DCDHF Fluorophores for Single‐Molecule Imaging in Cells

There is a persistent need for small‐molecule fluorescent labels optimized for single‐molecule imaging in the cellular environment. Application of these labels comes with a set of strict requirements: strong absorption, efficient and stable emission, water solubility and membrane permeability, low background emission, and red‐shifted absorption to avoid cell autofluorescence. We have designed and characterized several fluorophores, termed “DCDHF” fluorophores, for use in live‐cell imaging based on the push–pull design: an amine donor group and a 2‐dicyanomethylene‐3‐cyano‐2,5‐dihydrofuran (DCDHF) acceptor group, separated by a π‐rich conjugated network. In general, the DCDHF fluorophores are comparatively photostable, sensitive to local environment, and their chemistries and photophysics are tunable to optimize absorption wavelength, membrane affinity, and solubility. Especially valuable are fluorophores with sophisticated photophysics for applications requiring additional facets of control, such as photoactivation. For example, we have reengineered a red‐emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low‐intensity violet light. This molecule and its relatives provide a new class of bright photoactivatable small‐molecule fluorophores, which are needed for super‐resolution imaging schemes that require active control (here turning‐on) of single‐molecule emission.     

Manganese‐Induced Triplet Blinking and Photobleaching of Single Molecule Cyanine Dyes

Irradiation of solutions of the cyanine dyes Cy3, Cy3B, and Cy5 in the presence of Mn²⁺ causes an increase in the yield of formation of the triplet state of the dye. This results in increased photobleaching and triplet blinking. Experiments with other divalent ions and paramagnetic molecules suggest that the enhancement in the intersystem‐crossing rate is related to the paramagnetic nature of the Mn²⁺ cation. The results are consistent with a model in which the formation of a weak collisional complex between the dye and the ion results in mixing of the singlet and triplet states of the dye. These findings are particularly significant in single‐molecule spectroscopy and super‐resolution imaging methods, in which photobleaching and blinking play an important role.     

Fluorescence Detection of Single‐Nucleotide Polymorphisms with a Single,Self‐Complementary,Triple‐Stem DNA Probe

Singled out for its singularity : In a single‐step, single‐component, fluorescence‐based method for the detection of single‐nucleotide polymorphisms at room temperature, the sensor is comprised of a single, self‐complementary DNA strand that forms a triple‐stem structure. The large conformational change that occurs upon binding to perfectly matched (PM) targets results in a significant increase in fluorescence (see picture; F=fluorophore, Q=quencher).

     

Spectral Versatility of Single Reef Coral Fluorescent Proteins Detected by Spectrally‐Resolved Single Molecule Spectroscopy

We use spectrally‐resolved room temperature single molecule spectroscopy to yield insights into the occurrence and dynamics of spectral forms of single tetramers of DsRed and its variants DsRed2, Fluorescent Timer, DsRed_N42H and AG4. The red‐emitting chromophore in DsRed and all studied variants readily converts into a high quantum efficiency super‐red emitting form. We propose the existence of two super‐red forms of different quantum efficiencies. The observed emission from the green‐emitting chromophore is consistent with bulk spectroscopy. We further observe distinct new spectral forms from each variant, which we attribute to a photoinduced chemical reaction leading to a truncated form of the red‐emitting chromophore analogous to the chromophore in the visible fluorescent protein zFP538. Our results have implications for the accurate interpretation of biological and biochemical processes illuminated by fluorescent proteins as well as for choosing appropriate experimental configurations.     

Surface Immobilization of Redox‐Labile Fluorescent Probes: Enabling Single‐Cell Co‐Profiling of Aerobic Glycolysis and Oncogenic Protein Signaling Activities

An analytical method is described for profiling lactate production in single cells via the use of coupled enzyme reactions on surface‐grafted resazurin molecules. The immobilization of the redox‐labile probes was achieved through chemical modifications on resazurin, followed by bio‐orthogonal click reactions. The lactate detection was demonstrated to be sensitive and specific. The method was incorporated into a single‐cell barcode chip for simultaneous quantification of aerobic glycolysis activities and oncogenic signaling phosphoproteins in cancer. The interplay between glycolysis and oncogenic signaling activities was interrogated on a glioblastoma cell line. Results revealed a drug‐induced oncogenic signaling reliance accompanying shifted metabolic paradigms. A drug combination that exploits this induced reliance exhibited synergistic effects in growth inhibition.     

