Pentamethine Cyanine Research Articles

Excited state relaxation in cationic pentamethine cyanines studied by time-resolved spectroscopy

In this work, we examined the nature and pathways of electronic excitation relaxation at low temperature in cationic pentamethine pyrylocyanine dye, which in the ground state is characterized by symmetric and non-symmetric localization of cationic charge on the carbon chain between the terminal groups. The carbon chain in such symmetric and non-symmetric charge localizations is close to polymethine and polyene conformations, respectively. The effect of symmetry breaking during the two-way transition polymethine – polyene in the optically excited state on the electronic properties of dyes is considered. Combined quantum-chemical calculations and time-resolved spectral measurements allowed us to characterize the symmetric and non-symmetric structures in the ground and excited states with specific peaks of transitions and lifetimes. The features of the polymethine structure of the dye are attributed to large-radius polaron formation, whereas for the polyene structures the model of excitons formed on the double bonds of the carbon chain can be used to analyze the relaxation pathways. The energy diagram model for relaxation pathways of optically excited electronic states has been proposed. The proposed model can be characteristic for pentamethine cyanine dyes with the symmetric and non-symmetric distribution of cationic charge at the carbon chain between the terminal groups in the ground and excited states.

Defining the Basis of Cyanine Phototruncation Enables a New Approach to Single-Molecule Localization Microscopy.

The light-promoted conversion of extensively used cyanine dyes to blue-shifted emissive products has been observed in various contexts. However, both the underlying mechanism and the species involved in this photoconversion reaction have remained elusive. Here we report that irradiation of heptamethine cyanines provides pentamethine cyanines, which, in turn, are photoconverted to trimethine cyanines. We detail an examination of the mechanism and substrate scope of this remarkable two-carbon phototruncation reaction. Supported by computational analysis, we propose that this reaction involves a singlet oxygen-initiated multistep sequence involving a key hydroperoxycyclobutanol intermediate. Building on this mechanistic framework, we identify conditions to improve the yield of photoconversion by over an order of magnitude. We then demonstrate that cyanine phototruncation can be applied to super-resolution single-molecule localization microscopy, leading to improved spatial resolution with shorter imaging times. We anticipate these insights will help transform a common, but previously mechanistically ill-defined, chemical transformation into a valuable optical tool.

Synthesis of pH-sensitive benzothiazole cyanine dye derivatives containing a pyridine moiety at the meso position

Four benzothiazole-derived pentamethine cyanine dyes were synthesized with a pyridine moiety at the meso-position of the methine chain with a reaction yield of 89–93%. These dyes were prepared with high purity in a three-step synthesis as prospective pH-responsive probes. Each compound absorbed and fluoresced between 630 and 670 nm within the far-red range of the visible spectrum with high molar absorptivity values calculated between 134,910 L mol −1 cm−1 and 163,816 L mol −1 cm−1 and quantum yields between 9% and 17%. When a 20 μM solution of dye derivatives are exposed to hydrochloric acid in the range of pH 5–6 in ethanol, all the dyes experienced a blueshift in absorbance and emission as well as a decrease in spectral intensity that enables them to operate as pH probes. These properties were further validated via computational studies showing pyridine's influence on each molecules' spectral properties, and pathways for electron delocalization in the presence and absence of acid were proposed. © 2021 Elsevier Science. All rights reserved.

Engineering couplings for exciton transport using synthetic DNA scaffolds

Summary Control over excitons enables electronic energy to be harnessed and transported for light harvesting and molecular electronics. Such control requires nanoscale precision over the molecular components. Natural light-harvesting systems achieve this precision through sophisticated protein machinery, which is challenging to replicate synthetically. Here, we introduce a DNA-based platform that spatially organizes cyanine chromophores to construct tunable excitonic systems. We synthesized DNA-chromophore nanostructures and characterized them with ensemble ultrafast and single-molecule spectroscopy and structure-based modeling. This synthetic approach facilitated independent control over the coupling among the chromophores and between the chromophores and the environment. We demonstrated that the coupling between the chromophores and the environment could enhance exciton transport efficiency, highlighting the key role of the environment in driving exciton dynamics. Control over excitons, as reported here, offers a path toward the development of designer nanophotonic devices.

