Experimental and computational investigation of unsymmetrical cyanine dyes: understanding torsionally responsive fluorogenic dyes

Optimization of the fluorogen-activating protein tag for quantitative protein trafficking and colocalization studies in S. cerevisiae

Spatial and temporal tracking of fluorescent proteins (FPs) in live cells permits visualization of proteome remodeling in response to extracellular cues. Historically, protein dynamics during trafficking have been visualized using constitutively active FPs fused to proteins of interest. While powerful, such FPs label all cellular pools of a protein, potentially masking the dynamics of select subpopulations. To help study protein subpopulations, bioconjugate tags, including the fluorogen activation proteins (FAPs), were developed. FAPs are comprised of two components: a single-chain antibody (SCA) fused to the protein of interest and a malachite-green (MG) derivative, which fluoresces only when bound to the SCA. Importantly, the MG derivatives can be either cell-permeant or -impermeant, thus permitting isolated detection of SCA-tagged proteins at the cell surface and facilitating quantitative endocytic measures. To expand FAP use in yeast, we optimized the SCA for yeast expression, created FAP-tagging plasmids, and generated FAP-tagged organelle markers. To demonstrate FAP efficacy, we coupled the SCA to the yeast G-protein coupled receptor Ste3. We measured Ste3 endocytic dynamics in response to pheromone and characterized cis- and trans-acting regulators of Ste3. Our work significantly expands FAP technology for varied applications in S. cerevisiae.

Nucleic Acid-Binding Dyes as Versatile Photocatalysts for Atom-Transfer Radical Polymerization

Nucleic acid-binding dyes (NuABDs) are fluorogenic probes that light up after binding to nucleic acids. Taking advantage of their fluorogenicity, NuABDs have been widely utilized in the fields of nanotechnology and biotechnology for diagnostic and analytical applications. We demonstrate the potential of NuABDs together with an appropriate nucleic acid scaffold as an intriguing photocatalyst for precisely controlled atom-transfer radical polymerization (ATRP). Additionally, we systematically investigated the thermodynamic and electrochemical properties of the dyes, providing insights into the mechanism that drives the photopolymerization. The versatility of the NuABD-based platform was also demonstrated through successful polymerizations using several NuABDs in conjunction with diverse nucleic acid scaffolds, such as G-quadruplex DNA or DNA nanoflowers. This study not only extends the horizons of controlled photopolymerization but also broadens opportunities for nucleic acid-based materials and technologies, including nucleic acid-polymer biohybrids and stimuli-responsive ATRP platforms.

Effects of halogen atom substitution on luminescent radicals: a case study on tris(2,4,6-trichlorophenyl)methyl radical-carbazole dyads

A series of halogen-substitute carbazole TTM radicals was synthesized. The effect of halogen substituents on radical luminescence was systematically evaluated. It was found that the well-known heavy atom effect does not work in the emission of radicals and that halogen substitution of the donor carbazole can change the HOMO and alter the absorption and emission wavelengths. In addition, the photostability was found to be improved with respect to TTM but not significantly different from that of closed-shell fluorescent molecules.

Overcoming Resistance in Prostate Cancer Therapy Using a DZ-Simvastatin Conjugate

Prostate cancer (PC), particularly its metastatic castration-resistant form (mCRPC), is a leading cause of cancer-related deaths among men in the Western world. Traditional systemic treatments, including hormonal therapy and chemotherapy, offer limited effectiveness due to tumors' inherent resistance to these therapies. Moreover, they often come with significant side effects. We have developed a delivery method using a tumor-cell-specific heptamethine carbocyanine dye (DZ) designed to transport therapeutic agents directly to tumor cells. This research evaluated simvastatin (SIM) as the antitumor payload because of its demonstrated chemopreventive effects on human cancers and its well-documented safety profile. We designed and synthesized a DZ-SIM conjugate for tumor cell targeting. PC cell lines and xenograft tumor models were used to assess tumor-cell targeting specificity and killing activity and to investigate the corresponding mechanisms. DZ-SIM treatment effectively killed PC cells regardless of their androgen receptor status or inherent therapeutic resistance. The conjugate targeted and suppressed xenograft tumor formation without harming normal cells of the host. In cancer cells, DZ-SIM was enriched in subcellular organelles, including mitochondria, where the conjugate formed adducts with multiple proteins and caused the loss of transmembrane potential, promoting cell death. The DZ-SIM specifically targets PC cells and their mitochondria, resulting in a loss of mitochondrial function and cell death. With a unique subcellular targeting strategy, the conjugate holds the potential to outperform existing chemotherapeutic drugs. It presents a novel strategy to circumvent therapeutic resistance, offering a more potent treatment for mCRPC.

