Cyanine Fluorophores Research Articles

Development and Application of Cationic Nile Blue Probes in Live-Cell Super-Resolution Imaging and Specific Targeting to Mitochondria.

Mitochondria are essential organelles involved in various metabolic processes in eukaryotes. The imaging, targeting, and investigation of cell death mechanisms related to mitochondria have garnered significant interest. Small-molecule fluorescent probes have proven to be robust tools for utilizing light to advance the study of mitochondrial biology. In this study, we present the rational design of cationic Nile blue probes carrying a permanent positive charge for these purposes. The cationic Nile blue probes exhibit excellent mitochondrial permeability, unique solvatochromism, and resistance to oxidation. We observed weaker fluorescence in aqueous solutions compared to lipophilic solvents, thereby minimizing background fluorescence in the cytoplasm. Additionally, we achieved photoredox switching of the cationic Nile blue probes under mild conditions. This enabled us to demonstrate their application for the first time in single-molecule localization microscopy of mitochondria, allowing us to observe mitochondrial fission and fusion behaviors. Compared to conventional cyanine fluorophores, this class of dyes demonstrated prolonged resistance to photobleaching, likely due to their antioxidation properties. Furthermore, we extended the application of cationic Nile blue probes to the mitochondria-specific delivery of taxanes, facilitating the study of direct interactions between the drug and organelles. Our approach to triggering cell death without reliance on microtubule binding provides valuable insights into anticancer drug research and drug-resistance mechanisms.

New buffer systems for photopainting of single biomolecules.

We present newly developed buffer systems that significantly improve the efficiency of a photochemically induced surface modification at the single molecule level. Buffers with paramagnetic cations and radical oxygen promoting species facilitate laser-assisted protein adsorption by photobleaching (LAPAP) of single fluorescently labelled oligonucleotides or biotin onto multi-photon-lithography-structured 2D and 3D acrylate scaffolds. Single molecule fluorescence microscopy has been used to quantify photopainting efficiency. We identify specific cation interaction sites for members of the cyanine, coumarin and rhodamine classes of fluorophores using quantum mechanical calculations. We show that our buffer systems provide an up to three-fold LAPAP-efficiency increase for the cyanine fluorophore, while keeping excitation parameters constant.

Unexpected dual-functional cyanine fluorophores: NIR multifunctional fluorescent probes for simultaneous monitoring of mitochondrial cysteine /viscosity during kidney ferroptosis in vivo

Cysteine (Cys) level and mitochondrial viscosity are important factors controlling cellular lipid peroxide metabolism and are closely related to ferroptosis. However, simultaneous tracking of these two key target analytes in the context of ferroptosis has not been realized. In this study, we developed a series of novel NIR dual-functional cyanine fluorophores AR-Cy based on a modified Vilsmeier-Haack reaction for simultaneous visualizing of cysteine level and mitochondrial viscosity during kidney ferroptosis in vivo. Intriguingly, this modified Vilsmeier-Haack reaction provides additional electron-withdrawing molecular rotor for improving the sensing performance to Cys and mitochondrial viscosity at two separated fluorescence channels (λem = 650 nm, Cys; λem = 710 nm, viscosity). Notably, by dual-color fluorescent imaging with this excellent probe AR-Cy-3, we found that ferroptosis process (erastin, sorafenib and sulfasalazine as ferroptosis inducers) was accompanied by a slight decrease in Cys channel and a significant increase in mitochondrial viscosity channel for the first time. More importantly, we further revealed that Cys level gradually decreased and mitochondrial viscosity rapidly increased in mouse kidney ferroptosis model in vivo. Therefore, this work provides not only the first dual-functional probe for studying the dynamic changes between the Cys level and mitochondrial viscosity in kidney ferroptosis but also useful cyanine fluorophores for designing powerful probes of relevant analytes to other diseases.

Synthesis, Optical Properties, and In Vivo Biodistribution Performance of Polymethine Cyanine Fluorophores.

