Exploiting the Nitrilotriacetic Acid Moiety for Biolabeling with Ultrastable Perylene Dyes

Stimuli-fluorochromic smart organic materials

Smart materials based on stimuli-fluorochromic π-conjugated solids (SFCSs) have aroused significant interest due to their versatile and exciting properties, leading to advanced applications. In this review, we highlight the recent developments in SFCS-based smart materials, expanding beyond organometallic compounds and light-responsive organic luminescent materials, with a discussion on the design strategies, exciting properties and stimuli-fluorochromic mechanisms along with their potential applications in the exciting fields of encryption, sensors, data storage, display, green printing, etc. The review comprehensively covers single-component and multi-component SFCSs as well as their stimuli-fluorochromic behaviors under external stimuli. We also provide insights into current achievements, limitations, and major challenges as well as future opportunities, aiming to inspire further investigation in this field in the near future. We expect this review to inspire more innovative research on SFCSs and their advanced applications so as to promote further development of smart materials and devices.

Biosensors Based on the Binding Events of Nitrilotriacetic Acid-Metal Complexes

Molecular immobilization and recognition are two key events for the development of biosensors. The general ways for the immobilization and recognition of biomolecules include covalent coupling reactions and non-covalent interactions of antigen-antibody, aptamer-target, glycan-lectin, avidin-biotin and boronic acid-diol. Tetradentate nitrilotriacetic acid (NTA) is one of the most common commercial ligands for chelating metal ions. The NTA-metal complexes show high and specific affinity toward hexahistidine tags. Such metal complexes have been widely utilized in protein separation and immobilization for diagnostic applications since most of commercialized proteins have been integrated with hexahistidine tags by synthetic or recombinant techniques. This review focused on the development of biosensors with NTA-metal complexes as the binding units, mainly including surface plasmon resonance, electrochemistry, fluorescence, colorimetry, surface-enhanced Raman scattering spectroscopy, chemiluminescence and so on.

Recent Advances in Excimer-Based Fluorescence Probes for Biological Applications

The fluorescent probe is a powerful tool for biological sensing and optical imaging, which can directly display analytes at the molecular level. It provides not only direct visualization of biological structures and processes, but also the capability of drug delivery systems regarding the target therapy. Conventional fluorescent probes are mainly based on monomer emission which has two distinguishing shortcomings in practice: small Stokes shifts and short lifetimes. Compared with monomer-based emission, excimer-based fluorescent probes have large Stokes shifts and long lifetimes which benefit biological applications. Recent progress in excimer-based fluorescent sensors (organic small molecules only) for biological applications are highlighted in this review, including materials and mechanisms as well as their representative applications. The progress suggests that excimer-based fluorescent probes have advantages and potential for bioanalytical applications.

Design and Synthesis of Porphyrin-Nitrilotriacetic Acid Dyads with Potential Applications in Peptide Labeling through Metallochelate Coupling

The need to detect and monitor biomolecules, especially within cells, has led to the emerging growth of fluorescent probes. One of the most commonly used labeling techniques for this purpose is reversible metallochelate coupling via a nitrilotriacetic acid (NTA) moiety. In this study, we focus on the synthesis and characterization of three new porphyrin-NTA dyads, TPP-Lys-NTA, TPP-CC-Lys-NTA, and Py ₃ P-Lys-NTA composed of a porphyrin derivative covalently connected with a modified nitrilotriacetic acid chelate ligand (NTA), for possible metallochelate coupling with Ni²⁺ ions and histidine sequences. Emission spectroscopy studies revealed that all of the probes are able to coordinate with Ni²⁺ ions and consequently can be applied as fluorophores in protein/peptide labeling applications. Using two different histidine-containing peptides as His₆-tag mimic, we demonstrated that the porphyrin-NTA hybrids are able to coordinate efficiently with the peptides through the metallochelate coupling process. Moving one step forward, we examined the ability of these porphyrin-peptide complexes to penetrate and accumulate in cancer cells, exploring the potential utilization of our system as anticancer agents.

Fluorescent probes based on multifunctional encapsulated perylene diimide dyes for imaging of lipid droplets in live cells

A multifunctional encapsulation strategy confers perylene diimide dyes with high brightness, live-cell permeability, excellent anti-oxidation and lipid droplet-specific staining ability.

Fluorescent glycoconjugates and their applications

Fluorescent glycoconjugates are discussed for their applications in biology in vitro, in cell assays and in animal models. Advantages and limitations are presented for each design using a fluorescent core conjugated with glycosides, or vice versa.

