despite the established importance of CES1 in drug metabolism, methods to study factors that can vary CES1 activity are limited with only a few suitable for use in live cells. Herein, we report the development of FCP1, a new CES1 specific fluorescent probe with a unique carbonate substrate constructed from commercially available reagents. We show that FCP-1 can specifically report on endogenous CES1 activity with a robust fluorescence response in live HepG2 cells through studies with inhibitors and genetic knockdowns. Subsequently, we deployed FCP-1 to develop a live cell fluorescence microscopy-based approach to identify activity differences between CES1 isoforms. To the best of our knowledge, this is the first application of a fluorescent probe to measure the activity of CES1 sequence variants in live cells.     

Glycosyl‐Modified Diporphyrins for in Vitro and in Vivo Fluorescence Imaging

The application of probes for optical imaging is becoming popular as they have high safety and good biocompatibility. We prepared two kinds of glycosyl‐modified diporphyrins, and their potentials as fluorescent probes were tested for the first time. After preparation of the glycosyl‐modified porphyrin monomers, Ag‐promoted coupling of the monomers was used to obtain glucose‐modified porphyrin dimer (GPD) and lactose‐modified porphyrin dimer (LPD). The strong interaction between the two porphyrin rings achieves red‐shifted emission, and thus circumvents autofluorescence and light‐scattering in biological samples. Although the glycosylation improves solubility, it also yielded selective attachment to cell membranes, and to chorions of early developmental‐stage zebrafish. Patch‐clamp experiments revealed the biocompatibility and low toxicity of GPD and LPD. Moreover, an in vivo imaging experiment provided direct evidence that zebrafish chorion contains sugar‐binding proteins. The modification and derivatization make porphyrins potential bioimaging probes for specific optical imaging.     

High Spatial Resolution Imaging of Endogenous Hydrogen Peroxide in Living Cells by Solid‐State Fluorescence

Herein, we describe selective imaging of hydrogen peroxide using a precipitating dye conjugated to a boronic acid‐based immolative linker. We achieved visualization of endogenous hydrogen peroxide in phagosomes by solid‐state two‐photon fluorescence imaging in living cells with exceptionally high spatial resolution.     

Monitoring Biosensor Activity in Living Cells with Fluorescence Lifetime Imaging Microscopy

Live-cell microscopy is now routinely used to monitor the activities of the genetically encoded biosensor proteins that are designed to directly measure specific cell signaling events inside cells, tissues, or organisms. Most fluorescent biosensor proteins rely on Förster resonance energy transfer (FRET) to report conformational changes in the protein that occur in response to signaling events, and this is commonly measured with intensity-based ratiometric imaging methods. An alternative method for monitoring the activities of the FRET-based biosensor proteins is fluorescence lifetime imaging microscopy (FLIM). FLIM measurements are made in the time domain, and are not affected by factors that commonly limit intensity measurements. In this review, we describe the use of the digital frequency domain (FD) FLIM method for the analysis of FRET signals. We illustrate the methods necessary for the calibration of the FD FLIM system, and demonstrate the analysis of data obtained from cells expressing “FRET standard” fusion proteins. We then use the FLIM-FRET approach to monitor the changes in activities of two different biosensor proteins in specific regions of single living cells. Importantly, the factors required for the accurate determination and reproducibility of lifetime measurements are described in detail.     

Endo‐β‐Glucosidase Tag Allows Dual Detection of Fusion Proteins by Fluorescent Mechanism‐Based Probes and Activity Measurement

β‐Glucoside‐configured cyclophellitols are activity‐based probes (ABPs) that allow sensitive detection of β‐glucosidases. Their applicability to detect proteins fused with β‐glucosidase was investigated in the cellular context. The tag was Rhodococcus sp. M‐777 endoglycoceramidase II (EGCaseII), based on its lack of glycans and ability to hydrolyze fluorogenic 4‐methylumbelliferyl β‐d ‐lactoside (an activity absent in mammalian cells). Specific dual detection of fusion proteins was possible in vitro and in situ by using fluorescent ABPs and a fluorogenic substrate. Pre‐blocking with conduritol β‐epoxide (a poor inhibitor of EGCaseII) eliminated ABP labeling of endogenous β‐glucosidases. ABPs equipped with biotin allowed convenient purification of the fusion proteins. Diversification of ABPs (distinct fluorophores, fluorogenic high‐resolution detection moieties) should assist further research in living cells and organisms.     

一种检测环境样品和细胞中肼的香豆素类比率型荧光探针

以香豆素为荧光团,4-溴丁酰基为识别基团,设计合成了一种比率型肼荧光探针COCB。其结构通过1HNMR、13CNMR和HRMS确证。肼对探针COCB中溴代丁酰基的选择性脱保护使分子内电荷转移(ICT)过程恢复；COCB在 420 nm 处蓝色荧光衰减,而在 480 nm 处青色荧光增强,实现了对肼的比率检测。COCB对肼表现出高选择性、高灵敏度和强抗干扰能力,并能在较宽的线性范围(0~250 μmol/L)和pH范围(6~11)内检测肼,检出限低至0.15μmol/L。此外,COCB合成简便,细胞毒性较低,已成功用于实际水样、土壤以及活细胞中肼的检测。