Near-infrared (NIR) cyanine dyes showed enhanced properties for biomedical imaging. A systematic modification within the cyanine skeleton has been made through a facile design and synthetic route for optimal bioimaging. Herein, we report the synthesis of 11 NIR cyanine fluorophores and an investigation of their physicochemical properties, optical characteristics, photostability, and in vivo performance. All synthesized fluorophores absorb and emit within 610-817 nm in various solvents. These dyes also showed high molar extinction coefficients ranging from 27,000 to 270,000 cm-1 M-1, quantum yields 0.01 to 0.33, and molecular brightness 208-79,664 cm-1 M-1 in the tested solvents. Photostability data demonstrate that all tested fluorophores 28, 18, 20, 19, 25, and 24 are more photostable than the FDA-approved indocyanine green. In the biodistribution study, most compounds showed tissue-specific targeting to selectively accumulate in the adrenal glands, lymph nodes, or gallbladder while excreted to the hepatobiliary clearance route. Among the tested, compound 23 showed the best targetability to the bone marrow and lymph nodes. Since the safety of cyanine fluorophores is well established, rationally designed cyanine fluorophores established in the current study will expand an inventory of contrast agents for NIR imaging of not only normal tissues but also cancerous regions originating from these organs/tissues.

Combined Fluorescence Fluctuation and Spectrofluorometric Measurements Reveal a Red-Shifted, Near-IR Emissive Photo-Isomerized Form of Cyanine 5.

Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such experiments. Here, we studied the photo-isomerization of the pentamethine cyanine 5 (Cy5) by two similar, yet complementary means to follow fluorophore blinking dynamics: fluorescence correlation spectroscopy (FCS) and transient-state (TRAST) excitation-modulation spectroscopy. Additionally, we combined TRAST and spectrofluorimetry (spectral-TRAST), whereby the emission spectra of Cy5 were recorded upon different rectangular pulse-train excitations. We also developed a framework for analyzing transitions between multiple emissive states in FCS and TRAST experiments, how the brightness of the different states is weighted, and what initial conditions that apply. Our FCS, TRAST, and spectral-TRAST experiments showed significant differences in dark-state relaxation amplitudes for different spectral detection ranges, which we attribute to an additional red-shifted, emissive photo-isomerized state of Cy5, not previously considered in FCS and single-molecule experiments. The photo-isomerization kinetics of this state indicate that it is formed under moderate excitation conditions, and its population and emission may thus deserve also more general consideration in fluorescence imaging and spectroscopy experiments.

P800SO3-PEG: a renal clearable bone-targeted fluorophore for theranostic imaging

BackgroundDue to the deep tissue penetration and reduced scattering, NIR-II fluorescence imaging is advantageous over conventional visible and NIR-I fluorescence imaging for the detection of bone growth, metabolism, metastasis, and other bone-related diseases.MethodsBone-targeted heptamethine cyanine fluorophores were synthesized by substituting the meso-carbon with a sulfur atom, resulting in a bathochromic shift and increased fluorescence intensity. The physicochemical, optical, and thermal stability of newly synthesized bone-targeted NIR fluorophores was performed in aqueous solvents. Calcium binding, bone-specific targeting, biodistribution, pharmacokinetics, and 2D and 3D NIR imaging were performed in animal models.ResultsThe newly synthesized S-substituted heptamethine fluorophores demonstrated a high affinity for hydroxyapatite and calcium phosphate, which improved bone-specific targeting with signal-background ratios > 3.5. Particularly, P800SO3-PEG showed minimum nonspecific uptake, and most unbound molecules were excreted into the urinary bladder. Histological analyses demonstrated that P800SO3-PEG remained stable in the bone for over two weeks and was incorporated into bone matrices. Interestingly, the flexible thiol ethylene glycol linker on P800SO3-PEG induced a promising photothermal effect upon NIR laser irradiation, demonstrating potential theranostic imaging.ConclusionsP800SO3-PEG shows a high affinity for bone tissues, deeper tissue imaging capabilities, minimum nonspecific uptake in the major organs, and photothermal effect upon laser irradiation, making it optimal for bone-targeted theranostic imaging.