Selective Detection of Pyrophosphate Anions in Aqueous Medium Using Aggregation of Perylene Diimide as a Fluorescent Probe

A water-soluble perylene diimide, aspartic acid-functionalized perylene diimide (APDI), has shown significant sequential "turn-off" and "turn-on" responses toward Cu2+ and inorganic pyrophosphate (PPi), respectively. APDI was found to show selectivity toward Cu2+ and inorganic PPi over adenosine monophosphate, adenosine diphosphate, and adenosine triphosphate. The detection has been studied by absorption and emission spectroscopy techniques. Incorporation of Cu2+ into the solution of APDI results in a distinct quenching of the fluorescence intensity, while there was no spectral change in the presence of other metal ions. The formed APDI-Cu2+ ensemble can turn on its fluorescence signal when PPi is present. The detection of PPi could be traced by looking at the change in color of the solution under the naked eye. No interference was observed from other anions, making the APDI-Cu2+aggregate a highly selective biosensor for PPi.

Diels–Alder reaction on perylenediimides: synthesis and theoretical study of core-expanded diimides

(Un)substituted perylenediimides react with (un)functionalized benzynes yielding core-expanded diimides.

A label-free and fluorescence turn-on assay for sensitive detection of hyaluronidase based on hyaluronan-induced perylene self-assembly

A label-free and fluorescence turn-on assay for sensitive detection of HAase based on HA–PDI nanoaggregates was reported.

Fluorescent Polymer-Single-Walled Carbon Nanotube Complexes with Charged and Noncharged Dendronized Perylene Bisimides for Bioimaging Studies

Fluorescent nanomaterials are expected to revolutionize medical diagnostic, imaging, and therapeutic tools due to their superior optical and structural properties. Their inefficient water solubility, cell permeability, biodistribution, and high toxicity, however, limit the full potential of their application. To overcome these obstacles, a water-soluble, fluorescent, cytocompatible polymer-single-walled carbon nanotube (SWNT) complex is introduced for bioimaging applications. The supramolecular complex consists of an alkylated polymer conjugated with neutral hydroxylated or charged sulfated dendronized perylene bisimides (PBIs) and SWNTs as a general immobilization platform. The polymer backbone solubilizes the SWNTs, decorates them with fluorescent PBIs, and strongly improves their cytocompatibility by wrapping around the SWNT scaffold. In photophysical measurements and biological in vitro studies, sulfated complexes exhibit superior optical properties, cellular uptake, and intracellular staining over their hydroxylated analogs. A toxicity assay confirms the highly improved cytocompatibility of the polymer-wrapped SWNTs toward surfactant-solubilized SWNTs. In microscopy studies the complexes allow for the direct imaging of the SWNTs' cellular uptake via the PBI and SWNT emission using the 1st and 2nd optical window for bioimaging. These findings render the polymer-SWNT complexes with nanometer size, dual fluorescence, multiple charges, and high cytocompatibility as valuable systems for a broad range of fluorescence bioimaging studies.

A Fluorescent Chemosensor for Zn2+ Based on a C3-Symmetrical and Pre-Organized 2,2′,2″-Nitrilotribenzoic Acid Material

A C3-symmetrical 4,4″,4⁗-nitrilotris(2′-methyl-[1,1′-biphenyl]-3-carboxylic acid) (4) derived from nitrilotriacetic acid (NTA) was found to selectively bind Zinc(ii) ions both in DMSO or MeOH. A synergistic effect of the anionic counter ion SO42− on the sensing behaviour of 4 to metal ions was clearly observed in DMSO. Interestingly, 4 showed a rapid hypochromatic shift in emission ascribed to the deprotonation and the concomitant formation of a 4–metal complex upon the addition of Zn2+ ions, instead of the bathochromic shift and emission enhancement attributed to the SO42−-involved hydrogen-bonding interaction for Ni2+, Li+, Mg2+, and Na+ ions at ratios below 1:1 in DMSO. The observed sensing process of sulfate salts associated with the SO42−-involved hydrogen-bonding interaction, deprotonation, and the concomitant complexation can also be clearly monitored by titration methods utilising UV-vis, fluorescence, and NMR spectroscopy in solution. In comparison with 4, compound 1 showed an obvious difference in the binding interaction with zinc sulfate in MeOH, probably owing to the decreased acidity. Anion-induced hydrogen-bonding interactions and deprotonation of the COOH protons in the excited state also endowed 4 versatile spectroscopic properties. The addition of F− and SO42− anions resulted in a remarkable enhancement probably related with a rigidifying effect. 2,2′,2″-Nitrilotribenzoic acid can be utilised as a potential scaffold to build a series of conjugated fluorescent sensors by its chelation effect owing to the rigid cavity pre-organised by the triphenylamine moiety and the carboxylic groups and the conjugation extension in the 4,4′,4″ positions.