Analysis of DNA Origami Nanostructures Using Capillary Electrophoresis

DNA origami nanostructures are engineered nanomaterials (ENMs) that possess significant customizability, biocompatibility, and tunable structural and functional properties, making them potentially useful materials in fields, such as medicine, biocomputing, biomedical engineering, and measurement science. Despite the potential of DNA origami as a functional nanomaterial, a major barrier to its applicability is the difficulty associated with obtaining pure, well-folded structures. Therefore, rapid methods of analysis to ensure purity are needed to support the rapid development of this class of nanomaterials. Here, we present the development of capillary electrophoresis (CE) as an analytical tool for DNA origami. CE was investigated under both capillary zone electrophoresis (CZE) and capillary transient isotachophoresis (ctITP) modes. Optimization of both systems yielded baseline resolved separations of folded DNA origami nanostructures from excess staple strands. The ctITP separation mode demonstrated superior performance in terms of peak resolution (Rs = 2.05 ± 0.3), peak efficiency (N = 12,200 ± 230), and peak symmetry (As = 1.29 ± 0.032). The SYBR family dyes (Gold, Green I, and Green II) were investigated as highly efficient, noncovalent fluorophores for on-column labeling of DNA origami and detection using laser-induced fluorescence. Finally, ctITP analysis conditions were also applied to DNA origami nanostructures with different shapes and for the differentiation of DNA origami aggregates.

Real-time Imaging of Nascent DNA in Live Cells by Monitoring the Fluorescence Lifetime of DNA-Incorporated Thiazole Orange-Modified Nucleotides

A modified 2'-deoxycytidine triphosphate derivative (dCTO TP) bearing a thiazole orange moiety tethered via an oligoethylene glycol linker was designed and synthesized. The nucleotide was incorporated into DNA by DNA polymerases in vitro as well as in live cells. Upon incorporation of dCTO TP into DNA, the thiazole orange moiety exhibited a fluorescence lifetime that differed significantly from the non-incorporated (i.e. free and non-covalently intercalated) forms of dCTO TP. When dCTO TP was delivered into live U-2 OS cells using a synthetic nucleoside triphosphate transporter, it allowed us to distinguish and monitor cells that were actively synthesizing DNA in real time, from the very first moments after the treatment. We anticipate that this probe could be used to study chromatin organization and dynamics.

Development of Highly Fluorogenic Styrene Probes for Visualizing RNA in Live Cells

Styrene dyes are useful imaging probes and fluorescent sensors due to their strong fluorogenic responses to environmental changes or binding macromolecules. Previously, indole-containing styrene dyes have been reported to selectively bind RNA in the nucleolus and cytoplasm. However, the application of these indole-based dyes in cell imaging is limited by their moderate fluorescence enhancement and quantum yields, as well as relatively high background associated with these green-emitting dyes. In this work, we have investigated the positional and electronic effects of the electron donor by generating regioisomeric and isosteric analogues of the indole ring. Select probes exhibited large Stokes shifts, enhanced molar extinction coefficients, and bathochromic shifts in their absorption and fluorescence wavelengths. In particular, the indolizine analogues displayed high membrane permeability, strong fluorogenic responses upon binding RNA, compatibility with fluorescence lifetime imaging microscopy (FLIM), low cytotoxicity, and excellent photostability. These indolizine dyes not only give rise to rapid, sensitive, and intense staining of nucleoli in live cells but can also resolve subnucleolar structures enabling highly detailed studies of nucleolar morphology. Furthermore, our dyes can partition into RNA coacervates and resolve the formation of multiphase complex coacervate droplets. These indolizine-containing styrene probes offer the highest fluorescence enhancement among the RNA-selective dyes reported in the literature; thus, these new dyes are excellent alternatives to the commercially available RNA dye, SYTO RNASelect, for visualizing RNA in live cells and in vitro.

Conversion of Ketones into Blue-Emitting Electron-Deficient Benzofurans

A novel heavy metal-free and safe synthetic methodology enabling one-step conversion of ketones into corresponding 4,5,6,7-tetrafluorobenzofurans (F4 BFs) has been developed. The presented approach has numerous advantageous qualities, including utilization of readily available substrates, broad scope, scalability, and good reaction yields. Importantly, some of the benzofurans prepared by this method were heretofore inaccessible by any other known transformation. Importantly, furo[2,3-b]pyrazines and heretofore unexplored difuro[2,3-c:3',2'-e]pyridazine can be prepared using this strategy. Spectroscopic studies reveal that for simple systems, absorption and fluorescence maxima fall within the UV spectral range, while π-electron system expansion red-shifts both spectra. Moreover, the good fluorescence quantum yields observed in solution, up to 96 %, are also maintained in the solid state. Experimental results are supported by density functional theory (DFT) calculations. The presented methodology, combined with the spectroscopic characteristics, suggest the possibility of using F4 BFs in the optoelectronic industry (i. e., organic light emitting devices (OLED), organic field-effect transistors (OFET), organic photovoltaics (OPV)) as inexpensive and readily available emissive or semiconductor materials.