Macromolecular conjugated cyanine fluorophore nanoparticles for tumor-responsive photo nanotheranostics

For photothermal therapy (PTT), the improved targeting can decrease the dosage and promote the therapeutic function of photothermal agents, which would effectively improve the antitumor effect. The tumor microenvironment (TME) and cells are targets in designing intelligent and responsive theranostics. However, most of these schemes have been limited to the traditional visible and first near-infrared (NIR-I) regions, eager to expand to the second near-infrared (NIR-II) window. We designed and synthesized a polyethylene glycol conjugated and disulfide-modified macromolecule fluorophore (MPSS). MPSS could self-assemble into core–shell micelles in an aqueous solution (MPSS-NPS), while the small molecule probes were in a high aggregation arrangement inside the nanoparticle. The pronounced aggregation quenching (ACQ) effect caused them to the “sleeping” state. After entering the tumor cells, the disulfide bonds in MPSS-NPS broke in response to a high concentration of glutathione (GSH) in TME, and the molecule probes were released. The highly aggregated state was effectively alleviated, resulting in distinct absorption enhancement in the near-infrared region. Therefore, the fluorescence signal was recovered, and the photothermal performance was triggered. In vitro and in vivo studies reveal that the Nano-system is efficient for the smart NIR-II fluorescence imaging-guided PTT, even at a low dosage and density of irradiation.

Molecular Tuning of IR-786 for Improved Tumor Imaging and Photothermal Therapy.

A tumor-targeted near-infrared (NIR) fluorophore CA800Cl was developed based on commercially available IR-786 by modulating its physicochemical properties. IR-786, a hydrophobic cationic heptamethine cyanine fluorophore, was previously recognized as a mitochondria-targeting NIR agent with excellent optical properties. Owing to the poor tumor specificity of IR-786 itself, in vivo studies on tumor-targeted imaging have not yet been investigated. A chloro-cyclohexene ring and indolium side groups on the heptamethine chain are key structural features that improve tumor targetability, owing to better biodistribution and clearance. Thus, IR-786 should be designed to be more soluble in aqueous solutions so that it can preferentially accumulate in the tumor based on the structure-inherent targeting strategy. In this study, we developed a bifunctional NIR fluorophore CA800Cl by incorporating carboxylate moieties in the basic structure of IR-786. This improved its tumor targetability and water solubility, thereby enabling the use of CA800Cl for enhanced photothermal cancer therapy.

Recent Progress of Cyanine Fluorophores for NIR-II Sensing and Imaging.

The cyanine fluorophores, a kind of classic organic fluorophores, are famous for their high extinction coefficient, simple synthetic route, and relatively long absorption and emission wavelengths. Moreover, the excellent biocompatibility and low toxicity in biological samples make cyanine fluorophores show excellent application value in the biomedical field, especially in Near-Infrared II (NIR-II) sensing and imaging. In this review, we briefly outline the history, characteristics, and current state of development of cyanine fluorophores. In particular, we described the application of cyanine fluorophores in NIR-II sensing and imaging. We hope this review can help researchers grab the latest information in the fast-growing field of cyanine fluorophores for NIR-II sensing and imaging.

Building multipurpose nano-toolkit by rationally decorating NIR-II fluorophore to meet the needs of tumor diagnosis and treatment

Phototheranostics have attracted tremendous attention in cancer diagnosis and treatment because of the noninvasiveness and promising effectiveness. Developing advanced phototheranostic agents with long emission wavelength, excellent biocompatibility, great tumor-targeting capability, and efficient therapeutic effect is highly desirable. However, the mutual constraint between imaging and therapeutic functions usually hinders their wide applications in biomedical field. To balance this contradiction, we herein rationally designed and synthesized three novel tumor-targeted NIR-II probes (QR-2PEG321, QR-2PEG1000, and QR-2PEG5000) by conjugating three different chain lengths of PEG onto an integrin αvβ3-targeted NIR-II heptamethine cyanine fluorophore, respectively. In virtue of the essential amphiphilic characteristics of PEG polymers, these probes display various degree of aggregation in aqueous buffer accompanying with differential NIR-II imaging and photothermal (PTT) therapeutic performance. Both in vitro and in vivo results have demonstrated that probe QR-2PEG5000 has the best NIR-II imaging performance with prominent renal clearance, whereas QR-2PEG321 possesses excellent photoacoustic signal as well as PTT effect, which undoubtedly provides a promising toolbox for tumor diagnosis and therapy. We thus envision that these synthesized probes have great potential to be explored as a toolkit for precise diagnosis and treatment of malignant tumors.