Dual-dye systems comprising activatable fluorescein dye and hydrophobic or hydrophilic Cy5 reference fluorophore for ratiometric drug delivery monitoring

Ratiometric fluorescence detection in biological samples in vitro and in vivo mitigates several issues in conventional single-signal measurements such as light absorption and scattering, dye photobleaching, and instrumental parameters. Herein, two new systems for ratiometric monitoring of drug delivery are synthesized and investigated. These systems comprise a non-fluorescent fluorescein-based dye, Flu, bound to the anticancer drug, azatoxin (Aza), through a hydrolytically cleavable acrylate ester linker and either hydrophobic (Cy5h) or hydrophilic (Cy5s) pentamethine cyanine dye providing a red-light reference signal. Upon drug release, the green Flu fluorescence notably increases enabling ratiometric tracking of drug release events. The spectral properties of the developed conjugates and fluorescently monitored drug release rates are investigated in biologically relevant media with respect of the Cy5 dye hydrophilicity.

Unsymmetrical pentamethine cyanines for visualizing physiological acidities from the whole-animal to the cellular scale with pH-responsive deep-red fluorescence.

Acidity plays an important role in numerous physiological and pathological events. Non-invasively monitoring pH dynamics would be valuable for understanding pathological processes and optimizing therapeutic strategies. Although numerous near-infrared (NIR) fluorophores have been developed to monitor acidification in vivo, the experimental results are difficult to verify at the molecular or cellular level using a fluorescence microscope or flow cytometer due to the lack of lasers with excitation wavelengths in the NIR wavelength range. This work presents a sequential condensation strategy for obtaining unsymmetrical pentamethine cyanines with fine-tuned pKa values and improved yields. These deep-red fluorophores with pH responsiveness can not only be used to monitor acidification in live cells using confocal microscopic imaging and flow cytometry, but they can also be used to non-invasively identify infected tissue with a low pH value in live mouse models. In addition, the acidity in infected tissue slices was verified under a conventional confocal microscope. Overall, this work demonstrates a new synthetic method with improved yields for unsymmetrical pentamethine cyanines that can report acidity. These pH-responsive deep-red fluorophores not only provide new tools for accessing pH-associated physiological and pathological events, but they can also help in understanding in vivo imaging results at the molecular or cellular level due to their detectability by multiple imaging instruments.

Critical role of H-aggregation for high-efficiency photoinduced charge generation in pristine pentamethine cyanine salts.

The mechanism of photoinduced symmetry-breaking charge separation in solid cyanine salts at the base of organic photovoltaic and optoelectronic devices is still debated. Here, we employ femtosecond transient absorption spectroscopy (TAS) to monitor the charge transfer processes occurring in thin films of pristine pentamethine cyanine (Cy5). Oxidized dye species are observed in Cy5-hexafluorophosphate salts upon photoexcitation, resulting from electron transfer from monomer excited states to H-aggregates. The charge separation proceeds with a quantum yield of 86%, providing the first direct proof of high efficiency intrinsic charge generation in organic salt semiconductors. The impact of the size of weakly coordinating anions on charge separation and transport is studied using TAS alongside electroabsorption spectroscopy and time-of-flight techniques. The degree of H-aggregation decreases with increasing anion size, resulting in reduced charge transfer. However, there is little change in carrier mobility, as despite the interchromophore distance increasing, the decrease in energetic disorder helps to alleviate the trapping of charges by H-aggregates.

Fluorous Soluble Cyanine Dyes for Visualizing Perfluorocarbons in Living Systems.

The bioorthogonal nature of perfluorocarbons provides a unique platform for introducing dynamic nano- and microdroplets into cells and organisms. To monitor the localization and deformation of the droplets, fluorous soluble fluorophores that are compatible with standard fluorescent protein markers and applicable to cells, tissues, and small organisms are necessary. Here, we introduce fluorous cyanine dyes that represent the most red-shifted fluorous soluble fluorophores to date. We study the effect of covalently appended fluorous tags on the cyanine scaffold and evaluate the changes in photophysical properties imparted by the fluorous phase. Ultimately, we showcase the utility of the fluorous soluble pentamethine cyanine dye for tracking the localization of perfluorocarbon nanoemulsions in macrophage cells and for measurements of mechanical forces in multicellular spheroids and zebrafish embryonic tissues. These studies demonstrate that the red-shifted cyanine dyes offer spectral flexibility in multiplexed imaging experiments and enhanced precision in force measurements.