Metal-Assisted Complexation of Fluorogenic Dyes by Cucurbit[7]uril and Cucurbit[8]uril: A DFT Evaluation of the Key Factors Governing the Host-Guest Recognition

With the emergence of host-guest systems, a novel branch of complexation chemistry has found wide application in industries such as food, pharmacy, medicine, environmental protection and cosmetics. Along with the extensively studied cyclodextrins and calixarenes, the innovative cucurbiturils (CB) have enjoyed increased popularity among the scientific community as they possess even better qualities as cavitands as compared to the former molecules. Moreover, their complexation abilities could further be enhanced with the assistance of metal cations, which can interestingly exert a dual effect on the complexation process: either by competitively binding to the host entity or cooperatively associating with the CB@guest structures. In our previous work, two metal species (Mg²⁺ and Ga³⁺) have been found to bind to CB molecules in the strongest fashion upon the formation of host-guest complexes. The current study focuses on their role in the complex formation with three dye molecules: thiazole orange, neutral red, and thioflavin T. Various key factors influencing the process have been recognized, such as pH and the dielectric constant of the medium, the cavity size of the host, Mⁿ⁺ charge, and the presence/absence of hydration shell around the metal cation. A well-calibrated DFT methodology, solidly based and validated and presented in the literature experimental data, is applied. The obtained results shed new light on several aspects of the cucurbituril complexation chemistry.

Functional Cyanine-Based PVA:PVP Polymers as Antimicrobial Tools toward Food and Health-Care Bacterial Infections

The rising of multidrug-resistant bacteria and their associated proliferation as harmful microorganisms boosts the creation of new antibacterial surfaces and biomaterials with applications ranging from health to food packing. Herein, low-cost antibacterial PVA:PVP copolymers containing cyanine derivatives (1, 2, and 3) and their respective Cu²⁺ complexes are successfully obtained and tested against Gram-negative and Gram-positive bacteria. The possible application in food packing is addressed by covering the surface of typical paper mockups with the doped polymers. All dye-doped polymers present a broad-spectrum antibacterial effect against Gram-positive bacteria, especially for Bacillus cereus (B. cereus), Staphylococcus aureus (S. aureus), and methicillin-resistant S. aureus (MRSA) strains, with PVA:PVP@3 and PVA:PVP@3-Cu being the most effective. Moreover, polymers containing cyanine derivatives present interesting inhibition effects against Pseudomonas aeruginosa (P. aeruginosa), where the production of its characteristic blue/green virulent pigment is not observed. Of the coated paper mockups, PVA:PVP:paper@2 and PVA:PVP:paper@2-Cu are most effective against B. cereus and S. aureus, while PVA:PVP:paper@3 and PVA:PVP:paper@3-Cu are most effective against the MRSA strain. In these formulations, direct contact inhibition mechanisms appear to be more significant than diffusional mechanisms, due to cyanine release hindrance, making them very interesting and versatile platforms for medical and food applications.

Pharmaceutical Salts of Piroxicam and Meloxicam with Organic Counterions

Piroxicam (PRM) and meloxicam (MEL) are two nonsteroidal anti-inflammatory drugs, belonging to the Biopharmaceutics Classification System Class II drugs. In this study, six novel pharmaceutical salts of PRM and MEL with three basic organic counterions, that is, 4-aminopyridine (4AP), 4-dimethylaminopyridine (4DMP), and piperazine (PPZ), were prepared by both slurrying and slow evaporation. These salts were characterized by single-crystal and powder X-ray diffraction, thermal analysis, and Fourier transform infrared spectroscopy. All six salts, especially MEL-4DMP and MEL-4AP, showed a significantly improved apparent solubility and dissolution rate in sodium phosphate solution compared with the pure APIs. Notably, PRM-4AP and PRM-4DMP salts exhibited enhanced fluorescence, and the PRM-PPZ salt showed weaker fluorescence compared with that of pure PRM due to different luminescence mechanisms.

Informing geometric deep learning with electronic interactions to accelerate quantum chemistry

Predicting electronic energies, densities, and related chemical properties can facilitate the discovery of novel catalysts, medicines, and battery materials. However, existing machine learning techniques are challenged by the scarcity of training data when exploring unknown chemical spaces. We overcome this barrier by systematically incorporating knowledge of molecular electronic structure into deep learning. By developing a physics-inspired equivariant neural network, we introduce a method to learn molecular representations based on the electronic interactions among atomic orbitals. Our method, OrbNet-Equi, leverages efficient tight-binding simulations and learned mappings to recover high-fidelity physical quantities. OrbNet-Equi accurately models a wide spectrum of target properties while being several orders of magnitude faster than density functional theory. Despite only using training samples collected from readily available small-molecule libraries, OrbNet-Equi outperforms traditional semiempirical and machine learning-based methods on comprehensive downstream benchmarks that encompass diverse main-group chemical processes. Our method also describes interactions in challenging charge-transfer complexes and open-shell systems. We anticipate that the strategy presented here will help to expand opportunities for studies in chemistry and materials science, where the acquisition of experimental or reference training data is costly.