Fluorescent RAFT polymers bearing a nitrilotriacetic acid (NTA) ligand at the α-chain-end for the site-specific labeling of histidine-tagged proteins

Fluorescent polymer probes bearing a nitrilotriacetic acid ligand at the α−chain-end selectively labeled histidine-tagged recombinant proteins.

Fluoride-mediated alkoxylation and alkylthio-functionalization of halogenated perylenediimides

The presence of fluoride ions in the reaction of chloro- or bromo-PDIs with alcohols and thiols leads to a spectacular increase in the yields of substituted compounds.

Perylenediimide-based glycoclusters as high affinity ligands of bacterial lectins: synthesis, binding studies and anti-adhesive properties

Rapid access to perylenediimide-based glycoclusters allowed their evaluation as high affinity ligands of bacterial lectins and their potential as anti-adhesive antibacterials.

Synthesis, Photophysical, and Biological Evaluation of Sulfated Polyglycerol Dendronized Perylenebisimides (PBIs)--A Promising Platform for Anti-Inflammatory Theranostic Agents?

A set of four water-soluble perylene bisimides (PBI) based on sulfated polyglycerol (PGS) dendrons were developed, their photophysical properties determined via UV/vis and fluorescence spectroscopy, and their performance as possible anti-inflammatory agents evaluated via biological in vitro studies. It could be shown that in contrast to charge neutral PG-PBIs the introduction of the additional electrostatic repulsion forces leads to a decrease in the dendron generation necessary for aggregation suppression, allowing the preparation of PBIs with fluorescence quantum yields of >95% with a considerable decreased synthetic effort. Furthermore, the values determined for L-selectin binding down to the nanomolar range, their limited impact on blood coagulation, and their minor activation of the complement system renders these systems ideal for anti-inflammatory purposes.

Novel derivatives of 1,6,7,12-tetrachloroperylene-3,4,9,10-tetracarboxylic acid: synthesis, electrochemical and optical properties

Facile synthesis and opto-electrochemical properties of various unsymmetrically “peri”-substituted perylene derivatives, with four chloro-atoms at the bay-positions, have been reported.

Direct alkylthio-functionalization of unsubstituted perylenediimides

A simple fluoride-mediated reaction allows the synthesis of 1,6-dialkylthioperylenediimides from unsubstituted perylenediimides under very mild conditions.

Molecular size, shape, and electric charges: essential for perylene bisimide-based DNA intercalator to localize in cell nuclei and inhibit cancer cell growth

The molecular properties concerning size, shape, and electric charges of the planar aromatic DNA intercalators are still poorly understood. Herein, a series of water-soluble perylene bisimide (PBI) derivatives containing a rigid and planar aromatic nanoscaffold with different size, shape, and electric charges were synthesized. Using histochemistry and cell viability assays on animal tissues and cancer cells, we revealed the molecular properties required for successful DNA intercalators to localize in cell nuclei and inhibit cancer cells. Small molecular size and the strong polarity of hydrophilic substituents are prerequisites for PBI-based DNA intercalators. A large number of charges facilitate the nucleic accumulation of these DNA intercalators, while fewer charges and planar aromatic nanoscaffold more efficiently inhibit cancer cell growth.

Advances in chemical labeling of proteins in living cells

The pursuit of quantitative biological information via imaging requires robust labeling approaches that can be used in multiple applications and with a variety of detectable colors and properties. In addition to conventional fluorescent proteins, chemists and biologists have come together to provide a range of approaches that combine dye chemistry with the convenience of genetic targeting. This hybrid-tagging approach amalgamates the rational design of properties available through synthetic dye chemistry with the robust biological targeting available with genetic encoding. In this review, we discuss the current range of approaches that have been exploited for dye targeting or for targeting and activation and some of the recent applications that are uniquely permitted by these hybrid-tagging approaches.

Reversible and oriented immobilization of histidine-tagged protein on silica gel characterized by frontal analysis

Utilizing N,N′-bis(carboxymethyl)-L-lysine (ANTA) combined with bivalent metal cation Ni²⁺, which leaving free sites for the reversible binding of gene recombinant histidine-tagged β₂-adrenoceptor onto silica gel.

