DNA Framework-Engineered Assembly of Cyanine Dyes for Structural Identification of Nucleic Acids

DNA nanostructures serve as precise templates for organizing organic dyes, enabling the creation of programmable artificial photonic systems with efficient light-harvesting and energy transfer capabilities. However, regulating the organization of organic dyes on DNA frameworks remains a great challenge. In this study, we investigated the factors influencing the self-assembly behavior of cyanine dye K21 on DNA frameworks. We observed that K21 exhibited diverse assembly modes, including monomers, H-aggregates, J-aggregates, and excimers, when combined with DNA frameworks. By manipulating conditions such as the ion concentration, dye concentration, and structure of DNA frameworks, we successfully achieved precise control over the assembly modes of K21. Leveraging K21's microenvironment-sensitive fluorescence properties on DNA nanostructures, we successfully discriminated between the chirality and topology structures of physiologically relevant G-quadruplexes. This study provides valuable insights into the factors influencing the dynamic assembly behavior of organic dyes on DNA framework nanostructures, offering new perspectives for constructing functional supramolecular aggregates and identifying DNA secondary structures.

Polydopamine nanoplatform with near infrared light and pH dual stimuli-responsive for chemo-photothermal cancer therapy

Photothermal agent accompanying with thermally responsive materials, displays well controlled drug release property, which is well-received as an outstanding design strategy for simultaneous photothermal/chemotherapy in cancer. Cyanine dye, as the prestigious photothermal agent has shown great potential due to its preeminent near-infrared absorbance and excellent thermal conversion efficiency. However, their inherent defect such as inferior photothermal stability, high leakage risk and poor therapy efficacy limit their further application in cancer therapy. Hence, a facile and universal strategy to make up these deficiencies is developed. Chemotherapeutic drug DOX and cyanine dye were loaded into polydopamine (PDA) nanoparticles. The PDA encapsulation dramatically improved the photothermal stability of cyanine dye. Attributed by the PDA structure feature, the thermo-sensitive small molecule glyamine (Gla) is introduced into the PDA surface to lessen leakage. The Gla can form a dense encapsulation layer on the dopamine surface through hydrogen bond. This newly fabricated Cyanine/DOX@PDA-Gla nanopaltform is characterized with NIR light/pH dual-responsive property, high NIR photothermal conversion performance and fluorescence guided chemo-photothermal therapy.

Sensitive monitoring of NAD(P)H levels within cancer cells using mitochondria-targeted near-infrared cyanine dyes with optimized electron-withdrawing acceptors

A series of near-infrared fluorescent probes, labeled A to E, were developed by combining electron-rich thiophene and 3,4-ethylenedioxythiophene bridges with 3-quinolinium and various electron deficient groups, enabling the sensing of NAD(P)H. Probes A and B exhibit absorptions and emissions in the near-infrared range, offering advantages such as minimal interference from autofluorescence, negligible photo impairment in cells and tissues, and exceptional tissue penetration. These probes show negligible fluorescence when NADH is not present, and their absorption maxima are at 438 nm and 470 nm, respectively. In contrast, probes C-E feature absorption maxima at 450, 334 and 581 nm, respectively. Added NADH triggers the transformation of the electron-deficient 3-quinolinium units into electron-rich 1,4-dihydroquinoline units resulting in fluorescence responses which were established at 748, 730, 575, 625 and 661 for probes AH-EH, respectively, at detection limits of 0.15 μM and 0.07 μM for probes A and B, respectively. Optimized geometries based on theoretical calculations reveal non-planar geometries for probes A-E due to twisting of the 3-quinolinium and benzothiazolium units bonded to the central thiophene group, which all attain planarity upon addition of hydride resulting in absorption and fluorescence in the near-IR region for probes AH and BH in contrast to probes CH-EH which depict fluorescence in the visible range. Probe A has been successfully employed to monitor NAD(P)H levels in glycolysis and specific mitochondrial targeting. Furthermore, it has been used to assess the influence of lactate and pyruvate on the levels of NAD(P)H, to explore how hypoxia in cancer cells can elevate levels of NAD(P)H, and to visualize changes in levels of NAD(P)H under hypoxic conditions with CoCl2 treatment. Additionally, probe A has facilitated the examination of the potential impact of chemotherapy drugs, namely gemcitabine, camptothecin, and cisplatin, on metabolic processes and energy generation within cancer cells by affecting NAD(P)H levels. Treatment of A549 cancer cells with these drugs has been shown to increase NAD(P)H levels, which may contribute to their anticancer effects ultimately leading to programmed cell death or apoptosis. Moreover, probe A has been successfully employed in monitoring NAD(P)H level changes in D. melanogaster larvae treated with cisplatin.

Classification and naming of polymethine dyes used as staining agents for microscopy. A short guide for biomedical investigators

The scientific literature contains many accounts of application of polymethine dyes, including cyanine dyes, as imaging agents, i.e., "biological stains," for microscopic investigation of biological materials. Currently, many such dyes are used as probes for living cells, i.e., "fluorescent probes." Polymethine dyes are defined here by two criteria. First, they possess a conjugated chain of (2n + 1) sp2-hybridized carbon atoms that connect a terminal π-electron-accepting (π-electron withdrawing) group with a terminal π-electron-donating group. Second, they have an odd number (2n + 3) of π-centers and an even number (2n + 4) of π-electrons in this chain, where n equals the number of -CR2=CR3- groups, usually vinylene groups -CH=CH-. Commercialization of diverse chemical types of many polymethine dyes has been attempted. The dyes that have achieved wide application, however, are limited in number and it is these dyes that are emphasized here. Because these polymethine dyes sometimes have been described by confusing, and sometimes confused, names, we clarify here the chemical categories and names of such dyes for the nonchemist, biomedical end user of such imaging agents. Nevertheless, the nomenclature presented here is not intended to replace the traditional "chromophore" categories of dyestuff chemistry, because the latter are held in place both by wide usage and by venerable authorities, such as the Colour Index.

Metal-Coordination-Mediated H-Aggregates of Cyanine Dyes for Effective Photothermal Therapy

Integration of cyanine dyes and metal ions into one nanoplatform via metal-coordination interactions is an effective strategy to build multimodality phototheranostics. The multifunctionalities of the formed nanoscale metal-organic particles (NMOPs) have been widely explored. However, the effect of metal-coordination interaction on the aggregation behavior of cyanine dyes is rarely reported. Herein, we reported the H-aggregation behavior of cyanine dye Cy-3COOH induced by different metal ions M (Fe2+ or Mn2+ ). Moreover, the extent of H-aggregates varied with different metal-coordination interactions. Upon NIR irradiation, H-aggregates of Cy-3COOH remarkably promoted photothermal conversion efficiency. Interestingly, we also find that H-aggregates of Cy-3COOH induced by metal ions can generate the reactive oxygen species (ROS) involving singlet oxygen (1 O2 ) and superoxide anion radical (O2 - ⋅) upon light irradiation. In addition, the ROS efficiency varies depending on the extent of H-aggregates. Additionally, the photoinduced ROS could disassemble aggregates and decompose cyanine dye Cy-3COOH, which limits the photothermal capability of Cy-3COOH/M NPs. Therefore, the photothermal performance of Cy-3COOH/M NPs could be manipulated by the degree of H-aggregation. This would provide a new insight to develop efficient phototheranostics NMOPs for cancer treatment.

