Cyanine Dye Cy5 Research Articles

Red Fluorescent Aminoferrocene (Pro)Drugs for in Cellulo and in Vivo Imaging.

Red fluorescent dyes are usually charged, lipophilic molecules with relatively high molecular weight, which tend to localize in specific intracellular locations, e. g., a cyanine dye Cy5 is biased towards mitochondria. They are often used as markers of biomolecules including nucleic acids and proteins. Since the molecular weight of the dyes is much smaller than that of the biomolecules, the labelling has a negligible effect on the properties of the biomolecules. In contrast, conjugation of the dyes to low molecular weight (pro)drugs can dramatically alter their properties. For example, conjugates of Cy5 with lysosome-targeting aminoferrocenes accumulate in mitochondria and exhibit no intracellular effects characteristic for the parent (pro)drugs. Herein we tested several neutral and negatively charged dyes for labelling lysosome-targeting aminoferrocenes 7 and 8 as well as a non-targeted control 3. We found that a BODIPY derivative BDP-TR exhibits the desired unbiased properties: the conjugation does not disturb the intracellular localization of the (pro)drugs, their mode of action, and cancer cell specificity. We used the conjugates to clarify the mechanism of action of the aminoferrocenes. In particular, we identified new intermediates, explained why lysosome-targeting aminoferrocenes are more potent than their non-targeted counterparts, and evaluated their distribution in vivo.

Screening of Methyl-β-cyclodextrins as an Antifading Agent for Cyanine Dye-Labeled Streptavidin to Improve the Performance of Genotyping Chips.

As a photostabilizing agent for cyanine dye, methyl-β-cyclodextrin (MβCD) was investigated as a possible antifading agent for cyanine dye-labeled proteins. Cyanine-3 (Cy3)-labeled streptavidin (SA-Cy3) solutions containing MβCD exhibited improved resistance against photobleaching. Further research revealed that MβCD can be used as a coating material on the surface of gene chips. Chips loaded with cyanine dye (Cy3 and Cyanine-5 (Cy5))-conjugated model microbeads exhibited resistance against photobleaching with MβCD coatings. MβCD coatings improved the imaging quality of model chips and resulted in higher discrimination ratios (DR) of single base recognition by a set of control beads (NP68). In a whole genome genotyping assay for human samples, the MβCD-coated samples were found to have a better clustering performance than the noncoated ones for a group of randomly picked single nucleotide polymorphisms (SNPs).

An antioxidative-enhanced endoplasmic reticulum-targeted cyanine dye for efficient tumor immunotherapy

Excessive generation of reactive oxygen species (ROS) triggers intense endoplasmic reticulum (ER) stress, emerging as a key mechanism for arousing autoimmune therapy. Therefore, the development of an ER-targeted ROS generator is crucial for advancing self-immunotherapy. However, despite a clear demand for ER-targeting ROS generators, the high-efficiency agents are still limited. In this study, the pentamethine cyanine dye (Cy5) is used as a parent structure to explore the efficient ER-targeted immune activator. Three variants (PCy5-H, PCy5-Cl, and PCy5-2Cl) were synthesized by introducing benzene, chlorobenzene, and dichlorobenzene structures at the meso-position of the Cy5 scaffold. The electron-withdrawing groups (EWGs) effectively reduce the electron density on the conjugate chain, facilitating the intersystem crossing (ISC) process and enhancing the antioxidant capability. Consequently, the antioxidant properties and ROS generation capacity of PCy5-2Cl were enhanced. Furthermore, encapsulating PCy5-2Cl into liposomes significantly improves its retention at the tumor site, inducing robust ER stress. Upon accumulation at the ER sites in tumor cells, PCy5-2Cl nanoparticles induced strong ER stress under near-infrared (NIR) light irradiation. Exposure to necrotic fragments reverses the immunosuppressive microenvironment within the tumor, ultimately promoting dendritic cell maturation and infiltration of cytotoxic T lymphocytes (CTLs). As a result, significant inhibition is observed in both primary and distant tumors, underscoring the efficacy of this EWGs modification strategy for enhancing tumor immunotherapy.