Encapsulation of Trimethine Cyanine in Cucurbit[8]uril: Solution versus Solid‐State Inclusion Behavior

Inclusion of polymethine cyanine dyes in the cavity of macrocyclic receptors is an effective strategy to alter their absorption and emission behavior in aqueous solution. In this paper, the effect of the host‐guest interaction between cucurbit[8]uril (CB[8]) and a model trimethine indocyanine (Cy3) on dye spectral properties and aggregation in water is investigated. Solution studies, performed by a combination of spectroscopic and calorimetric techniques, indicate that the addition of CB[8] disrupts Cy3 aggregates, leading to the formation of a 1 : 1 host‐guest complex with an association constant of 1.5×10⁶ M⁻¹. At concentrations suitable for NMR experiments, the slow formation of a supramolecular polymer was observed, followed by precipitation. Single crystals X‐ray structure elucidation confirmed the formation of a polymer with 1 : 1 stoichiometry in the solid state.

Recent advances in bioprobes and biolabels based on cyanine dyes

As a functional dye, cyanine dye promotes the widespread application of bioprobes in the fields of medicine, genetics and environment, owing to its advantages of good photophysical properties, excellent biocompatibility and low toxicity to biological systems. Nowadays, it is mainly used in the fields of life sciences such as fluorescent labeling of biological macromolecules, disease diagnosis, immunoassay and DNA detection, all of which lie at the core of this review. First, we briefly introduced the characteristics and principles of the cyanine dye bioprobe. Afterward, we paid attention to the recent progress of cyanine dye bioprobes widely used in the 10 years from 2010 to 2020. The application of cyanine dyes as bioprobes with different identification elements, including enzymes, organelles, immunity and DNAs, was mainly summarized. Finally, this review gave an outlook on the future development trend of cyanine dye bioprobes. This facilitates the construction of a new type of multifunctional fluorescent probe and promotes its clinical application.

From the Physicochemical Characteristic of Novel Hesperetin Hydrazone to Its In Vitro Antimicrobial Aspects

Microorganisms are able to give rise to biofilm formation on food matrixes and along food industry infrastructures or medical equipment. This growth may be reduced by the application of molecules preventing bacterial adhesion on these surfaces. A new Schiff base ligand, derivative of hesperetin, HABH (2-amino-N'-(2,3-dihydro-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chromen-4-ylidene)benzohydrazide), and its copper complex, CuHABH [CuLH₂(OAc)], were designed, synthesized and analyzed in terms of their structure and physicochemical properties, and tested as antibacterial agents. Their structures both in a solid state and in solution were established using several methods: FT-IR, ¹H NMR, ¹³C NMR, UV-Vis, FAB MS, EPR, ESI-MS and potentiometry. Coordination binding of the copper(II) complex dominating at the physiological pH region in the solution was found to be the same as that detected in the solid state. Furthermore, the interaction between the HABH and CuHABH with calf-thymus DNA (CT-DNA) were investigated. These interactions were tracked by UV-Vis, CD (circular dichroism) and spectrofluorimetry. The results indicate a stronger interaction of the CuHABH with the CT-DNA than the HABH. It can be assumed that the nature of the interactions is of the intercalating type, but in the high concentration range, the complex can bind to the DNA externally to phosphate residues or to a minor/major groove. The prepared compounds possess antibacterial and antibiofilm activities against Gram-positive and Gram-negative bacteria. Their antagonistic activity depends on the factor-strain test system. The glass was selected as a model surface for the experiments on antibiofilm activity. The adhesion of bacterial cells to the glass surface in the presence of the compounds was traced by luminometry and the best antiadhesive action against both bacterial strains was detected for the CuHABH complex. This molecule may play a crucial role in disrupting exopolymers (DNA/proteins) in biofilm formation and can be used to prevent bacterial adhesion especially on glass equipment.

Immobilization of Cyanines in DNA Produces Systematic Increases in Fluorescence Intensity

Cyanines are useful fluorophores for a myriad of biological labeling applications, but their interactions with biomolecules are unpredictable. Cyanine fluorescence intensity can be highly variable due to complex photoisomerization kinetics, which are exceedingly sensitive to the surrounding environment. This introduces large errors in Förster resonance energy transfer (FRET)-based experiments where fluorescence intensity is the output parameter. However, this environmental sensitivity is a strength from a biological sensing point of view if specific relationships between biomolecular structure and cyanine photophysics can be identified. We describe a set of DNA structures that modulate cyanine fluorescence intensity through the insertion of adenine or thymine bases. These structures simultaneously provide photophysical predictability and tunability. We characterize these structures using steady-state fluorescence measurements, fluorescence correlation spectroscopy (FCS), and time-resolved photoluminescence (TRPL). We find that the photoisomerization rate decreases over an order of magnitude across the adenine series, which is consistent with increasing immobilization of the cyanine moiety by the surrounding DNA structure.

Photophysics of thiazole orange in deep eutectic solvents

Photophysics and torsional dynamics of thiazole orange (TO) as a function of temperature have been studied in two deep eutectic solvents (DESs) using spectroscopic techniques. Two DESs are used as a solvent namely DES-I (choline chloride + urea, mole ratio 1: 2) and DES-II (N,N diethyl ethanol ammonium chloride + urea, mole ratio 1: 2). We explore the influence of DESs on the photophysical properties of TO. The fluorescence quantum yield and fluorescence lifetime of TO decreases with increasing temperature due to thermal deactivation. At higher temperature, fluorescence quantum yield of TO decreases in DESs may be due to the molecular rotor nature of TO, with the benzothiazole and quinoline ring of this dye being able to be rotated relative to each other in the excited state. In these solvents, the free volume idea was found to provide a truthful report of the solvent viscosity-temperature behavior, and the probe torsional dynamics. Fluorescence lifetime imaging microscopy (FLIM) was used to insight and observed the distribution of lifetime of TO in the surface of both DESs. The contact angle was determined to show the hygroscopic nature of the DESs.