Multifunctional Near-Infrared Dye IR-817 Encapsulated in Albumin Nanoparticles for Enhanced Imaging and Photothermal Therapy in Melanoma

Background

Near-infrared cyanine dyes have high sensitivity and spatial resolution imaging capabilities, but they also have unavoidable drawbacks such as photobleaching, low water solubility, fluorescence quenching, and toxic side effects. As an effective biologic drug carrier, albumin combines with cyanine dyes to form albumin@dye nanoparticles. These nanoparticles can alleviate the aforementioned issues and are widely used in tumor imaging and photothermal therapy.

Methods

Herein, a newly synthesized near-infrared dye IR-817 was combined with bovine serum albumin (BSA) to create BSA@IR-817 nanoparticles. Through the detection of fluorescence emission and absorption, the optimal concentration and ratio of BSA and IR-817 were determined. Subsequently, dynamic light scattering (DLS) measurements and scanning electron microscopy (SEM) were used for the physical characterization of the BSA@IR-817 nanoparticles. Finally, in vitro and in vivo experiments were conducted to assess the fluorescence imaging and photothermal therapeutic potential of BSA@IR-817 nanoparticles.

Results

IR-817 was adsorbed onto the BSA carrier by covalent conjugation and supramolecular encapsulation, resulting in the formation of dispersed, homogeneous, and stable nanoparticles with a particle size range of 120-220 nm. BSA@IR-817 not only improved the poor water solubility, fluorescence quenching, and toxic side effects of IR-817 but also enhanced the absorption and fluorescence emission peaks in the near-infrared region, as well as the fluorescence in the visible spectrum. In addition, BSA@IR-817 combined with laser 808 irradiation was able to convert light energy into heat energy with temperatures exceeding 50 °C. By creating a mouse model of subcutaneous melanoma, it was discovered that the tumor inhibition rate of BSA@IR-817 was greater than 99% after laser irradiation and that it achieved nearly complete tumor ablation without causing significant toxicity.

Conclusion

Our research, therefore, proposes the use of safe and effective photothermal nanoparticles for the imaging, diagnosis, and treatment of melanoma, and offers a promising strategy for future biomedical applications.

Low-Dose NIR-II Preclinical Bioimaging Using Liposome-Encapsulated Cyanine Dyes

Fluorescence imaging in the second near-infrared window (NIR-II, 1000-1700 nm) provides a powerful tool for in vivo structural and functional imaging in deep tissue. However, the lack of biocompatible contrast agents with bright NIR-II emission has hindered its application in fundamental research and clinical trials. Herein, a liposome encapsulation strategy for generating ultrabright liposome-cyanine dyes by restricting dyes in the hydrophobic pockets of lipids and inhibiting the aggregation, as corroborated by computational modeling, is reported. Compared with free indocyanine green (ICG, an US Food and Drug Administration-approved cyanine dye), liposome-encapsulated ICG (S-Lipo-ICG) shows a 38.7-fold increase in NIR-II brightness and enables cerebrovascular imaging at only one-tenth dose over a long period (30 min). By adjusting the excitation wavelength, two liposome-encapsulated cyanine dyes (S-Lipo-ICG and S-Lipo-FD1080) enable NIR-II dual-color imaging. Moreover, small tumor nodules (2-5 mm) can be successfully distinguished and removed with S-Lipo-ICG image-guided tumor surgery in rabbit models. This liposome encapsulation maintains the metabolic pathway of ICG, promising for clinical implementation.

Aminooxy Click Modification of a Periodate-Oxidized Immunoglobulin G: A General Approach to Antibody-Drug Conjugates with Dye-Mediated Expeditious Stoichiometry Control

A universal approach to the construction of antibody-drug conjugates (ADCs) has been developed. It relies on periodate oxidation of naturally present glycans of immunoglobulin G, followed by oxime ligation and, optionally, copper(I)-catalyzed alkyne-azide cycloaddition for conjugation with a toxic payload. The introduction of highly absorbing cyanine dyes into the linker allows for facile determination of the drug-antibody ratio. We applied this methodology to the synthesis of cytotoxic conjugates of an antibody against the tumor-associated antigen PRAME with doxorubicin and monomethyl auristatin E (MMAE). The resultant conjugates retained their affinity to a large extent, yet their cytotoxicity in vitro varied dramatically: while the doxorubicin-based conjugate did not produce any effect on cells, the MMAE-based one demonstrated specific activity against PRAME-expressing cancer cell lines. Importantly, the latter conjugate constitutes the first reported example of a PRAME-targeting ADC.

Mueller Matrix Polarimetry on Cyanine Dye J-Aggregates

Cyanine dyes are known to form H- and J-aggregates in aqueous solutions. Here we show that the cyanine dye, S0271, assembles in water into vortex induced chiral J-aggregates. The chirality of the J-aggregates depends on the directionality of the vortex. This study utilised both conventional benchtop CD spectropolarimeters and Mueller matrix polarimetry. It was found that J-aggregates have real chirality alongside linear dichroism and linear and circular birefringence. We identify the factors that are key to the formation of metastable chiral J-aggregates and propose a mechanism for their assembly.

Near-Unity Superradiant Emission from Delocalized Frenkel Excitons in a Two-Dimensional Supramolecular Assembly

We demonstrate three general effective strategies to mitigate non-radiative losses in the superradiant emission from supramolecular assemblies. We focus on J-aggregates of 5,5',6,6'-tetrachloro-1,1'-diethyl-3,3'-di(4-sulfobutyl)-benzimidazolocarbocyanine (TDBC) and elucidate the nature of their nonradiative processes. We show that self-annealing at room temperature, photo-brightening, and the purification of the dye monomers all lead to substantial increases in emission quantum yields (QYs) and a concomitant lengthening of the emission lifetime, with purification of the monomers having the largest effect. We use structural and optical measurements to support a microscopic model that emphasizes the deleterious effects of a small number of impurity and defect sites that serve as non-radiative recombination centers. This understanding has yielded a room temperature molecular fluorophore in solution with an unprecedented combination of fast emissive lifetime and high QY. We obtain superradiant emission from J-aggregates of TDBC in solution at room temperature with a QY of 82% coupled with an emissive lifetime of 174 ps. This combination of high QY and fast lifetime at room temperature makes supramolecular assemblies of purified TDBC a model system for the study of fundamental superradiance phenomena. High QY J-aggregates are uniquely suited for the development of applications that require high speed and high brightness fluorophores such as devices for high speed optical communication.

A Selenium-Substituted Heptamethine Cyanine Photosensitizer for Near-Infrared Photodynamic Therapy

Photodynamic therapy (PDT) is a relatively safe approach to cancer treatment without significant systemic side effects or drug resistance. However, the current PDT efficiency is unsatisfactory due to the lack of near-infrared (NIR) photosensitizers. Heptamethine cyanine (Cy7) dyes are well-known NIR fluorophores and are also used as photosensitizers. But their singlet oxygen quantum yields (Φ_Δ ) are not ideal. Herein, we developed an NIR photosensitizer with a long-lived excited triplet state (τ=4.3 μs) by introducing a selenium atom into the structure of a Cy7 dye. The new NIR photosensitizer exhibits a significantly high singlet oxygen quantum yield (Φ_Δ =0.11). Its good PDT effect was demonstrated in the living cells. Considering that the selenium-substituted photosensitizer has a very low dark cytotoxicity and good chemical stability, we conclude that it will have a promising future in biomedical and clinical applications.