Aggregation deaggregation influenced selective and sensitive detection of Cu2+ and ATP by histidine functionalized water-soluble fluorescent perylene diimide under physiological conditions and in living cells

A novel PDI-HIS probe detects Cu²⁺ to form aggregated nonfluorescent complex. Addition of 0.58 ppm ATP to this complex causes its rapid disaggregation thereby recovering the fluorescence by ∼99% in vitro and in A549 living cells.

Assembly modulation of PDI derivative as a supramolecular fluorescence switching probe for detection of cationic surfactant and metal ions in aqueous media

We report an amphiphilic perylene diimide (1), a bimolecular analog of l-3,4-dihydroxyphenylalanine (L-DOPA), as a reversible fluorescence switching probe for the detection and sensing of cationic surfactants and Fe(3+)/Cu(2+) in an aqueous media respectively by means of host-guest interactions driven assembly and disassembly of 1. Photophysical studies of 1, going from dimethyl sulfoxide (DMSO) (State-I) to pure aqueous medium (State-II), suggested the formation of self-assembled aggregates by displaying very weak fluorescence emission along with red shifted broad absorption bands. Interestingly, the cationic surfactant cetyltrimethylammonium bromide (CTAB) could disassemble 1 in miceller conditions by restoring bright yellow fluorescence and vibronically well-defined (Franck-Condon progressions A0-0/A0-1 ≈ 1.6) absorption bands of 1 over other neutral and anionic surfactants (State-III). Owing to the metal chelating nature of L-DOPA, 1 was able to sense Fe(3+) and Cu(2+) among a pool of other metal ions by means of fluorescence switching off state, attributed to metal interaction driven assembly of 1 (State-IV). Such metallosupramolecular assemblies were found to reverse back to the fluorescence switching on state using a metal ion chelator, diethylenetriaminepentaacetic acid (DTPA, State-III), further signifying the role of metal ions toward assembly of 1. Formation of assembly and disassembly could be visualized by the diminished and increased yellow emission under green laser light. Further, the assembly-disassembly modulation of 1 has been extensively characterized using infrared (IR), mass spectrometry, microscopy and dynamic light scattering (DLS) techniques. Therefore, modulation of the molecular self-assembly of PDI derivative 1 in aqueous media (assembled state, State-II) by means of host-guest interactions provided by micellar structures of CTAB (disassembled state, State-III), metal ion (Fe(3+) and Cu(2+)) interactions (assembled state, State-IV) and metal ion sequestration using DTPA (disassembled state, State-III) is viewed as a supramolecular reversible fluorescence switching off-on probe for cationic surfactant CTAB and Fe(3+)/Cu(2+).

Perylene-cored star-shaped polycations for fluorescent gene vectors and bioimaging

Two star polycations, poly(2-aminoethyl methacrylate) (PAEMA, P1) and poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA, P2), have been synthesized with perylene diimide (PDI) as the central fluorophore. (1)H NMR and (13)C NMR are used to confirm the successful synthesis of a macromolecular initiator. Using ATRP strategy, P1 and P2 are obtained with narrow molecular weight distribution. The star polymers have good fluorescence properties in aqueous solution, which provides fluorescent tracing and imaging during gene delivery. Both P1 and P2 can efficiently condense DNA into stable nanoparticles. Transfection studies demonstrate that P1 and P2 deliver DNA into live cells with higher efficiency and lower cytotoxicity than polyethylenimine (PEI, 25 kDa). P2 shows higher capacity for gene delivery than P1 due to its better buffering and faster rate of cellular internalization.

The regulatory switch of F1-ATPase studied by single-molecule FRET in the ABEL Trap

F₁-ATPase is the soluble portion of the membrane-embedded enzyme F_oF₁-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F₁ part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis by F₁ (or F_oF₁) must be minimized in the cell. In bacteria, the ε subunit is thought to control and block ATP hydrolysis by mechanically inserting its C-terminus into the rotary motor region of F₁. We investigate this proposed mechanism by labeling F₁ specifically with two fluorophores to monitor the C-terminus of the ε subunit by Förster resonance energy transfer. Single F₁ molecules are trapped in solution by an Anti-Brownian electrokinetic trap which keeps the FRET-labeled F₁ in place for extended observation times of several hundreds of milliseconds, limited by photobleaching. FRET changes in single F₁ and FRET histograms for different biochemical conditions are compared to evaluate the proposed regulatory mechanism.