Rational Structure‐Based Design of Bright GFP‐Based Complexes with Tunable Dimerization

Fluorescent proteins are transformative tools; thus, any brightness increase is a welcome improvement. We invented the “vGFP strategy” based on structural analysis of GFP bound to a single‐domain antibody, predicting tunable dimerization, enhanced brightness (ca. 50 %), and improved pH resistance. We verified all of these predictions using biochemistry, crystallography, and single‐molecule studies. We applied the vsfGFP proteins in three diverse scenarios: single‐step immunofluorescence in vitro (3× brighter due to dimerization); expression in bacteria and human cells in vivo (1.5× brighter); and protein fusions showing better pH resistance in human cells in vivo. The vGFP strategy thus allows upgrading of existing applications, is applicable to other fluorescent proteins, and suggests a method for tuning dimerization of arbitrary proteins and optimizing protein properties in general.     

Construction of a Selective Fluorescent Probe for GSH Based on a Chloro‐Functionalized Coumarin‐enone Dye Platform

Glutathione (GSH), the most abundant intracellular biothiol, protects cellular components from damage caused by free radicals and reactive oxygen species (ROS), and plays a crucial role in human pathologies. A fluorescent probe that can selectively sense intracellular GSH would be very valuable for understanding of its biological functions and mechanisms of diseases. In this work, a 3,4‐dimethoxythiophenol‐substituted coumarin‐enone was exploited as a reaction‐type fluorescent probe for GSH based on a chloro‐functionalized coumarin‐enone platform. In the probe, the 3,4‐dimethoxythiophenol group functions not only as a fluorescence quencher through photoinduced electron transfer (PET) to ensure a low background fluorescence, but also as a reactive site for biothiols. The probe displays a dramatic fluorescence turn‐on response toward GSH with the long‐wavelength emission (600 nm) and significant Stokes shift (100 nm). The selectivity of the probe toward GSH over cysteine (Cys), homocysteine (Hcy), and other amino acids was demonstrated. Assisted by laser‐scanning confocal microscopy, we have demonstrated that the probe could specifically sense GSH over Cys/Hcy in human renal cell carcinoma SiHa cells.     

Utilizing a pH‐Sensitive Dye in the Selective Fluorescent Recognition of Sulfate

A receptor containing amidopyrrole binding subunits and free amino groups, conjugated to a naphthalimide dye, has been designed and synthesized. The intrinsic selectivity of the binding motif for phosphate present in DMSO completely disappears in 10 % DMSO aqueous buffer at pH 3.6, at which the receptor is protonated. The electrostatic interactions between the receptor and an anion start to dominate, thus leading to selectivity for sulfate. The ability of the HSO₄^? anion to transfer the proton to the amino group during the recognition event suppresses the photoinduced electron transfer (PET) on the dye, resulting in a selective turn‐on fluorescent response. The choice of pH of the solution for sensing is dictated by the pK_a value of the dye.     

Linking Phospholipase Mobility to Activity by Single‐Molecule Wide‐Field Microscopy

Many of the biological processes taking place in cells are mediated by enzymatic reactions occurring in the cell membrane. Understanding interfacial enzymatic catalysis is therefore crucial to the understanding of cellular function. Unfortunately, a full picture of the overall mechanism of interfacial enzymatic catalysis, and particularly the important diffusion processes therein, remains unresolved. Herein we demonstrate that single‐molecule wide‐field fluorescence microscopy can yield important new information on these processes. We image phospholipase enzymes acting upon bilayers of their natural phospholipid substrate, tracking the diffusion of thousands of individual enzymes while simultaneously visualising local structural changes to the substrate layer. We study several enzyme types with different affinities and catalytic activities towards the substrate. Analysis of the trajectories of each enzyme type allows us successfully to correlate the mobility of phospholipase with its catalytic activity at the substrate. The methods introduced herein represent a promising new approach to the study of interfacial/heterogeneous catalysis systems.     