An Approach to Developing Cyanines with Upconverted Photosensitive Efficiency Enhancement for Highly Efficient NIR Tumor Phototheranostics

Upconverted reactive oxygen species (ROS) photosensitization with one-photon excitation mode is a promising tactic to elongate the excitation wavelengths of photosensitive dyes to near-infrared (NIR) light region without the requirement of coherent high-intensity light sources. However, the photosensitization efficiencies are still finite by the unilateral improvement of excited-state intersystem crossing (ISC) via heavy-atom-effect, since the upconverted efficiency also plays a decisive role in upconverted photosensitization. Herein, a NIR light initiated one-photon upconversion heavy-atom-free small molecule system is reported. The meso-rotatable anthracene in pentamethine cyanine (Cy5) is demonstrated to enrich the populations in high vibrational-rotational energy levels and subsequently improve the hot-band absorption (HBA) efficiency. Moreover, the spin-orbit charge transfer intersystem crossing (SOCT-ISC) caused by electron donated anthracene can further amplify the triplet yield. Benefiting from the above two aspects, the ¹ O₂ generation significantly increases with over 2-fold improved performance compared with heavy-atom-modified method under upconverted light excitation, which obtains efficient in vivo phototheranostic results and provides new opportunities for other applications such as photocatalysis and fine chemical synthesis.

An Insight into Symmetrical Cyanine Dyes as Promising Selective Antiproliferative Agents in Caco-2 Colorectal Cancer Cells

Cancer remains one of the diseases with the highest worldwide incidence. Several cytotoxic approaches have been used over the years to overcome this public health threat, such as chemotherapy, radiotherapy, and photodynamic therapy (PDT). Cyanine dyes are a class of compounds that have been extensively studied as PDT sensitisers; nevertheless, their antiproliferative potential in the absence of a light source has been scarcely explored. Herein, the synthesis of eighteen symmetric mono-, tri-, and heptamethine cyanine dyes and their evaluation as potential anticancer agents is described. The influences of the heterocyclic nature, counterion, and methine chain length on the antiproliferative effects and selectivities were analysed, and relevant structure-activity relationship data were gathered. The impact of light on the cytotoxic activity of the most promising dye was also assessed and discussed. Most of the monomethine and trimethine cyanine dyes under study demonstrated a high antiproliferative effect on human tumour cell lines of colorectal (Caco-2), breast (MCF-7), and prostate (PC-3) cancer at the initial screening (10 µM). However, concentration-viability curves showed higher potency and selectivity for the Caco-2 cell line. A monomethine cyanine dye derived from benzoxazole was the most promising compound (IC₅₀ for Caco-2 = 0.67 µM and a selectivity index of 20.9 for Caco-2 versus normal human dermal fibroblasts (NHDF)) and led to Caco-2 cell cycle arrest at the G0/G1 phase. Complementary in silico studies predicted good intestinal absorption and oral bioavailability for this cyanine dye.

The Unexpected Selectivity Switching from Mitochondria to Lysosome in a D-π-A Cyanine Dye

Two interesting benzothizolium-based D-π-A type hemicyanine dyes (3a-3b) with a diphenylamine (-NPh₂) donor group were evaluated for fluorescence confocal microscopy imaging ability in live cells (MO3.13, NHLF). In sharp contrast to previously reported D-π-A dyes with alkyl amine donor (-NR₂) groups (1), 3a and 3b exhibited significantly different photophysical properties and organelle selectivity. Probes 3a and 3b were nearly non-fluorescent in many polar and non-polar solvents but exhibited a bright red fluorescence (λ_em ≈ 630-640 nm) in stained MO3.13 and NHLF with very low probe concentrations (i.e., 200 nM). Fluorescence confocal microscopy-based co-localization studies revealed excellent lysosome selectivity from the probes 3a-3b, which is in sharp contrast to previously reported D-π-A type benzothiazolium dyes (1) with an alkyl amine donor group (-NR₂) (exhibiting selectivity towards cellular mitochondria). The photostability of probe 3 was found to be dependent on the substituent (R') attached to the quaternary nitrogen atom in the cyanine dye structure. The observed donor-dependent selectivity switching phenomenon can be highly useful in designing novel organelle-targeted fluorescent probes for live-cell imaging applications.

"Invisible" Digital Light Processing 3D Printing with Near Infrared Light

The ability to 3D print structures with low-intensity, long-wavelength light will broaden the materials scope to facilitate inclusion of biological components and nanoparticles. Current materials limitations arise from the pervasive absorption, scattering, and/or degradation that occurs upon exposure to high-intensity, short-wavelength (ultraviolet) light, which is the present-day standard used in light-based 3D printers. State-of-the-art techniques have recently extended printability to orange/red light. However, as the wavelength of light increases, so do the inherent challenges to match the speed and resolution of traditional UV light-induced solidification processes (i.e., photocuring). Herein, a photosystem is demonstrated to enable low-intensity (<5 mW/cm2), long-wavelength (∼850 nm) near-infrared (NIR) light-driven 3D printing, "invisible" to the human eye. The combination of a NIR absorbing cyanine dye with electron-rich and -deficient redox pairs was required for rapid photocuring in a catalytic manner. The rate of polymerization and time to solidification upon exposure to NIR light were characterized via in situ spectroscopic and rheological monitoring. Translation to NIR digital light processing (projection-based) 3D printing was accomplished through rigorous optimization of resin composition and printing parameters to balance the speed (<60 s/layer) and resolution (<300 μm features). As a proof-of-concept, composite 3D printing with nanoparticle-infused resins was accomplished. Preliminary analysis showed improved feature fidelity for structures produced with NIR relative to UV light. The present report provides key insight that will inform next-generation light-based photocuring technology, such as wavelength-selective multimaterial 3D bio- and composite-printing.

Copper-Catalyzed Covalent Dimerization of Near-Infrared Fluorescent Cyanine Dyes: Synergistic Enhancement of Photoacoustic Signals for Molecular Imaging of Tumors

Photoacoustic (PA) imaging relies on the absorption of light by chromophores to generate acoustic waves used to delineate tissue structures and physiology. Here, we demonstrate that Cu(II) efficiently catalyzes the dimerization of diverse near-infrared (NIR) cyanine molecules, including a peptide conjugate. NMR spectroscopy revealed a C-C covalent bond along the heptamethine chains, creating stable molecules under conditions such as a wide range of solvents and pH mediums. Dimerization achieved >90% fluorescence quenching, enhanced photostability, and increased PA signals by a factor of about 4 at equimolar concentrations compared to the monomers. In vivo study with a mouse cancer model revealed that dimerization enhanced tumor retention and PA signal, allowing cancer detection at doses where the monomers are less effective. While the dye dimers highlighted peritumoral blood vessels, the PA signal for dimeric tumor-targeting dye-peptide conjugate, LS301, was diffuse throughout the entire tumor mass. A combination of the ease of synthesis, diversity of molecules that are amenable to Cu(II)-catalyzed dimerization, and the high acoustic wave amplification by these stable dimeric small molecules ushers a new strategy to develop clinically translatable PA molecular amplifiers for the emerging field of molecular photoacoustic imaging.