Rapid Estimation of Membrane Protein Orientation in Liposomes.

The topological organization of proteins embedded in biological membranes is crucial for the tight interplay between these enzymes and their accessibility to substrates in order to fulfil enzymatic activity. The orientation of a membrane protein reconstituted in artificial membranes depends on many parameters and is hardly predictable. Here, we present a convenient approach to assess this important property independent of the enzymatic activity of the reconstituted protein. Based on cysteine‐specific chemical modification of a target membrane protein with a cyanine fluorophore and a corresponding membrane‐impermeable fluorescence quencher, the novel strategy allows rapid evaluation of the distribution of the two orientations after reconstitution. The assay has been tested for the respiratory complexes bo3 oxidase and ATP synthase of Escherichia coli and the results agree well with other orientation determination approaches. Given the simple procedure, the proposed method is a powerful tool for optimization of reconstitution conditions or quantitative orientation information prior to functional measurements.

Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series.

The front cover artwork was provided by Gabriel Moya, a PhD student in the Cordes lab (LMU Biocenter Munich, Germany). The cover image shows an artistic impression of the chemical structures of two fluorophores investigated in the paper. Read the full text of the Article at 10.1002/cphc.202000935.

Front Cover: Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series (15/2021)

Front Cover: Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series (15/2021)

Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series*.

The use of fluorescence techniques has an enormous impact on various research fields including imaging, biochemical assays, DNA‐sequencing and medical technologies. This has been facilitated by the development of numerous commercial dyes with optimized photophysical and chemical properties. Often, however, information about the chemical structures of dyes and the attached linkers used for bioconjugation remain a well‐kept secret. This can lead to problems for research applications where knowledge of the dye structure is necessary to predict or understand (unwanted) dye‐target interactions, or to establish structural models of the dye‐target complex. Using a combination of optical spectroscopy, mass spectrometry, NMR spectroscopy and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we propose a structure for Alexa Fluor 555 and refine that of AF555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647 maleimide. We also conducted a comprehensive comparison between Alexa Fluor and AF dyes by continuous‐wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein‐attached dyes. All these data support the idea that Alexa Fluor and AF dyes have a cyanine core and are a derivative of Cy3 and Cy5. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single‐molecule FRET applications. Both pairs showed excellent performance in solution‐based smFRET experiments using alternating laser excitation. Minor differences in apparent dye‐protein interactions were investigated by molecular dynamics simulations. Our findings clearly demonstrate that the AF‐fluorophores are an attractive alternative to Alexa‐ and Cy‐dyes in smFRET studies or other fluorescence applications.

γ-Glutamyl transpeptidase-activatable near-infrared nanoassembly for tumor fluorescence imaging-guided photothermal therapy.

Rationale: Precise treatment of tumors is attracting increasing attention. Molecular probes simultaneously demonstrating the diagnostic signal and pharmacological effect in response to tumor microenvironment are highly desired. γ-glutamyl transpeptidase (GGT) is a biomarker with significantly up-regulated expression in the tumor area. We developed a GGT responsive near-infrared (NIR) nanoassembly for tumor-specific fluorescence imaging-guided photothermal therapy.Methods: The GGT responsive NIR probe was constructed by conjugating GGT-specific substrate γ-glutamic acid (γ-Glu) with cyanine fluorophore (NRh-NH2) via amide reaction. The resulting NRh-G spontaneously assembled into nanoparticles (NRh-G-NPs) around 50 nm. The NPs were characterized and the properties evaluated in the presence or absence of GGT. Subsequently, we studied fluorescence imaging and photothermal therapy of NRh-G-NPs in vitro and in vivo.Results: NRh-G-NPs, upon specific reaction with GGT, turned into NRh-NH2-NPs, showing a ~180-fold fluorescence enhancement and excellent photothermal effect recovery. NRh-G-NPs could selectively light up U87MG tumor cells while their fluorescence was weak in L02 human normal liver cells. The NPs also showed excellent tumor cell ablation upon laser irradiation. After intravenous injection into tumor-bearing mice, NRh-G-NPs could arrive in the tumor area and specifically light up the tumor. Following laser irradiation, the tumor could be completely erased with no tumor reoccurrence for up to 40 days.Conclusions: NRh-G-NPs were specifically responsive to GGT overexpressed in U87MG tumor cells and selectively lit up the tumor for imaging-guided therapy. Besides, the recovery of photothermal property in the tumor area could improve cancer therapy precision and decreased side effects in normal tissues.