Evaluation of asymmetric orthogonal cyanine fluorophores

Pentamethine cyanine (Cy5) fluorophores have proven to be versatile imaging agents (i.e., tracers) for a range of micro- and macroscopic imaging applications, including image-guided surgery. In this study the relationship between the structure of asymmetric Cy5 fluorophores and their photophysical properties was studied. To this end, seven Cy5 analogues, bearing orthogonal N-indole substituents (H, SO3−, or benzene), were synthesised and evaluated. In-depth analysis revealed that introduction of sulfonates enhanced the fluorescence brightness and photostability, while reducing the lipophilicity, serum binding and stacking tendency. The addition of benzene moieties induced a bathochromic shift of 10–20 nm, increased the lipophilicity (LogP = -1.56–1.23) and serum binding (67.3–93.8% bound), as well as negatively impacted the brightness (0.74–42.9 · 103 M−1 cm−1), photostability (24.4–90.6% remaining), and stacking tendency. Chemical stability was uninfluenced by the substitution pattern. Additionally, the generation of a c[RGDyK]-based hybrid tracer based on one of these fluorophores in combination with a diethylenetriaminepentaacetic acid (DTPA) chelate and an 111In-isotope was reported. This compound was evaluated in vitro using αvβ3-overexpressing Geβ3 cells and in vivo using a 4T1 mouse tumour model. Overall, the presented results imply that alterations of the asymmetrical orthogonal Cy5 fluorophore structure have impact on the (photo)physical properties. Furthermore, the orthogonal Cy5 fluorophore framework can readily be applied in tracer development.

High-Yielding Water-Soluble Asymmetric Cyanine Dyes for Labeling Applications

A simple and efficient microwave-assisted synthesis of asymmetric pentamethine cyanine dyes with various functional groups was developed, which allows high-yielding results. The synthesized dyes are modifiable and suitable for single-molecule imaging in biological and medical sciences by application of click chemistry or classic esterification and amidation.

Far-red pentamethine cyanine dyes as fluorescent probes for the detection of serum albumins.

Benzothiazole based cyanine dyes with bridged groups in the pentamethine chain were studied as potential far-red fluorescent probes for protein detection. Spectral-luminescent properties were characterized for unbound dyes and in the presence of serum albumins (bovine (BSA), human (HSA), equine (ESA)), and globular proteins (β-lactoglobulin, ovalbumin). We have observed that the addition of albumins leads to a significant increase in dyes fluorescence intensity. However, the fluorescent response of dyes in the presence of other globular proteins was notably lower. The value of fluorescence quantum yield for dye bearing a sulfonate group complexed with HSA amounted to 42% compared with 0.2% for the free dye. The detection limit of HSA by this dye was greater than 0.004 mg ml−1 which indicates the high sensitivity of dye to low HSA concentrations. Modelling of structure of the dyes complexes with albumin molecules was performed by molecular docking. According to these data, dyes could bind to up to five sites on the HSA molecule; the most preferable are the haemin-binding site in subdomain IB and the dye-binding site in the pocket between subdomains IA, IIA and IIIA. This work confirms that pentamethine cyanine dyes could be proposed as powerful far-red fluorescent probes applicable for highly sensitive detection of albumins.

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.

Synthesis and characterization of new derivatives of bis(1,4‐diazepinium) salts and bis(γ‐substituted pentamethine cyanine(dyes using vinamidinium salt

AbstractThe preparation of several bis(1,4‐diazepinium) salts from the reaction of three 1,2‐diamines with a bis(vinamidinium) salt is described. Bis(γ‐substituted pentamethine cyanine(dyes are also prepared from the reaction of vinamidinium salt with 1,2‐dimethylquinolinium perchlorate and 1,2,3,3‐tetramethyl‐3H‐indolium perchlorate. Data from elemental analyzes, IR, 1H‐NMR, 13C‐NMR, and mass spectra (MS) confirm the molecular structure of the obtained products.

Optimizing the Biodistribution of Radiofluorinated Barbiturate Tracers for Matrix Metalloproteinase Imaging by Introduction of Fluorescent Dyes as Pharmacokinetic Modulators.