Targetable Conformationally Restricted Cyanines Enable Photon-Count-Limited Applications*

Cyanine dyes are exceptionally useful probes for a range of fluorescence-based applications, but their photon output can be limited by trans-to-cis photoisomerization. We recently demonstrated that appending a ring system to the pentamethine cyanine ring system improves the quantum yield and extends the fluorescence lifetime. Here, we report an optimized synthesis of persulfonated variants that enable efficient labeling of nucleic acids and proteins. We demonstrate that a bifunctional sulfonated tertiary amide significantly improves the optical properties of the resulting bioconjugates. These new conformationally restricted cyanines are compared to the parent cyanine derivatives in a range of contexts. These include their use in the plasmonic hotspot of a DNA-nanoantenna, in single-molecule Förster-resonance energy transfer (FRET) applications, far-red fluorescence-lifetime imaging microscopy (FLIM), and single-molecule localization microscopy (SMLM). These efforts define contexts in which eliminating cyanine isomerization provides meaningful benefits to imaging performance.

A NIR Emitting Cyanine with Large Stokes' Shift for Mitochondria and Identification of their Membrane Potential Disruption

An NIR emitting (λ_em ≈730 nm) cyanine probe ExCy was synthesized in good yields by extending the π-conjugation length (i. e., with furan moiety) to the donor-accepter system. ExCy exhibited a large Stokes' shift (Δλ≈100 nm) due to strong intramolecular charge transfer (ICT), and high fluorescence quantum yield (Φ_fl ≈0.47 in DCM). Due to its low fluorescence in an aqueous environment (Φ_fl ≈0.007 in H₂ O), the probe exhibited the potential of achieving a large fluorescence turn-on upon entering a hydrophobic cellular environment. Fluorescence confocal microscopy studies revealed that ExCy was readily excitable with a far-red laser line (i. e., 640 nm) while the corresponding emission was collected in the NIR region. ExCy exhibited excellent selectivity towards live cell mitochondria according to the co-localization studies. The probe also exhibited high photostability, long-term imaging ability and wash-free staining ability, when being applied to live cells. Our studies indicated that the mitochondrial localization of ExCy was dependent on the membrane potential of the mitochondria. ExCy was successfully utilized as a mitochondrial membrane potential dysfunction indicator to visually identify cells with mitochondrial dysfunction via fluorescence confocal microscopy. ExCy was further examined for potential in vivo imaging of zebrafish.

DNA Aptamer-Cyanine Complexes as Generic Colorimetric Small-Molecule Sensors

Aptamers are promising biorecognition elements for sensors. However, aptamer-based assays often lack the requisite levels of sensitivity and/or selectivity because they typically employ structure-switching aptamers with attenuated affinity and/or utilize reporters that require aptamer labeling or which are susceptible to false positives. Dye-displacement assays offer a label-free, sensitive means for overcoming these issues, wherein target binding liberates a dye that is complexed with the aptamer, producing an optical readout. However, broad utilization of these assays has been limited. Here, we demonstrate a rational approach to develop colorimetric cyanine dye-displacement assays that can be broadly applied to DNA aptamers regardless of their structure, sequence, affinity, or the physicochemical properties of their targets. Our approach should accelerate the development of mix-and-measure assays that could be applied for diverse analytical applications.

Photodynamic Therapy with Tumor Cell Discrimination through RNA-Targeting Ability of Photosensitizer

Photodynamic therapy (PDT) represents an effective treatment to cure cancer. The targeting ability of the photosensitizer is of utmost importance. Photosensitizers that discriminate cancer cells can avoid the killing of normal cells and improve PDT efficacy. However, the design and synthesis of photosensitizers conjugated with a recognition unit of cancer cell markers is complex and may not effectively target cancer. Considering that the total RNA content in cancer cells is commonly higher than in normal cells, this study has developed the photosensitizer QICY with RNA-targeting abilities for the discrimination of cancer cells. QICY was specifically located in cancer cells rather than normal cells due to their stronger electrostatic interactions with RNA, thereby further improving the PDT effects on the cancer cells. After intravenous injection into mice bearing a xenograft tumor, QICY accumulated into the tumor location through the enhanced permeability and retention effect, automatically targeted cancer cells under the control of RNA, and inhibited tumor growth under 630 nm laser irradiation without obvious side effects. This intelligent photosensitizer with RNA-targeting ability not only simplifies the design and synthesis of cancer-cell-targeting photosensitizers but also paves the way for the further development of highly efficient PDTs.

Aggregate Formation of Boron-Containing Molecules in Thermal Vacuum Deposited Films

The spectral properties of new boron-containing dyes were studied. One-component (pure dyes) and composite "Alq₃+dye" thin films were fabricated using the thermal vacuum deposition method. The positions of the transmission spectra maxima in a one-component film are different for different film thicknesses. The best correlation of the maxima positions of the dye transmission spectra in solid and liquid solutions was observed for thicknesses of films close to a few (up to 10) monolayers. On the other hand, the absorption spectra maxima positions of one-component dye films (upper 10 nm) and composite films with high concentration, did not match the corresponding positions of absorption spectra maxima recorded in solutions. Comparison of the absorption spectra in one-component dye films and in solutions indicates the presence of both monomers and their aggregates in one-component films (contrary to solutions where such processes of aggregation do not take place, even at very high concentrations). Simultaneously with aggregation manifestation in the absorption spectra, the intensity of fluorescence of one-component dye films dramatically decreases. A quantum chemical simulation of the possible relative arrangement of two dye molecules indicates that the most possible of the simplest types of aggregates are physical dimers. Films of practical importance (due to efficient energy transfer from host to guest molecules when all singlet excitons are captured) possess a high quantum yield of fluorescence when reaching an impurity concentration of a few percent (aggregation does not take place yet).

Photoactivated In Situ Generation of Near Infrared Cyanines for Spatiotemporally Controlled Fluorescence Imaging in Living Cells

Photoactivated trimerization of 2,3,3-trimethyl-3H-indole derivatives created near infrared fluorophore Cy5. The synthetic method is air-tolerant, photosensitizer free, metal free, and condensation agent free. Living cells make Cy5 on a time scale of minutes under white light irradiation at a low power intensity, with the monomer as the only exogenous agent. The new method is promising to find applications in cell studies for in situ spatiotemporally controlled fluorescence imaging in living cells.