The Efficacy of Hybridization Analysis of DNA Labeled with Red and Near-Infrared Cyanine Dyes

We present a study of the sensitivity of a hybridization microarray analysis of DNA labeled with 2'‑deoxyuridine-5'-triphosphate derivatives that contain the Cy5 and Cy7 cyanine fluorophore dyes. Two Cy5-dUTP and two Cy7-dUTP derivatives that can be effectively incorporated into a newly synthesized DNA strand during PCR were chosen for this study. PCR products fluorescently labeled with different dyes were hybridized with a matrix of oligonucleotide probes immobilized in the microchip hydrogel cells. Fluorescent signals were recorded on a digital fluorescence microscope in the red (for Cy5-dUTP) and near-infrared (for Cy7-dUTP) range. Using the serial dilution method, the minimum DNA concentration was evaluated, which is necessary for genotyping by the specific interaction between the fluorescently labeled PCR product and oligonucleotide probes on the microarray. It has been shown that the fluorescently labeled Cy7-dUTP, unlike Cy5-dUTP, provides greater sensitivity of the hybridization analysis.

Design, synthesis and application of a dual-functional fluorescent probe for reactive oxygen species and viscosity.

A fluorescence probe based on cyanine fluorophore was designed and synthesized in this work, which can be used to determine viscosity and reactive oxygen species (e.g., OCl-, ONOO-) at different wavelengths. Under a low viscosity medium, the fluorescence quantum yield of the probe is very low; however, with the increase of the medium viscosity, the probe's emission at 571nm is enhanced by nearly 25-fold due to the inhibition of intramolecular rotations. On the other hand, the probe shows a rapid and linear fluorescence response at 710nm to OCl- or ONOO- within 1min. The different spectral response regions of the probe permit the selective detection of both viscosity and reactive oxygen species. Furthermore, the probe is demonstrated to be cell permeable and capable of detecting the viscosity and the total amount of OCl-/ONOO- in living cells with the help of confocal microscope fluorescence imaging.

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.

Fluorescent H2 Receptor Squaramide-Type Antagonists: Synthesis, Characterization, and Applications.

Fluorescence labeled ligands have been gaining importance as molecular tools, enabling receptor-ligand-binding studies by various fluorescence-based techniques. Aiming at red-emitting fluorescent ligands for the hH2R, a series of squaramides labeled with pyridinium or cyanine fluorophores (19-27) was synthesized and characterized. The highest hH2R affinities in radioligand competition binding assays were obtained in the case of pyridinium labeled antagonists 19-21 (pK i: 7.71-7.76) and cyanine labeled antagonists 23 and 25 (pK i: 7.67, 7.11). These fluorescent ligands proved to be useful tools for binding studies (saturation and competition binding as well as kinetic experiments), using confocal microscopy, flow cytometry, and high content imaging. Saturation binding experiments revealed pK d values comparable to the pK i values. The fluorescent probes 21, 23, and 25 could be used to localize H2 receptors in HEK cells and to determine the binding affinities of unlabeled compounds.

Ratiometric Photoacoustic Chemical Sensor for Pd2+ Ion

Recently, small molecule photoacoustic sensors have emerged prominently in chem/biosensing owing to their excellent performance of high contrast, high resolution, and deep penetration depth. However, there has been little report on a photoacoustic sensor for Pd2+ detection so far. Herein, a ratiometric photoacoustic Pd2+ sensor, Cy-DPA, based on cyanine fluorophore has been developed. The absorbance peak of Cy-DPA shifts from 710 to 770 nm after the interaction with Pd2+, thus producing a strong PA signal output at 770 nm. As-prepared Cy-DPA could sensing palladium with high sensitivity (27 nM) and selectivity in a fast response (<30 s), which opened new avenue for Pd2+ real-time detection in vivo.