Machine Learning for Electronically Excited States of Molecules

Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.

Machine Learning for Electronically Excited States of Molecules

Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.

Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy

We have studied spectral-luminescent properties of the monomethine cyanine dyes both in their free states and in the presence of either double-stranded deoxyribonucleic acids (dsDNAs) or single-stranded ribonucleic acids (RNAs). The dyes possess low fluorescence intensity in an unbound state, which is increased up to 479 times in the presence of the nucleic acids. In the presence of RNAs, the fluorescence intensity increase was stronger than that observed in the presence of dsDNA. Next, we have performed staining of live and fixed cells by all prepared dyes. The dyes proved to be cell and nuclear membrane permeant. They are photostable and brightly stain RNA-containing organelles in both live and fixed cells. The colocalization confirmed the specific nucleoli staining with anti-Ki-67 antibodies. The RNA digestion experiment has confirmed the selectivity of the dyes toward intracellular RNA. Based on the obtained results, we can conclude that the investigated monomethine cyanine dyes are useful fluorescent probes for the visualization of intracellular RNA and RNA-containing organelles such as nucleoli by using fluorescence microscopy.

Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold

SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its chemical structure is unknown and its binding mode to DNA remains controversial. Here, we solve the structure of SYBR Gold by NMR and mass spectrometry to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium] and determine its extinction coefficient. We quantitate SYBR Gold binding to DNA using two complementary approaches. First, we use single-molecule magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length and twist. The MT assay reveals systematic lengthening and unwinding of DNA by 19.1° ± 0.7° per molecule upon binding, consistent with intercalation, similar to the related dye SYBR Green I. We complement the MT data with spectroscopic characterization of SYBR Gold. The data are well described by a global binding model for dye concentrations ≤2.5 μM, with parameters that quantitatively agree with the MT results. The fluorescence increases linearly with the number of intercalated SYBR Gold molecules up to dye concentrations of ∼2.5 μM, where quenching and inner filter effects become relevant. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold.

Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions

Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.

Supramolecular Dipeptide-Based Near-Infrared Fluorescent Nanotubes for Cellular Mitochondria Targeted Imaging and Early Apoptosis

Herein, we have designed and synthesized unsymmetrical visible Cy-3 and near-infrared (NIR) Cy-5 chromophores anchoring mitochondria targeting functional group conjugated with a Phe-Phe dipeptide by a microwave-assisted Fmoc solid phase peptide synthesis method on Wang resin. These dipeptide-based Cy-3-TPP/FF as well as Cy-5-TPP/FF molecules self-assemble to form fluorescent nanotubes in solution, and it has been confirmed by TEM, SEM, and AFM. The Cy-3-TPP/FF and Cy-5-TPP/FF molecules in solution exhibit narrow excitation as well as emission bands in the visible and NIR region, respectively. These lipophilic cationic fluorescent peptide molecules spontaneously and selectively accumulate inside the mitochondria of human carcinoma cells that have been experimentally validated by live cell confocal laser scanning microscopy and display a high Pearson's correlation coefficient in a colocalization assay. Live cell multicolor confocal imaging using the NIR Cy-5-TPP/FF in combination with other organelle specific dye is also accomplished. Moreover, these lipophilic dipeptide-based cationic molecules reach the critical aggregation concentration inside the mitochondria because of the extremely negative inner mitochondrial membrane potential [(ΔΨ_m)_cancer ≈ -220 mV] and form supramolecular nanotubes which are accountable for malignant mitochondria targeted early apoptosis. The early apoptosis is arrested using Cy-5-TPP/FF and confirmed by annexin V-FITC/PI apoptosis detection assay.

Cyanine Dyes Containing Quinoline Moieties: History, Synthesis, Optical Properties, and Applications

Cyanine dyes carrying quinoline moieties are an important class of organic molecules that are of great interest for applications in many fields like medicine, pharmacology, and engineering. Despite their exceptional properties, such as stability, high molar extinction coefficients, and high pH-sensitivity, this class of dyes has been less analyzed and reviewed in the last few decades. Therefore, this review article focuses on discussing the history of quinoline compounds, various synthetic routes to prepare quinolinium salts and symmetrical and asymmetrical mono-, di-, tri-, penta- and heptamethine cyanine dyes, containing quinoline moieties, together with their optical properties and applications as photosensitizers in photodynamic therapy, probes in biomolecules for labeling of nucleic acids, as well as imaging agents.

Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO

Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)_n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)₆. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π^* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.