A non-spherical nanoparticles system for the delivery of peptides using polymer grafted nanocellulose

AbstractPeptide drugs are increasingly used to treat a variety of diseases ranging from cancer, and infections to cardiovascular diseases. However, peptides can suffer from low stability in the bloodstream. Entrapment of peptides into nano-sized carriers of various types has widely been explored, but all of them have spherical shapes. Nanocellulose can in contrast serve as a non-spherical nanoparticle with a high aspect ratio. After the isolation of nanocellulose by TEMPO-mediated oxidation, the material needs to be modified with polymers to generate nanoparticles with high water-solubility that can also favourably interact with peptide drugs. We have here chosen insulin as the model drug, which can strongly interact with cationic polymers. As it is known that cationic polymer may retain charged drugs too tightly, we have selected poly(2-(dimethylamino)ethyl acrylate) PDMAEA as a degradable polymer that undergoes self-hydrolysis to poly(acrylic acid) in water. This polymer was compared to poly(N-(3-(dimethylamino)propyl) acrylamide) PDMAPAA, which is a stable cationic polymer. The cationic polymer was co-grafted with poly(2-hydroxyethyl acrylate) PHEA as a water-soluble neutral polymer using the three-component Passerini reaction. A combination of fluorescence and UV-Vis techniques were used to quantify the amount of polymer that was conjugated to the surface. The polymer-coated nanocellulose was labelled with the fluorescent cyanine dye Cy5 while insulin was labelled with Cy3 creating a FRET system that allows monitoring of the interaction between insulin and polymer in cell growth media. We observed that despite the self-hydrolysis of PDMAEA into a negatively charged polymer, the negatively charged insulin was not released in buffer solution according to the FRET studies. Only the addition of serum-supplemented cell growth media led to insulin release. The limited release was explained with the fact that insulin, as well as other peptides, have a mixture of negative and positive charges, with the pH value and the isoelectric point determining the balance between both. Negative-charged polymers can therefore still interact favourably with negatively charged peptides by interacting with cationic amino acids. Graphical Abstract

Selective Accumulation of Poly(Lactic-Co-Glycolic Acid) Nanoparticles in Endotheliocytes and Mesenchymal Stromal Cells Cultured as Mixed-Cell Spheroids.

The use of drug-loaded nanoparticles is an actively developed approach in targeted cancer therapy. Prevascularized spheroids generated from mesenchymal stem cells and endotheliocytes are considered as a model to evaluate the tropism of therapeutic nanoparticles to a specific tissue. Nanoparticles based on co-polymer of lactic and glycolic acids (poly(lactic-co-glycolic acid; PLGA) labeled with cyanine dye (Cy5) were incubated with prevascularized spheroids, and the rate of their penetration and their distribution in the spheroid-forming cells were evaluated. Endotheliocytes more intensively accumulated nanoparticles than mesenchymal stem cells: the number of nanoparticles in mixed-cell spheroids of mesenchymal stem cells and endotheliocytes was greater than in spheroids built solely of mesenchymal stem cells by 5±1.2 times. The developed 3D in vitro cell model provides a low-cost way to assess tissue tropism of therapeutic nanoparticles under conditions closer to natural in comparison with 2D culture.

Superior Photoprotection of Cyanine Dyes with Thio-imidazole Amino Acids.

Preventing fluorophore photobleaching and unwanted blinking is crucial for single-molecule fluorescence (SMF) studies. Reductants achieve photoprotection via quenching excited triplet states, yet either require counteragents or, for popular alkyl-thiols, are limited to cyanine dye Cy3 protection. Here, we provide mechanistic and imaging results showing that the naturally occurring amino acid ergothioneine and its analogue dramatically enhance photostability for Cy3, Cy5, and their conformationally restrained congeners, providing a biocompatible universal solution for demanding fluorescence imaging.

Synthesis and biological evaluation of theranostic Trastuzumab–SN38 conjugate for Near-IR fluorescence imaging and targeted therapy of HER2+ breast cancer

Here, we report on the design, synthesis, and biological evaluation of a new theranostic antibody drug conjugate (ADC), Cy5-Ab-SS-SN38, that consists of the HER2-specific antibody trastuzumab (Ab) connected to the near infrared (NIR) pentamethine cyanine dye Cy5 and SN38, which is a bioactive metabolite of the anticancer drug irinotecan. SN38 is bound to an antibody through a glutathione-responsive self-immolative disulfide carbamate linker. For the first time, we explored this linker in ADC and found that it to reduce the drug release rate, which is important for safe drug delivery. The developed ADC exhibited specific accumulation and nanomolar anti-breast cancer activity on HER2-positive (HER2+) cell lines but no effect on HER2-. Animals treated with this ADC exhibited good tolerance. In vivo studies have shown that the ADC had good targeting ability for HER2+ tumors with much higher anticancer potency than trastuzumab itself or a mixture of trastuzumab with SN38. Side-by-side HER2+/HER2-xenograft at the 10 mg/kg dose exhibited specific accumulation and reduction of HER2+ tumor but not accumulation or growth inhibition of HER2-counterpart. The self-immolative disulfide linker implemented in this study was proven to be successful, broadening its utilization with other antibodies for targeted anticancer therapy in general. We believe that the theranostic ADCs comprising the glutathione-responsive self-immolative disulfide carbamate linker are applicable for the treatment and fluorescent monitoring of malignancies and anticancer drug delivery.

Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures.

Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self-assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N-terminus. Microscopic techniques, in particular cryogenic TEM (cryo-TEM) and cryo-electron tomography technique (cryo-ET), reveal two types of highly ordered three-dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two-dimensional membrane-like assemblies at pH 3.4, both species displaying spectral features of H-aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three-dimensional organization.

Cyanine Dye Coupling Mediates Self‐assembly of a pH Sensitive Peptide into Novel 3D Architectures

AbstractSynthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self‐assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N‐terminus. Microscopic techniques, in particular cryogenic TEM (cryo‐TEM) and cryo‐electron tomography technique (cryo‐ET), reveal two types of highly ordered three‐dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two‐dimensional membrane‐like assemblies at pH 3.4, both species displaying spectral features of H‐aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three‐dimensional organization.

Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes.

Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates—aggregates of chemically distinct dyes—rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm–1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays.

Development of fluorescence-based nucleic acid blot hybridization method using Cy5.5 labeled DNA probes

Near-infrared (NIR) fluorophores are widely used as fluorescent probes for bioimaging because of their minimal photodamage to biological samples, deep penetration, and low interference from background autofluorescence. Here, we employed a NIR fluorescent cyanine dye Cy5.5 to label DNA probes for nucleic acid blot hybridization. The specificity and sensitivity of fluorescent DNA probes were proven by both Southern blot and Northern blot using cellulolytic bacterium Ruminiclostridium cellulolyticum as a model. Furthermore, employing the method, we successfully identified the gene disruption of ClosTron to rule out off-target, analyzed the differential transcription of genes under different conditions, and confirmed RNA cleavage. Compared to other nonradioactive probes, the preparation and detection of Cy5.5-labeled probes are more simple, more economical, and versatile, suggesting that the Cy5.5-labeled probes are suitable for nucleic acid blot hybridization in addition to bioimaging.

Counterion-insulated near-infrared dyes in biodegradable polymer nanoparticles for in vivo imaging.

Polymeric nanoparticles (NPs) are highly attractive for biomedical applications due to their potential biodegradability and capacity to encapsulate different loads, notably drugs and contrast agents. For in vivo optical bioimaging, NPs should operate in the near-infrared region (NIR) and exhibit stealth properties. In the present work, we applied the approach of ionic dye insulation with bulky hydrophobic counterions for encapsulation of near-infrared cyanine dyes (Cy5.5 and Cy7 bearing two octadecyl chains) into biodegradable polymer (PLGA) NPs. We found that at high dye loading (20–50 mM with respect to the polymer), the bulkiest fluorinated tetraphenylborate counterion minimized best the aggregation-caused quenching and improved fluorescence quantum yields of both NIR dyes, especially of Cy5.5. In addition, bulky counterions also enabled formation of small 40 nm polymeric NPs in contrast to smaller counterions. To provide them stealth properties, we prepared 40 nm dye-loaded PEGylated NPs through nanoprecipitation of synthetic PLGA–PEG block copolymer with the dye/counterion salt. The obtained NIR NPs loaded with Cy5.5 dye salt allowed in vivo imaging of wild-type mice with a good contrast after IV injection. Compared to the bare PLGA NPs, PLGA–PEG NPs exhibited significantly slower accumulation in the liver. Biodistribution studies confirmed the preferential accumulation in the liver, although PLGA and PLGA–PEG NPs could also be distributed in other organs, with the following tendency: liver > spleen > lungs > kidney > heart > testis > brain. Overall, the present work validated the counterion approach for encapsulation of NIR cyanine dyes into biodegradable polymer NPs bearing covalently attached PEG shell. Thus, we propose a simple and robust methodology for preparation of NIR fluorescent biodegradable polymer NPs, which could further improve the existing optical imaging for biomedical applications.