Regulatory conformational changes of the ε subunit in single FRET-labeled FoF1-ATP synthase

Subunit ε is an intrinsic regulator of the bacterial F_oF₁-ATP synthase, the ubiquitous membrane-embedded enzyme that utilizes a proton motive force in most organisms to synthesize adenosine triphosphate (ATP). The C-terminal domain of ε can extend into the central cavity formed by the α and β subunits, as revealed by the recent X-ray structure of the F₁ portion of the Escherichia coli enzyme. This insertion blocks the rotation of the central γ subunit and, thereby, prevents wasteful ATP hydrolysis. Here we aim to develop an experimental system that can reveal conditions under which ε inhibits the holoenzyme F_oF₁-ATP synthase in vitro. Labeling the C-terminal domain of ε and the γ subunit specifically with two different fluorophores for single-molecule Förster resonance energy transfer (smFRET) allowed monitoring of the conformation of ε in the reconstituted enzyme in real time. New mutants were made for future three-color smFRET experiments to unravel the details of regulatory conformational changes in ε.

Grafting perylenes to ZnO nanoparticles

A new prototype of dendritic perylenes suitable for the chemical functionalization of inorganic nanoparticles was synthesized and characterized. The bay-functionalized perylene core of these molecular architectures was coupled to a catechol moiety, which serves as an anchor group for the functionalization of metal oxides, in particular ZnO. To increase the solubility of both the perylene and the targeted hybrid nanostructures, a Newkome-type dendron bearing nine positive charges was introduced. This charge was also employed to stabilize the nanoparticles and further protect them from Ostwald ripening through Coulombic repulsion. ZnO quantum dots with an average diameter of 5 nm were synthesized and functionalized with the perylene derivative. Successful functionalization was clearly demonstrated by dynamic light scattering, zeta-potential measurements, thermogravimetric analysis/MS, and UV/Vis and fluorescence spectroscopy. The generated particle dispersions were stable against agglomeration for more than eight weeks.

pH-sensitive perylene bisimide probes for live cell fluorescence lifetime imaging

Several new perylene bisimide (PBI) probes comprising oligo-guanidine conjugates and cationic hydrogel nanoparticle structures were designed for sensing intracellular pH in live cell fluorescence lifetime imaging microscopy (FLIM).

Novel EDTA-ligands containing an integral perylene bisimide (PBI) core as an optical reporter unit

The synthesis, characterization and metal complexation of a new class of perylene bisimides (PBIs) as an integral part of ethylenediaminetetraacetic acid (EDTA) are reported.

Twisting and subunit rotation in single F(O)(F1)-ATP synthase

F(O)F(1)-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single F(O)F(1)-ATP synthases.

Polyglycerol-Dendronized Perylenediimides as Stable, Water-Soluble Fluorophores

The synthesis and photophysical properties of water-soluble, fluorescent polyglycerol-dendronized perylenediimides 1-4 are reported. The polyglycerol dendrons, which are known to be highly biocompatible, are found to confer high water-solubility on the perylenediimide in aqueous media while retaining its excellent fluorescent properties. Furthermore, intramolecular cross-linking of the polyglycerol dendrons using the ring-closing metathesis reaction not only enhances the photostability but also reduces the size of perylenediimide-cored dendrimers. The permeability of the various dendritic shells is probed using heavy metal ion quenchers and compared to non-dendritic but water-soluble perylenediimide 5.

Isothermally reversible fluorescence switching of a mechanochromic perylene bisimide dye

Isothermally rewritable fluorescence mechanochromism has been realized for a perylene bisimide dye with bulky and flexible substituents. Fluorescent patterns drawn by mechanical stimuli can be erased by thermal stimuli, treatment with solvent vapors, or spontaneous structural transition from orange-fluorescent to green-fluorescent states. The isothermal fluorescence switching of solid dye films is applicable to displays and sensory materials.

A turn-on fluorescent sensor for pyrophosphate based on the disassembly of Cu2+-mediated perylene diimide aggregates

A complex between an anionic perylene diimide derivative (PDI-GlyAsp) and cupric ion has been prepared and applied to be turn-on fluorescent probe for the detection of pyrophosphate (PPi) in 100% aqueous solution. The complex formation process and PPi detection have been studied by absorption and emission spectroscopy. It was confirmed that the introduction of cupric ion into PDI-GlyAsp solution resulted in the assembly of PDI-GlyAsp into PDI-GlyAsp/Cu(2+) aggregates, leading to the fluorescence quenching of PDI-GlyAsp. Upon addition of PPi into the above solution led to the disassembly of the aggregates due to the competitive binding of PPi with Cu(2+) in the PDI-GlyAsp/Cu(2+) complex, and a recovery of PDI-GlyAsp emission was observed. Therefore, the PDI-GlyAsp/Cu(2+) complex can be applied as a turn-on fluorescent probe for detecting PPi with high selectivity and sensitivity.