Dysregulated expression or activation of matrix metalloproteinases (MMPs) is observed in many kinds of life-threatening diseases. Therefore, MMP imaging-for example, with radiolabeled MMP inhibitors (MMPIs)-potentially represents a valuable tool for clinical diagnostics using noninvasive single photon emission computed tomography (SPECT) or positron emission tomography (PET) imaging. Despite numerous preclinical imaging approaches, translation to a clinical setting has not yet been successful. We introduce and oppose three potential radiofluorinated MMP-targeted imaging probes, modified by the introduction of pentamethine cyanine (Cy5) dyes and therefore containing both radio- as well as fluorescent label with respect to their capability to assess MMP activity in vivo by means of scintigraphic (PET) and/or fluorescent (NIRF) imaging. New hybrid MMPI tracer candidates, structurally based on radiofluorinated pyrimidine-2,4,6-triones (barbiturates) from previous approaches, were synthesized by convenient two-step syntheses. In the first step, Cy5 dyes, varying in the number of sulfonate groups (nSO3- = 1, 2, or 4) and bearing an additional "clickable" alkyne moiety, were coupled to the barbiturate MMPI by amide formation. In the second step, the [18F]fluoride radiolabel was introduced into the resulting Cy5 dye conjugates by "radio-click" chemistry. Biodistribution studies of these hybrid tracer candidates were assessed and compared in C57BL/6 mice by PET as well as fluorescence imaging. MMP activity was imaged in a MMP-positive mouse model of irritant contact dermatitis (ICD) by PET and sequential fluorescence reflectance imaging (FRI), respectively. In vivo data were validated by scintillation counting, gelatin zymography, and MMP-histology. Three new potential hybrid MMP imaging probes were prepared, differing essentially in the number of sulfonate groups, introduced by Cy5 dye components. Although the hydrophilicity of these compounds was substantially increased, 10a (nSO3- = 1) and 10b (nSO3- = 2) were still rapidly eliminated via unfavorable hepatobiliary pathways, as observed in earlier approaches. Only 11 (nSO3- = 4) showed delayed in vivo clearance and a shift towards higher renal elimination. In the chosen mouse model of ICD, only 11 (nSO3- = 4) significantly accumulated in the inflamed mouse ear, which could be precisely visualized by means of PET and FRI.

Conformationally restrained pentamethine cyanines and use in reductive single molecule localization microscopy.

Pentamethine cyanines are a class of far-red fluorophores that find extensive use in single-molecule localization microscopy (SMLM), as well as a broad range of other techniques. A drawback of this scaffold is its relatively low quantum yields, which is due to excited state deactivation via trans-to-cis chromophore isomerization. Here we describe a synthetic strategy to improve the photon output of these molecules. In the key synthetic transformation, a protected dialdehyde precursor undergoes a cascade reaction that forms a tetracyclic ring system. The resulting conformationally restrained analogs exhibit improved fluorescence quantum yield and extended fluorescence lifetimes. These properties, together with their ability to efficiently recover from hydride reduction, enable a uniquely simple form of single-molecule localization microscopy (SMLM).

Anti-quenching NIR-II molecular fluorophores for in vivo high-contrast imaging and pH sensing

The contrast and sensitivity of in vivo fluorescence imaging has been revolutionized by molecular fluorophores operating in the second near-infrared window (NIR-II; 1000-1700 nm), but an ongoing challenge is the solvatochromism-caused quenching in aqueous solution for the long-wavelength absorbing fluorophores. Herein, we develop a series of anti-quenching pentamethine cyanine fluorophores that significantly overcome the severe solvatochromism, thus affording stable absorption/emission beyond 1000 nm with up to ~ 44-fold enhanced brightness and superior photostability in aqueous solution. These advantages allow for deep optical penetration (8 mm) as well as high-contrast and highly-stable lymphatic imaging superior to clinical-approved indocyanine green. Additionally, these fluorophores exhibit pH-responsive fluorescence, allowing for noninvasive ratiometric fluorescence imaging and quantification of gastric pH in vivo. The results demonstrate reliable accuracy in tissue as deep as 4 mm, comparable to standard pH electrode method. This work unlocks the potential of anti-quenching pentamethine cyanines for NIR-II biological applications.

Harnessing Cyanine Reactivity for Optical Imaging and Drug Delivery.