Self‐Pillared,Single‐Unit‐Cell Sn‐MFI Zeolite Nanosheets and Their Use for Glucose and Lactose Isomerization

Single‐unit‐cell Sn‐MFI, with the detectable Sn uniformly distributed and exclusively located at framework sites, is reported for the first time. The direct, single‐step, synthesis is based on repetitive branching caused by rotational intergrowths of single‐unit‐cell lamellae. The self‐pillared, meso‐ and microporous zeolite is an active and selective catalyst for sugar isomerization. High yields for the conversion of glucose into fructose and lactose to lactulose are demonstrated.     

Loading of a Coordination Polymer Nanobelt on a Functional Carbon Fiber: A Feasible Strategy for Visible‐Light‐Active and Highly Efficient Coordination‐Polymer‐Based Photocatalysts

To improve the photocatalytic properties of coordination polymers under irradiation in the visible‐light region, coordination polymer nanobelts (CPNB) were loaded on functional carbon fiber (FCF) through the use of a simple colloidal blending process. The resulting coordination polymer nanobelt loaded functional carbon fiber composite material (CPNB/FCF) exhibited dramatically improved photocatalytic activity for the degradation of rhodamine B (RhB) under visible‐light irradiation. Optical and electrochemical methods illustrated the enhanced photocatalytic activity of CPNB/FCF originated from high separation efficiency of photogenerated electrons and holes on the interface of CPNB and FCF, which was produced by the synergy effect between them. In the composite material, the role of FCF could be described as photosensitizer and good electron transporter. For FCF, the number of functional groups on its surface has a significant influence on the photocatalytic performance of the resulting CPNB/FCF composite material, and an ideal FCF carrier was obtained as a highly efficient CPNB/FCF photocatalyst. CPNB/FCF showed outstanding stability during the degradation of rhodamine B (RhB); thus, the material is suitable for use as a photocatalyst in the treatment of organic dyes in water.     

Far‐Red and Near‐IR AIE‐Active Fluorescent Organic Nanoprobes with Enhanced Tumor‐Targeting Efficacy: Shape‐Specific Effects

The rational design of high‐performance fluorescent materials for cancer targeting in vivo is still challenging. A unique molecular design strategy is presented that involves tailoring aggregation‐induced emission (AIE)‐active organic molecules to realize preferable far‐red and NIR fluorescence, well‐controlled morphology (from rod‐like to spherical), and also tumor‐targeted bioimaging. The shape‐tailored organic quinoline–malononitrile (QM) nanoprobes are biocompatible and highly desirable for cell‐tracking applications. Impressively, the spherical shape of QM‐5 nanoaggregates exhibits excellent tumor‐targeted bioimaging performance after intravenously injection into mice, but not the rod‐like aggregates of QM‐2.     

High‐Throughput Development of a Hybrid‐Type Fluorescent Glutamate Sensor for Analysis of Synaptic Transmission

Fluorescent sensors are powerful tools for visualizing cellular molecular dynamics. We present a high‐throughput screening system, designated hybrid‐type fluorescence indicator development (HyFInD), to identify optimal position‐specific fluorophore labeling in hybrid‐type sensors consisting of combinations of ligand‐binding protein mutants with small molecular fluorophores. We screened sensors for glutamate among hybrid molecules obtained by the reaction of four cysteine‐reactive fluorescence probes with a set of cysteine‐scanning mutants of the 274 amino acid S1S2 domain of AMPA‐type glutamate receptor GluA2 subunit. HyFInD identified a glutamate‐responsive probe (enhanced glutamate optical sensor: eEOS) with a dynamic range >2400 %, good photostability, and high selectivity. When eEOS was specifically tethered to neuronal surfaces, it reliably visualized the spatiotemporal dynamics of glutamate release at single synapses, revealing synapse‐to‐synapse heterogeneity of short‐term plasticity.     

Second‐Generation Fluorescent Quadracyclic Adenine Analogues: Environment‐Responsive Probes with Enhanced Brightness

Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two‐step pathway with the Suzuki–Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦ_F) of 1700 and 2300, respectively, in water and behave as wavelength‐ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity‐sensitive dual‐band emissions that could prove useful to investigate DNA structural changes induced by DNA–protein or –drug interactions. The four qANs are very promising microenvironment‐sensitive fluorescent adenine analogues that display considerable brightness for such compounds.