Plant Nanobionic Sensors for Arsenic Detection

Arsenic is a highly toxic heavy-metal pollutant which poses a significant health risk to humans and other ecosystems. In this work, the natural ability of wild-type plants to pre-concentrate and extract arsenic from the belowground environment is exploited to engineer plant nanobionic sensors for real-time arsenic detection. Near-infrared fluorescent nanosensors are specifically designed for sensitive and selective detection of arsenite. These optical nanosensors are embedded in plant tissues to non-destructively access and monitor the internal dynamics of arsenic taken up by the plants via the roots. The integration of optical nanosensors with living plants enables the conversion of plants into self-powered autosamplers of arsenic from their environment. Arsenite detection is demonstrated with three different plant species as nanobionic sensors. Based on an experimentally validated kinetic model, the nanobionic sensor could detect 0.6 and 0.2 ppb levels of arsenic after 7 and 14 days respectively by exploiting the natural ability of Pteris cretica ferns to hyperaccumulate and tolerate exceptionally high level of arsenic. The sensor readout could also be interfaced with portable electronics at a standoff distance, potentially enabling applications in environmental monitoring and agronomic research.

Synthesis of fluorescent G-quadruplex DNA binding ligands for the comparison of terminal group effects in molecular interaction: Phenol versus methoxybenzene

A number of new fluorescent nucleic acid binding ligands were synthesized by utilizing the non-specific thiazole orange dye as the basic scaffold for molecular design. Under simple synthetic conditions, the molecular scaffold of thiazole orange bridged with a terminal side-group (phenol or methoxybenzene) becomes more flexible because the newly added ethylene bridge is relatively less rigid than the methylene of thiazole orange. It was found that these molecules showed better selectivity towards G-quadruplex DNA structure in molecular interactions with different type of nucleic acids. The difference in terms of induced DNA-ligand interaction signal, selectivity, and binding affinity of the ligands with the representative nucleic acids including single-stranded DNA, double-stranded DNA, telomere and promoter G4-DNA and ribosomal RNA were investigated. The position of the terminal methoxyl groups was found showing strong influence both on binding affinity and fluorescent discrimination among 19 nucleic acids tested. The ligand with a methoxyl group substituted at the meta-position of the styryl moiety exhibited the best fluorescent recognition performance towards telo21 G4-DNA. A good linear relationship between the induced fluorescent binding signal and the concentration of telo21 was obtained. The comparison of ligand-DNA interaction properties including equilibrium binding constants, molecular docking, G4-conformation change and stabilization ability for G4-structures was also conducted. Two cancer cell lines (human prostate cancer cell (PC3) and human hepatoma cell (hepG2)) were selected to explore the inhibitory effect of the ligands on the cancer cell growth. The IC₅₀ values obtained in the MTT assay for the two cancer cells were found in the range of 3.4-10.8 μM.

Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials

Optically active molecular materials, such as organic conjugated polymers and biological systems, are characterized by strong coupling between electronic and vibrational degrees of freedom. Typically, simulations must go beyond the Born-Oppenheimer approximation to account for non-adiabatic coupling between excited states. Indeed, non-adiabatic dynamics is commonly associated with exciton dynamics and photophysics involving charge and energy transfer, as well as exciton dissociation and charge recombination. Understanding the photoinduced dynamics in such materials is vital to providing an accurate description of exciton formation, evolution, and decay. This interdisciplinary field has matured significantly over the past decades. Formulation of new theoretical frameworks, development of more efficient and accurate computational algorithms, and evolution of high-performance computer hardware has extended these simulations to very large molecular systems with hundreds of atoms, including numerous studies of organic semiconductors and biomolecules. In this Review, we will describe recent theoretical advances including treatment of electronic decoherence in surface-hopping methods, the role of solvent effects, trivial unavoided crossings, analysis of data based on transition densities, and efficient computational implementations of these numerical methods. We also emphasize newly developed semiclassical approaches, based on the Gaussian approximation, which retain phase and width information to account for significant decoherence and interference effects while maintaining the high efficiency of surface-hopping approaches. The above developments have been employed to successfully describe photophysics in a variety of molecular materials.

Divergent synthesis of 5',7'-difluorinated dihydroxanthene-hemicyanine fused near-infrared fluorophores

We describe an expedient access to a 5',6',7'-trifluoro dihydroxanthene-hemicyanine fused scaffold in 2 steps and 54% overall yield from the corresponding salicylic aldehyde. A 6'-regioselective nucleophilic aromatic substitution (SNAr) reaction with a wide range of nitrogen, sulfur or selenium nucleophiles then gives access to 16 near-infrared (NIR) fluorophores emitting in the 710-750 nm range. We also report the experimental and theoretical photophysical investigations of these unique optical agents that include the first series of 6'-heavy atom substituted dihydroxanthenes, extending the pool of polyfluorinated markers for biomedical and material applications.