Optical approaches that visualize and manipulate biological processes have transformed modern biomedical research. An enduring challenge is to translate these powerful methods into increasingly complex physiological settings. Longer wavelengths, typically in the near-infrared (NIR) range (∼650-900 nm), can enable advances in both fundamental and clinical settings; however, suitable probe molecules are needed. The pentamethine and heptamethine cyanines, led by prototypes Cy5 and Cy7, are among the most useful compounds for fluorescence-based applications, finding broad use in a range of contexts. The defining chemical feature of these molecules, and the key chromophoric element, is an odd-numbered polymethine that links two nitrogen atoms. Not only a light-harvesting functional group, the cyanine chromophore is subject to thermal and photochemical reactions that dramatically alter many properties of these molecules. This Account describes our recent studies to define and use intrinsic cyanine chromophore reactivity. The hypothesis driving this research is that novel chemistries that manipulate the cyanine chromophore can be used to address challenging problems in the areas of imaging and drug delivery. We first review reaction discovery efforts that seek to address two limitations of long-wavelength fluorophores: undesired thiol reactivity and modest fluorescence quantum yield. Heptamethine cyanines with an O-alkyl substituent at the central C4' carbon were prepared through a novel N- to O-transposition reaction. Unlike commonly used C4'-phenol variants, this new class of fluorophores is resistant to thiol modification and exhibits improved in vivo imaging properties when used as antibody tags. We have also developed a chemical strategy to enhance the quantum yield of far-red pentamethine cyanines. Using a synthetic strategy involving a cross metathesis/tetracyclization sequence, this approach conformationally restrains the pentamethine cyanine scaffold. The resulting molecules exhibit enhanced quantum yield (ΦF = 0.69 vs ΦF = 0.15). Furthermore, conformational restraint improves interconversion between reduced hydrocyanine and intact cyanine forms, which enables super resolution microscopy. This Account then highlights efforts to use cyanine photochemical reactivity for NIR photocaging. Our approach involves the deliberate use of cyanine photooxidation, a reaction previously only associated with photodegradation. The uncaging reaction sequence is initiated by photooxidative chromophore cleavage (using wavelengths of up to 780 nm), which prompts a C-N bond hydrolysis/cyclization sequence resulting in phenol liberation. This approach has been applied to generate the first NIR-activated antibody-drug conjugates. Tumor uptake can be monitored in vivo using NIR fluorescence, prior to uncaging with an external irradiation source. This NIR uncaging strategy can slow tumor progression and increase survival in a MDA-MB-468- luc mouse model. Broadly, the vantage point of cyanine reactivity is providing novel probe molecules with auspicious features for use in complex imaging and drug delivery settings.

Bifunctional reactive pentamethine cyanine dyes for biomedical applications

New unsymmetrical pentamethine cyanine dyes containing two non-equivalent reactive groups selected from carboxyl, amino and hydroxyl in different combinations were synthesized and their spectral properties investigated. Amino and hydroxy groups were used for binding the dyes to the anticancer drug, chlorambucil (CLB) via biodegradable amide or ester linker while the second reactive functionality could be utilized for attachment at mild conditions to a targeting carrier such as an antibody or peptide. These conjugates can thereby potentially be suitable for fluorescence-based monitoring of drug delivery. The CLB release profiles triggered by biodegradable linker were investigated in buffer solutions and cell medium using LC-MS and spectrofluorimetric methods.

Design and synthesis of symmetrical pentamethine cyanine dyes as NIR photosensitizers for PDT

Herein, we report the synthesis and spectroscopic characterization of novel Near Infra-Red (NIR) pentamethine cyanine dyes, as potential photosensitizers for Photodynamic Therapy (PDT) characterized by a strong absorption in the tissue transparency window (600–800 nm). The heteroaromatic benzoindolenine ring of various symmetrical cyanine dyes has been differently functionalized and quaternarized as a result of a structure-activity study and to determine the substituent effect on the cellular uptake, ROS production and photodynamic activity. These probes present low cytotoxicity in dark, but promote phototoxic effect, upon irradiation, in human fibrosarcoma cell line (HT-1080) with interesting and unexpected structure to property activity.

PH-Responsive Cy5 dyes having nucleophilic substituents for molecular imaging

pH-Responsive fluorescent pentamethine cyanine (Cy5) derivatives having nucleophilic substituents were synthesized. Cy5 derivatives 1-O having mercaptopropyl, hydroxypropyl, and aminopropyl groups on an indole nitrogen atom showed pH-dependent equilibria between a fluorescent open-ring structure (1-O) and a non-fluorescent closed-ring structure (1-C) in pH ranges 3–7, 6–7.5, and 8–9, respectively. pH-Responsive dyes 1a-C having a 1,3-thiazinane structure were easily internalized into A549 cells and converted to open-ring structure 1a-O in response to the relatively low pH of acidic compartments in the cells.