Azulene-Substituted Donor-Acceptor Polymethines and 1,6'-Bi-, 1,6';3,6''-Ter-, and Quinqueazulenes via Zincke Salts: Synthesis, and Structural, Optical, and Electrochemical Properties

Azulene-substituted donor-acceptor polymethines, bi-, ter-, and quinqueazulenes composed of the 1,6'-biazulene unit have been successfully prepared from corresponding Zincke salts. The synthesis of polymethines through the reaction of Zincke salts with several amines, followed by a Knoevenagel reaction with malononitrile, was accomplished in moderate to high yields (40-92 %). Meanwhile, the reaction of Zincke salts with secondary amines and the subsequent sequential condensation-cyclization with cyclopentadienide ions, so-called Ziegler-Hafner method, produced the corresponding 1,6'-biazulenes, 1,6';3,6''-terazulenes, and quinqueazulene, respectively. The structural, optical, and electrochemical properties of the azulene-substituted donor-acceptor polymethines, bi-, ter-, and quinqueazulenes were revealed by single-crystal X-ray structure analysis, UV/vis spectroscopy, voltammetry analysis, spectroelectrochemistry, and theoretical calculations. These results suggested that the substituents on the azulene ring and their substitution positions directly affect their reactivities, optical and electrochemical properties.

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.

pH-Activatable Cyanine Dyes for Selective Tumor Imaging Using Near-Infrared Fluorescence and Photoacoustic Modalities

Photoacoustic (PA) imaging is an emerging molecular imaging modality that complements fluorescence imaging and enables high resolution within deep tissue. Fluorescence/PA multimodality imaging would be a powerful technique to extract more comprehensive information from targets than traditional single-modality imaging. In this paper, we developed a new pH-activatable sensor, CypHRGD, which is applicable to both fluorescence and PA detection. CypHRGD was derived from our previous near-infrared pH-sensing platform, in which substitution with a bulky phenyl group and functionalization with a cRGD peptide remarkably improved the sensor's biocompatibility with attenuated dye aggregation. The multimodality imaging applications of CypHRGD were demonstrated in cultured cells and cancer-xenografted mice with rapid kinetics and high sensitivity and specificity, which relies on cRGD-facilitated tumor targeting, probe accumulation and subsequent activation in the acidic organelles after endocytosis.

Lab-on-Microsphere-FRET-Based Multiplex Sensor Platform

Here we report on the development and investigation of a novel multiplex assay model based on polymer microspheres (PMS) encoded with ternary AIS/ZnS quantum dots (QDs). The system was prepared via layer-by-layer deposition technique. Our studies of Förster resonance energy transfer (FRET) between the QD-encoded microspheres and two different cyanine dyes have demonstrated that the QD photoluminescence (PL) quenching steadily increases with a decrease in the QD-dye distance. We have found that the sensitized dye PL intensity demonstrates a clear maximum at two double layers of polyelectrolytes between QDs and Dye molecules on the polymer microspheres. Time resolved PL measurements have shown that the PL lifetime decreases for the QDs and increases for the dyes due to FRET. The designed system makes it possible to record spectrally different bands of FRET-induced dye luminescence with different decay times and thereby allows for the multiplexing by wavelength and photoluminescence lifetimes of the dyes. We believe that PMS encoded with AIS/ZnS QDs have great potential for the development of new highly selective and sensitive sensor systems for multiplex analysis to detect cell lysates and body fluids' representative biomarkers.

FRET-Based Analysis of AgInS2/ZnAgInS/ZnS Quantum Dot Recombination Dynamics

Ternary quantum dots (QDs) are very promising nanomaterials with a range of potential applications in photovoltaics, light-emitting devices, and biomedicine. Despite quite intensive studies of ternary QDs over the last years, the specific relaxation channels involved in their emission mechanisms are still poorly understood, particularly in the corresponding core-shell nanostructures. In the present work, we have studied the recombination pathways of AgInS₂ QDs stabilized with the ZnAgInS alloy layer and the ZnS shell (AIS/ZAIS/ZnS QDs) using time-resolved fluorescence spectroscopy. We have also investigated FRET in complexes of AIS/ZAIS/ZnS QDs and cyanine dyes with the absorption bands overlapping in the different regions of the QD emission spectrum, which allowed us to selectively quench the radiative transitions of the QDs. Our studies have demonstrated that FRET from QDs to dyes results in decreasing of all QD PL decay components with the shortest lifetime decreasing the most and the longest one decreasing the least. This research presents important approaches for the investigation of ternary QD luminescence mechanisms by the selective quenching of recombination pathways. These studies are also essential for potential applications of ternary QDs in photodynamic therapy, multiplex analysis, and time-resolved FRET sensing.

Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate

Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism (ICD; λ = 450-550 nm) recognition between A-T(U) and G-C basepair containing polynucleotides. The benzothiazole-isostere showed pronounced (four-fold) fluorimetric selectivity toward ds-RNA in comparison to any ds-DNA, at variance to its quinoline-analogue fluorescence being weakly selective to GC-DNA. Preliminary screening on human tumor and normal lung cell lines showed that both dyes very efficiently enter living cells and accumulate in mitochondria, causing moderate cytotoxic effects, and thus could be considered as lead compounds toward novel theragnostic mitochondrial dyes.

The chemistry of 4-(dicyanomethylene)-3-methyl-l-phenyl-2-pyrazoline-5- ones as a privileged scaffold in synthesis of heterocycles

BACKGROUND

The reactivity of 4-(dicyanomethylene)-3-methyl-l-phenyl-2-pyrazoline-5-one DCNP 1 and its derivatives makes it valuable as a building block for the synthesis of heterocyclic compounds like pyrazolo-imidazoles, - thiazoles, spiropyridines, spiropyrroles, spiropyrans and others. As a number of publications have reported on the reactivity of DCNP and its derivatives, we compiled some features of this interesting molecule.

OBJECTIVE

This article aims to review the preparation of DCNP, its reactivity and application in heterocyclic and dyes synthesis.

CONCLUSION

In this review we have provided an overview of recent progress in the chemistry of DCNP and its significance in synthesis of various classes of heterocyclic compounds and dyes. The unique reactivity of DCNP offers unprecedentedly mild reaction conditions for the generation of versatile cynomethylene dyes from a wide range of precursors including amines, α-aminocarboxylic acids, their esters, phenols, malononitriles and azacrown ethers. We anticipate that more innovative transformations involving DCNP will continue to emerge in the near future.

Bioinspired Heterocyclic Partnership in a Cyanine-Type Acidichromic Chromophore

A new red hair-inspired 1,4-benzothiazine-based scaffold is disclosed herein, built upon a modular D-π-A architecture via condensation of the easily accessible 3-phenyl-2H-1,4-benzothiazine with indole-3-carboxaldehyde. The compound was obtained in around 50% yields and was characterized by complete spectroscopic analysis. The new benzothiazine-based cyanine displayed a characteristic reversible acidichromic behavior with a marked bathochromic shift upon acidification. The chromophore resisted at least fifteen hydrochloric acid/sodium hydroxide cycles without appreciable alterations. The expedient and scalable synthetic procedure together with the pH sensitive chromophoric properties would make the new compound an attractive prototype for novel modular chromophore for pH-sensing and other applications.