Photo-isomerization of the Cyanine Dye Alexa-Fluor 647 (AF-647) in the Context of dSTORM Super-Resolution Microscopy

Cyanine dyes, as used in super-resolution fluorescence microscopy, undergo light-induced "blinking", enabling localization of fluorophores with spatial resolution beyond the optical diffraction limit. Despite a plethora of studies, the molecular origins of this blinking are not well understood. Here, we examine the photophysical properties of a bio-conjugate cyanine dye (AF-647), used extensively in dSTORM imaging. In the absence of a potent sacrificial reductant, light-induced electron transfer and intermediates formed via the metastable, triplet excited state are considered unlikely to play a significant role in the blinking events. Instead, it is found that, under conditions appropriate to dSTORM microscopy, AF-647 undergoes reversible photo-induced isomerization to at least two long-lived dark species. These photo-isomers are characterized spectroscopically and their interconversion probed by computational means. The first-formed isomer is light sensitive and transforms to a longer-lived species in modest yield that could be involved in dSTORM related blinking. Permanent photobleaching of AF-647 occurs with very low quantum yield and is partially suppressed by the anaerobic redox buffer.

Supramolecular Assembly Induced Emission of Thiazole Orange with Sulfobutylether β-cyclodextrin: A Stimuli-Responsive Fluorescence Sensor for Tyramine

Modulation and control of stimuli responsive features of molecular assemblies in organized assemblies/cavitand macrocycles have received immense attention in many areas. In this study, we have established the formation of a discrete molecular assembly of thiazole orange (TO) dyes at the portals of the sulfobutylether β-cyclodextrin (SBE₇ βCD) macrocycle leading to the evolution of a strong and distinct emission band from aggregated TO. The supramolecular assembly promoted portal aggregation of TO in its 1 : 4 (SBE₇ βCD : TO) composition, characterized by absorption, fluorescence, circular dichroism, ITC and ¹ H NMR measurements, was probed to be selectively responsive to tyramine among other biogenic amines/neurotransmitters. For the first time, the different extent of emission quenching of SBE₇ βCD : TO assembly in the presence of biogenic amines/neurotransmitters is translated to achieve a selective on-off fluorescence sensor for the detection of tyramine against other neurotransmitters with a limit-of-detection (LOD) as low as ∼575 nM (79 ppb). The emission features of the assembly with changes in temperature is found to be highly reproducible even after several temperature cycles and is promising to design an optical supramolecular thermometer in the ambient temperature range.

Red-emitting FIT-PNAs: "On site" detection of RNA biomarkers in fresh human cancer tissues

To date, there are limited approaches for the direct and rapid visualization (on site) of tumor tissues for pathological assessment and for aiding cytoreductive surgery. Herein, we have designed FIT-PNAs (forced-intercalation-peptide nucleic acids) to detect two RNA cancer biomarkers. Firstly, a lncRNA (long noncoding RNA) termed CCAT1, has been shown as an oncogenic lncRNA over-expressed in a variety of cancers. The latter, an mRNA termed KRT20, has been shown to be over-expressed in metastases originating from colorectal cancer (CRC). To these FIT-PNAs, we have introduced the bis-quinoline (BisQ) cyanine dye that emits light in the red region (605-610 nm) of the visible spectrum. Most strikingly, spraying fresh human tissue taken from patients during cytoreductive surgery for peritoneal metastasis of colon cancer with an aqueous solution of CCAT1 FIT-PNA results in bright fluorescence in a matter of minutes. In fresh healthy tissue (from bariatric surgeries), no appreciable fluorescence is detected. In addition, a non-targeted FIT-PNA shows no fluorescent signal after spraying this FIT-PNA on fresh tumor tissue emphasizing the specificity of these molecular sensors. This study is the first to show on-site direct and immediate visualization of an RNA cancer biomarker on fresh human cancer tissues by topical application (spraying) of a molecular sensor.

Meso-Substituent-Directed Aggregation Behavior and Water Solubility: Direct Functionalization of Methine Chain in Thiazole Orange and Biological Applications in Aqueous Buffer

A new strategy is presented to preclude aggregation and enhance water solubility of cyanine dyes. Namely, a heteroatom-containing substituent, for distorting molecular plane and increasing interaction with water molecules, is introduced to the methine chain of 2-thiazole orange (1, a monocyanine) via one-step, and 2-thiazole orange derivatives 2a-g are prepared accordingly. The X-ray crystal structures show that the molecular plane of 2a-g is drastically twisted, which reduces intermolecular π-π stacking. The derivatives 2a-g exhibit good to excellent water solubility and can be dissolved in aqueous phosphate-buffered saline (PBS) at concentrations suitable for biomedical applications. No aggregation in aqueous PBS, relatively high molar extinction coefficients, and low solvatochromism of 2a-g are reflected by the UV-vis spectra. Compound 2b shows fast response and high selectivity for biothiols (Cys, Hcy, and GSH) in aqueous PBS and is further employed to detect endogenous biothiols with decent biocompatibility as demonstrated by live cell fluorescence imaging.