Spectral-Time Multiplexing in FRET Complexes of AgInS2/ZnS Quantum Dot and Organic Dyes

Nowadays, multiplex analysis is very popular, since it allows to detect a large number of biomarkers simultaneously. Traditional multiplex analysis is usually based on changes of photoluminescence (PL) intensity and/or PL band spectral positions in the presence of analytes. Using PL lifetime as an additional parameter might increase the efficiency of multiplex methods. Quantum dots (QDs) can be used as luminescent markers for multiplex analysis. Ternary in-based QDs are a great alternative to the traditional Cd-based one. Ternary QDs possess all advantages of traditional QDs, including tunable photoluminescence in visible range. At the same time ternary QDs do not have Cd-toxicity, and moreover they possess long spectral dependent lifetimes. This allows the use of ternary QDs as a donor for time-resolved multiplex sensing based on Förster resonance energy transfer (FRET). In the present work, we implemented FRET from AgInS₂/ZnS ternary QDs to cyanine dyes absorbing in different spectral regions of QD luminescence with different lifetimes. As the result, FRET-induced luminescence of dyes differed not only in wavelengths but also in lifetimes of luminescence, which can be used for time-resolved multiplex analysis in biology and medicine.

DNA Photocleavage in the Near-Infrared Wavelength Range by 2-Quinolinium Dicarbocyanine Dyes

Here, we report the syntheses of two pentamethine cyanine dyes containing quinolinium rings and substituted with either hydrogen (3) or bromine (4) at the meso carbon. The electron withdrawing bromine atom stabilizes dye 4 in aqueous buffer, allowing complex formation to occur between the dye and double-helical DNA. UV–visible, CD, and fluorescence spectra recorded at low DNA concentrations suggest that dye 4 initially binds to the DNA as a high-order aggregate. As the ratio of DNA to dye is increased, the aggregate is converted to monomeric and other low-order dye forms that interact with DNA in a non-intercalative fashion. The brominated dye 4 is relatively unreactive in the dark, but, under 707–759 nm illumination, generates hydroxyl radicals that cleave DNA in high yield (pH 7.0, 22 °C). Dye 4 is also taken up by ES2 ovarian carcinoma cells, where it is non-toxic under dark conditions. Upon irradiation of the ES2 cells at 694 nm, the brominated cyanine reduces cell viability from 100 ± 10% to 14 ± 1%. Our results suggest that 2-quinolinium-based carbocyanine dyes equipped with stabilizing electron withdrawing groups may have the potential to serve as sensitizing agents in long-wavelength phototherapeutic 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.

Near-Infrared-II Molecular Dyes for Cancer Imaging and Surgery

Fluorescence bioimaging affords a vital tool for both researchers and surgeons to molecularly target a variety of biological tissues and processes. This review focuses on summarizing organic dyes emitting at a biological transparency window termed the near-infrared-II (NIR-II) window, where minimal light interaction with the surrounding tissues allows photons to travel nearly unperturbed throughout the body. NIR-II fluorescence imaging overcomes the penetration/contrast bottleneck of imaging in the visible region, making it a remarkable modality for early diagnosis of cancer and highly sensitive tumor surgery. Due to their convenient bioconjugation with peptides/antibodies, NIR-II molecular dyes are desirable candidates for targeted cancer imaging, significantly overcoming the autofluorescence/scattering issues for deep tissue molecular imaging. To promote the clinical translation of NIR-II bioimaging, advancements in the high-performance small molecule-derived probes are critically important. Here, molecules with clinical potential for NIR-II imaging are discussed, summarizing the synthesis and chemical structures of NIR-II dyes, chemical and optical properties of NIR-II dyes, bioconjugation and biological behavior of NIR-II dyes, whole body imaging with NIR-II dyes for cancer detection and surgery, as well as NIR-II fluorescence microscopy imaging. A key perspective on the direction of NIR-II molecular dyes for cancer imaging and surgery is also discussed.

Superweak Coordinating Anion as Superstrong Enhancer of Cyanine Organic Semiconductor Properties

The superweak tetrakis(nonafluoro-tert-butoxy)aluminate coordinating anion was employed to introduce pseudo-gas-phase conditions to the 2-[5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indolium chromophore. The resulting formation of a photoactive organic-inorganic hybrid salt has led to a highly stabilized excited state of the organic chromophore mainly due to the minimized lattice energy and Coulomb interactions. These highly beneficial features caused by the well dispersed negative charge of the anion have led to an enhanced neat spin-casted film fluorescence intensity, prolonged fluorescence lifetime, smooth thin film surfaces and a record power photovoltaic efficiency of 3.8 % when compared to organic salts of this particular chromophore containing anions with localised negative charge. Clear evidence is given that a superweak coordinating anion is an emerging key parameter in cyanine dye photochemistry. This approach can be seen as a general guideline to prepare highly efficient ionic dyes for organic semiconductor applications.

[Substrate Properties of New Fluorescently Labeled Deoxycytidine Triphosphates in Enzymatic Synthesis of DNA with Polymerases of Families A and B]

The efficiency of the incorporation of fluorescently labeled derivatives of 2'-deoxycytidine in DNA synthesized de novo has been studied using PCR with Taq and Tth polymerases of family A and Vent (exo-) and Deep Vent (exo-) polymerases of family B. Four derivatives of 5'-triphosphate-2'-deoxycytidine (dCTP) have different chemical structures of the indodicarbocyanine dye and Cy5 analogue attached to position 5 of cytosine. The kinetics of the accumulation of the PCR products and the intensity of the fluorescent signals in the hybridization analysis with immobilized DNA probes depend on the modification of the fluorescently labeled dCTP counterpart, its concentration, and the type of DNA polymerase. All labeled triphosphates showed some inhibitory effects on PCR. The best balance between the efficiency of incorporating labeled cytidine derivatives and the negative effect on the PCR kinetics has been shown in the case of Hot Taq polymerase in combination with the Cy5-dCTP analogue, which contains containing electrically neutral chro-mophore, the axis of which is a continuation of the linker between the chromophore and the pyrimidine base.

Near-Infrared-II (NIR-II) Bioimaging via Off-Peak NIR-I Fluorescence Emission

Significantly reduced photon scattering and minimal tissue autofluorescence levels in the second biological transparency window (NIR-II; 1000-1700 nm) facilitate higher resolution in vivo biological imaging compared to tradition NIR fluorophores (~700-900 nm). However, the existing palette of NIR-II fluorescent agents including semiconducting inorganic nanomaterials and recently introduced small-molecule organic dyes face significant technical and regulatory hurdles prior to clinical translation. Fortunately, recent spectroscopic characterization of NIR-I dyes (e.g., indocyanine green (ICG), IRDye800CW and IR-12N3) revealed long non-negligible emission tails reaching past 1500 nm. Repurposing the most widely used NIR dye in medicine, in addition to those in the midst of clinical trials creates an accelerated pathway for NIR-II clinical translation. This review focuses on the significant advantage of imaging past 1000 nm with NIR-I fluorophores from both a basic and clinical viewpoint. We further discuss optimizing NIR-I dyes around their NIR-II/shortwave infrared (SWIR) emission, NIR-II emission tail characteristics and prospects of NIR-II imaging with clinically available and commercially available dyes.