Targeting Burkitt lymphoma with a tumor cell-specific heptamethine carbocyanine-cisplatin conjugate

BACKGROUND

Burkitt lymphoma is a fast-growing mature B cell malignancy, whose genetic hallmark is translocation and activation of the c-myc gene. Prompt multiagent immunochemotherapy regimens can have favorable outcomes, but prognosis is poor in refractory or relapsed disease. We previously identified a novel family of near-infrared heptamethine carbocyanine fluorescent dyes (HMCD or DZ) with tumor-homing properties via organic anion-transporting peptides. These membrane carriers have uptake in tumor cells but not normal cells in cell culture, mouse and dog tumor models, patient-derived xenografts, and perfused kidney cancers in human patients.

METHODS

Here we report the cytotoxic effects of a synthesized conjugate of DZ with cisplatin (CIS) on B cell lymphoma CA46, Daudi, Namalwa, Raji, and Ramos cell lines in cell culture and in xenograft tumor formation. Impaired mitochondrial membrane permeability was examined as the mechanism of DZ-CIS-induced lymphoma cell death.

RESULTS

The new conjugate, DZ-CIS, is cytotoxic against Burkitt lymphoma cell lines and tumor models. DZ-CIS retains tumor-homing properties to mitochondrial and lysosomal compartments, does not accumulate in normal cells and tissues, and has no nephrotoxicity in mice. DZ-CIS accumulated in Burkitt lymphoma cells and tumors induces apoptosis and retards tumor cell growth in culture and xenograft tumor growth in mice.

CONCLUSION

DZ-CIS downregulated c-myc and overcame CIS resistance in myc-driven TP53-mutated aggressive B cell Burkitt lymphoma. We propose that DZ-CIS could be used to treat relapsed/refractory aggressive Burkitt lymphomas.

A cell surface display fluorescent biosensor for measuring MMP14 activity in real-time

Despite numerous recent advances in imaging technologies, one continuing challenge for cell biologists and microscopists is the visualization and measurement of endogenous proteins as they function within living cells. Achieving this goal will provide a tool that investigators can use to associate cellular outcomes with the behavior and activity of many well-studied target proteins. Here, we describe the development of a plasmid-based fluorescent biosensor engineered to measure the location and activity of matrix metalloprotease-14 (MMP14). The biosensor design uses fluorogen-activating protein technology coupled with a MMP14-selective protease sequence to generate a binary, “switch-on” fluorescence reporter capable of measuring MMP14 location, activity, and temporal dynamics. The MMP14-fluorogen activating protein biosensor approach is applicable to both short and long-term imaging modalities and contains an adaptable module that can be used to study many membrane-bound proteases. This MMP14 biosensor promises to serve as a tool for the advancement of a broad range of investigations targeting MMP14 activity during cell migration in health and disease.

Halogen-containing thiazole orange analogues - new fluorogenic DNA stains

Novel asymmetric monomeric monomethine cyanine dyes 5a–d, which are analogues of the commercial dsDNA fluorescence binder thiazole orange (TO), have been synthesized. The synthesis was achieved by using a simple, efficient and environmetally benign synthetic procedure to obtain these cationic dyes in good to excellent yields. Interactions of the new derivatives of TO with dsDNA have been investigated by absorption and fluorescence spectroscopy. The longest wavelength absorption bands in the UV–vis spectra of the target compounds are in the range of 509–519 nm and these are characterized by high molar absorptivities (63000–91480 L·mol⁻¹·cm⁻¹). All investigated dyes from the series are either not fluorescent or their fluorescence is quite low, but they become strongly fluorescent after binding to dsDNA. The influence of the substituents attached to the chromophores was investigated by combination of spectroscopic (UV–vis and fluorescence spectroscopy) and theoretical (DFT and TDDFT calculations) methods.

Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications

An RNA-based fluorogenic module consists of a light-up RNA aptamer able to specifically interact with a fluorogen to form a fluorescent complex. Over the past decade, significant efforts have been devoted to the development of such modules, which now cover the whole visible spectrum, as well as to their engineering to serve in a wide range of applications. In this review, we summarize the different strategies used to develop each partner (the fluorogen and the light-up RNA aptamer) prior to giving an overview of their applications that range from live-cell RNA imaging to the set-up of high-throughput drug screening pipelines. We then conclude with a critical discussion on the current limitations of these modules and how combining in vitro selection with screening approaches may help develop even better molecules.

Unsymmetrical Relaxation Paths of the Excited States in Cyanine Dyes Detected by Time-Resolved Fluorescence: Polymethinic and Polyenic Forms

Novel applications of organic dyes and vast opportunities for their molecular tailoring keep the focus of the scientific community on the issues of symmetry breaking in the systems having different location of uncompensated charge, which has tremendous impact on photoluminescent properties of the dyes. In this article, we provide distinctive experimental evidence of three relaxation paths (one symmetrical and two unsymmetrical) of excited states by analysis of lifetime and spectra of time-resolved fluorescence at low temperature with strong support of quantum-chemical modeling. Importantly, the studied cyanine dye (astraphloxin) in aqueous solution has two different unsymmetrical relaxation paths of excited states in the polymethinic and donor-acceptor polyenic forms, where the last form strongly diminishes in less polar media. The experimental and computational results provide essential fundamental knowledge of molecular electronic relaxations substantially affected by matrix rigidity and polarity for design and photonic applications of elongated π-electronic systems.