Tracers for Fluorescence-Guided Surgery: How Elongation of the Polymethine Chain in Cyanine Dyes Alters the Pharmacokinetics of a Dual-Modality c[RGDyK] Tracer

The potential of receptor-mediated fluorescence-based image-guided surgery tracers is generally linked to the near-infrared emission profile and good-manufacturing-production availability of fluorescent dyes. Surprisingly, little is known about the critical interaction between the structural composition of the dyes and the pharmacokinetics of the tracers. In this study, a dual-modality tracer design was used to systematically and quantitatively evaluate the influence of elongation of the polymethine chain in a fluorescent cyanine dye on the imaging potential of a targeted tracer. Methods: As a model system, the integrin marker α_vβ₃ was targeted using arginylglycylaspartisc acid [RGD]-based vectors functionalized with a ¹¹¹In-diethylenetriaminepentaacetic acid (DTPA) chelate and a fluorescent dye: (Cy3-(SO₃)methyl-COOH [emission wavelength (λ_em), 580 nm], Cy5-(SO₃)methyl-COOH [λ_em, 680 nm], or Cy7-(SO₃)methyl-COOH [λ_em, 780 nm]). Tracers were analyzed for differences in photophysical properties, serum protein binding, chemical or optical stability, and signal penetration through tissue. Receptor affinities were evaluated using saturation and competition experiments. In vivo biodistribution (SPECT imaging and percentage injected dose per gram of tissue) was assessed in tumor-bearing mice and complemented with in vivo and ex vivo fluorescence images obtained using a clinical-grade multispectral fluorescence laparoscope. Results: Two carbon-atom-step variations in the polymethine chain of the fluorescent cyanine dyes were shown to significantly influence the chemical and photophysical characteristics (e.g., stability, brightness, and tissue penetration) of the hybrid RGD tracers. DTPA-Cy5-(SO₃)methyl-COOH-c[RGDyK] structurally outperformed its Cy3 and Cy7 derivatives. Radioactivity-based evaluation of in vivo tracer pharmacokinetics yielded the lowest nonspecific uptake and highest tumor-to-background ratio for DTPA-Cy5-(SO₃)methyl-COOH-c[RGDyK] (13.2 ± 1.7), with the Cy3 and Cy7 analogs trailing at respective tumor-to-background ratios of 5.7 ± 0.7 and 4.7 ± 0.7. Fluorescence-based assessment of tumor visibility revealed a similar trend. Conclusion: These findings underline that variations in the polymethine chain lengths of cyanine dyes have a profound influence on the photophysical properties, stability, and in vivo targeting capabilities of fluorescent imaging tracers. In a direct comparison, the intermediate-length dye (Cy5) yielded a superior c[RGDyK] tracer, compared with the shorter (Cy3) and longer (Cy7) analogs.

Increasing Photovoltaic Performance of an Organic Cationic Chromophore by Anion Exchange

A symmetrical cyanine dye chromophore is modified with different counteranions to study the effect on crystal packing, polarizability, thermal stability, optical properties, light absorbing layer morphology, and organic photovoltaic (OPV) device parameters. Four sulfonate-based anions and the bulky bistriflylimide anion are introduced to the 2-[5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indolium chromophore using an Amberlyst A26 (OH^- form) anion exchanger. Anionic charge distribution clearly correlates with device performance, whereby an average efficiency of 2% was reached in a standard bilayer organic solar. Evidence is given that the negative charge of the anion distributed over a large number of atoms is significantly more important than the size of the organic moieties of the sulfonate charge carrying group. This provides a clear strategy for future design of more efficient cyanine dyes for OPV applications.

Increasing Photovoltaic Performance of an Organic Cationic Chromophore by Anion Exchange

A symmetrical cyanine dye chromophore is modified with different counteranions to study the effect on crystal packing, polarizability, thermal stability, optical properties, light absorbing layer morphology, and organic photovoltaic (OPV) device parameters. Four sulfonate-based anions and the bulky bistriflylimide anion are introduced to the 2-[5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indolium chromophore using an Amberlyst A26 (OH^- form) anion exchanger. Anionic charge distribution clearly correlates with device performance, whereby an average efficiency of 2% was reached in a standard bilayer organic solar. Evidence is given that the negative charge of the anion distributed over a large number of atoms is significantly more important than the size of the organic moieties of the sulfonate charge carrying group. This provides a clear strategy for future design of more efficient cyanine dyes for OPV applications.

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.

Energy Transfer between Spatially Separated Entangled Molecules

Light–matter strong coupling allows for the possibility of entangling the wave functions of different molecules through the light field. We hereby present direct evidence of non‐radiative energy transfer well beyond the Förster limit for spatially separated donor and acceptor cyanine dyes strongly coupled to a cavity. The transient dynamics and the static spectra show an energy transfer efficiency approaching 37 % for donor–acceptor distances ≥100 nm. In such systems, the energy transfer process becomes independent of distance as long as the coupling strength is maintained. This is consistent with the entangled and delocalized nature of the polaritonic states.

A Conjugate of Pentamethine Cyanine and 18F as a Positron Emission Tomography/Near-Infrared Fluorescence Probe for Multimodality Tumor Imaging

The novel synthesis of a dual-modality, pentamethine cyanine (Cy5) fluorescent, ¹⁸F positron emission tomography (PET) imaging probe is reported. The probe shows a large extinction coefficient and large quantum yield in the biologically transparent, near-infrared window (650–900 nm) for in vivo fluorescent imaging. This fluorophore bears the isotope, ¹⁸F, giving a ¹⁸F-PET/near-infrared fluorescent (NIRF), bi-modal imaging probe, that combines the long-term stability of NIRF and the unlimited penetration depth of PET imaging. The bi-modal probe is labeled with ¹⁸F in a quick, one-step reaction, which is important in working with the rapid decay of ¹⁸F. The bi-modal probe bears a free carboxyl group, highlighting a PET/NIRF synthon that can be conjugated onto many advanced biomolecules for biomarker-specific in vivo dual-modal PET/NIR tumor imaging, confocal histology, and utility in multi-fluorophore, fluorescence-guided surgery. Its potential in vivo biocompatibility is explored in a quick proof-of-principal in vivo study. The dye is delivered to A549 xenograft flank-tumors to generate PET and NIRF signals at the tumor site. The tumor distribution is confirmed in ex vivo gamma counting and imaging. Pentamethine cyanine (Cy5) has the ability to preferentially accumulate in tumor xenografts. We substitute the PET/NIRF probe for Cy5, and explore this phenomenon.

A Highly Selective Sensor for Cyanide in Organic Media and on Solid Surfaces

The application of IR 786 perchlorate (IR-786) as a selective optical sensor for cyanide anion in both organic solution (acetonitrile (MeCN), 100%) and solvent-free solid surfaces was demonstrated. In MeCN, IR-786 was selective to two anions in the following order: CN(-) > OH(-). A significant change in the characteristic dark green color of IR-786 in MeCN to yellow was observed as a result of nucleophilic addition of CN(-) to the fluorophore, i.e., formation of IR 786-(CN), which was also verified by a blue shift in the 775 nm absorbance peak to 430 nm. A distinct green fluorescence emission from the IR-786-(CN) in MeCN was also observed, which demonstrated the selectivity of IR-786 towards CN(-) in MeCN. Fluorescence emission studies of IR-786 showed that the lower detection limit and the sensitivity of IR-786 for CN(-) in MeCN was 0.5 μM and 0.5 to 8 μM, respectively. The potential use of IR-786 as a solvent-free solid state sensor for the selective sensing and monitoring of CN(-) in the environment was also demonstrated. On solvent-free solid state surfaces, the sensitivity of the IR-786 to CN(-) in water samples was in the range of 50-300 μM with minimal interference by OH(-).

2, 2'- and 4, 4'-Cyanines are transporter-independent in vitro dopaminergic toxins with the specificity and mechanism of toxicity similar to MPP⁺

Specific uptake through dopamine transporter followed by the inhibition of the mitochondrial complex-I have been accepted as the cause of the specific dopaminergic toxicity of 1-methyl-4-phenylpyridinium (MPP(+) ). However, MPP(+) is taken up into many cell types through other transporters, suggesting that, in addition to the efficient uptake, intrinsic vulnerability of dopaminergic cells may also contribute to their high sensitivity to MPP(+) and similar toxins. To test this possibility, two simple cyanines were employed in a comparative study based on their unique characteristics and structural similarity to MPP(+) . Here, we show that they freely accumulate in dopaminergic (MN9D and SH-SY5Y) as well as in liver (HepG2) cells, but are specifically and highly toxic to dopaminergic cells with IC50s in the range of 50-100 nM, demonstrating that they are about 1000-fold more toxic than MPP(+) under similar experimental conditions. They cause mitochondrial depolarization non-specifically, but increase the reactive oxygen species specifically in dopaminergic cells leading to the apoptotic cell death parallel to MPP(+) . These and other findings suggest that the specific dopaminergic toxicity of these cyanines is due to the inherent vulnerability of dopaminergic cells toward mitochondrial toxins that lead to the excessive production of reactive oxygen species. Therefore, the specific dopaminergic toxicity of MPP(+) must also be, at least partly, due to the specific vulnerability of dopaminergic neurons. Thus, these cyanines could be stronger in vivo dopaminergic toxins than MPP(+) and their in vivo toxicities must be evaluated. Here, we show that cationic lipophilic cyanines with structural similarity to 1-methyl-4-phenylpyridinium (MPP(+) ) freely accumulate non-specifically, but only toxic to dopaminergic cells. They are 1000-fold more toxic than MPP(+) under similar conditions. They cause mitochondrial depolarization non-specifically, but increase the ROS specifically in dopaminergic cells leading to the apoptotic cell death parallel to MPP(+) . Thus, the specific dopaminergic toxicity of MPP(+) and related toxins could be due to the intrinsic vulnerability of dopaminergic cells toward mitochondrial oxidative stress.

Trichocyanines: a Red-Hair-Inspired Modular Platform for Dye-Based One-Time-Pad Molecular Cryptography

Current molecular cryptography (MoCryp) systems are almost exclusively based on DNA chemistry and reports of cryptography technologies based on other less complex chemical systems are lacking. We describe herein, as proof of concept, the prototype of the first asymmetric MoCryp system, based on an 8-compound set of a novel bioinspired class of cyanine-type dyes called trichocyanines. These novel acidichromic cyanine-type dyes inspired by red hair pigments were synthesized and characterized with the aid of density functional theory (DFT) calculations. Trichocyanines consist of a modular scaffold easily accessible via an expedient condensation of 3-phenyl- or 3-methyl-2H-1,4-benzothiazines with N-dimethyl- or o-methoxyhydroxy-substituted benzaldehyde or cinnamaldehyde derivatives. The eight representative members synthesized herein can be classified as belonging to two three-state systems tunable through four different control points. This versatile dye platform can generate an expandable palette of colors and appears to be specifically suited to implement an unprecedented single-use asymmetric molecular cryptography system. With this system, we intend to pioneer the translation of digital public-key cryptography into a chemical-coding one-time-pad-like system.

A unique type of pyrrole-based cyanine fluorophores with turn-on and ratiometric fluorescence signals at different pH regions for sensing pH in enzymes and living cells

The development of new functional fluorescent dyes has attracted great attention. Herein we have described a novel strategy to design a unique type of cyanine dyes by attaching two indolium moieties at the α-positions of the pyrrole core. The new type of cyanine dyes is named as PyCy fluorophores. Importantly, PyCy dyes can exhibit an exceptional feature, fluorescence turn-on response at pH varying from acidic to near-neutral conditions, and a ratiometric fluorescence response at pH varying from near-neutral to basic conditions. By taking advantage of the fluorescence turn-on response of PyCy2 at pH varying from acidic to near-neutral conditions and emission properties of PyCy2, we have demonstrated that a small-molecule fluorescent probe can image pH variations in living cells. Furthermore, we have demonstrated that PyCy2 can sense real-time pH changes under alkaline conditions induced by enzymes based on the ratiometric fluorescence response of PyCy2 at pH varying from near-neutral to basic conditions. We expect that the new design strategy for PyCy fluorophores may prompt the development of a wide variety of cyanine derivatives with desirable properties.

Increasing the brightness of cyanine fluorophores for single-molecule and superresolution imaging

In spite of their relatively low fluorescence quantum yield, cyanine dyes such as Cy3, Cy5, or Cy7 are widely used in single-molecule fluorescence applications due to their high extinction coefficients and excellent photon yields. We show that the fluorescence quantum yield and lifetime of red-emitting cyanine dyes can be substantially increased in heavy water (D2 O) compared with water (H2 O). We find that the magnitude of the quantum yield increase in D2 O scales with the emission wavelength, reaching a particularly high value of 2.6-fold for the most red-emitting dye investigated, Cy7. We further demonstrate a higher photon yield in single-molecule superresolution experiments in D2 O compared to H2 O, which leads to an improved localization precision and hence better spatial resolution. This finding is especially beneficial for biological applications of fluorescence microscopy, which are typically carried out in aqueous media and which greatly profit from the red spectral range due to reduced cellular auto-fluorescence.

All-near-infrared multiphoton microscopy interrogates intact tissues at deeper imaging depths than conventional single- and two-photon near-infrared excitation microscopes

The era of molecular medicine has ushered in the development of microscopic methods that can report molecular processes in thick tissues with high spatial resolution. A commonality in deep-tissue microscopy is the use of near-infrared (NIR) lasers with single- or multiphoton excitations. However, the relationship between different NIR excitation microscopic techniques and the imaging depths in tissue has not been established. We compared such depth limits for three NIR excitation techniques: NIR single-photon confocal microscopy (NIR SPCM), NIR multiphoton excitation with visible detection (NIR/VIS MPM), and all-NIR multiphoton excitation with NIR detection (NIR/NIR MPM). Homologous cyanine dyes provided the fluorescence. Intact kidneys were harvested after administration of kidney-clearing cyanine dyes in mice. NIR SPCM and NIR/VIS MPM achieved similar maximum imaging depth of ∼100 μm. The NIR/NIR MPM enabled greater than fivefold imaging depth (>500 μm) using the harvested kidneys. Although the NIR/NIR MPM used 1550-nm excitation where water absorption is relatively high, cell viability and histology studies demonstrate that the laser did not induce photothermal damage at the low laser powers used for the kidney imaging. This study provides guidance on the imaging depth capabilities of NIR excitation-based microscopic techniques and reveals the potential to multiplex information using these platforms.