Aminoferrocene‐Based Anticancer Prodrugs Labelled with Cyanine Dyes for in vivo Imaging

AbstractN‐alkylaminoferrocene‐based (NAAF) prodrugs are activated in the presence of reactive oxygen species (ROS), based on which these prodrugs target cancer cells (high ROS) and do not affect normal cells (low ROS). To gain some insights into their mode of action in vivo, we have investigated the biodistribution of 18F‐labelled NAAF prodrugs in tumor‐bearing mice by positron emission tomography (PET). Due to the short half‐life of 18F, the experimental time frame was restricted to 60 min. To extend the observation window, a more stable marker is required. In this paper, we report on conjugates of NAAF prodrugs with two cyanine dyes Cy5 and Cy7 including details of their synthesis, characterization and basic properties in cell free settings and their cellular uptake in representative human cancer cells. Finally, the Cy5 conjugate was subjected to in vivo fluorescence imaging studies to determine the prodrug biodistribution over 24 h.

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3.

Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments. Many methods have been used to model the excitonic coupling in molecules with varying degrees of accuracy. The atomic transition charge model offers a high-accuracy and cost-effective way to calculating the excitonic coupling. The main focus of this work is to generate high-quality atomic transition charges that can accurately model the Cy3 dye's transition density. The transition density of the excitation of the ground to first excited state is calculated using configuration-interaction singles and time-dependent density functional theory and is benchmarked against the algebraic diagrammatic construction method. Using the transition density we derived the atomic transition charges using two approaches: Mulliken population analysis and charges fitted to the transition electrostatic potential. The quality of the charges is examined, and their ability to accurately calculate the excitonic coupling is assessed via comparison to experimental data of an artificial biscyanine construct. Theoretical comparisons to the supermolecule ab initio couplings and the widely used point-dipole approximation are also made. Results show that using the transition electrostatic potential is a reliable approach for generating the transition atomic charges. A high-quality set of charges, that can be used to model the Cy3 dye dimer excitonic coupling with high-accuracy and a reasonable computational cost, is obtained.

Intraoperative visualization of nerves using a myelin protein-zero specific fluorescent tracer

BackgroundSurgically induced nerve damage is a common but debilitating side effect in oncological surgery. With the aim to use fluorescence guidance to enable nerve-sparing interventions in future surgery, a fluorescent tracer was developed that specifically targets myelin protein zero (P0).ResultsTruncated homotypic P0 protein-based peptide sequences were C-terminally functionalized with the far-red cyanine dye Cy5. The lead compound Cy5-P0101–125 was selected after initial solubility, (photo)physical and in vitro evaluation (including P0-blocking experiments). Cy5-P0101–125 (KD = 105 ± 17 nM) allowed in vitro and ex vivo P0-related staining. Furthermore, Cy5-P0101–125 enabled in vivo fluorescence imaging of the Sciatic nerve in mice after local intravenous (i.v.) administration and showed compatibility with a clinical fluorescence laparoscope during evaluation in a porcine model undergoing robot-assisted surgery. Biodistribution data revealed that i.v. administered [111In]In-DTPA-P0101–125 does not enter the central nervous system (CNS).ConclusionP0101–125 has proven to be a potent nerve-specific agent that is able to target P0/myelin under in vitro, ex vivo, and in vivo conditions without posing a threat for CNS-related toxicity.

Donor-conformation-dependent energy transfer for dual-color fluorescent probe with high-resolution imaging

Herein, we presented a brand-new concept to construct the Forster resonance energy transfer (FRET) based cassette by integrating a vibration-induced emission (VIE) chromophore as the donor. Different from traditional donors only with a single emission, the VIE donor possessed well-separated dual emission bands by altering the excited state molecular configuration from bent state to the planar state. By linking an acceptor such as a cyanine dye (Cy5), a novel VIE-FRET cassette (PPCy5) was prepared. The planar emission profile of VIE donor moiety could fully cover the absorption of Cy5, thus the complete FRET process enabled the excellent bimodal spectra difference of 142 nm and ultra-large pseudo-Stokes shift of up to 300 nm. Benefiting from the viscosity-dependent characteristic of the VIE donor, PPCy5 could clearly and intuitively reveal the different viscosity regions in vivo by dual-color and high-resolution imaging. The VIE-FRET paradigm provides an optional platform for developing donor-acceptor based dual-color fluorescent probes with high-resolution imaging ability.

Peg derivatives for the synthesis of water-soluble cyanine dye Cy5

An effective method for the preparation of water-soluble cyanine dye Cy5 using the soluble polymers supported liquid-phase organic synthesis (LPOS) was proposed. Poly (ethylene glycol) methyl ether with a molecular weight of 2000 was used as a polymer substrate, which allowed us to simplify the characterization of products at intermediate stages of synthesis by NMR spectroscopy. This approach makes it easy to obtain the necessary cyanine dyes, which are widely used as fluorescent labels and are popular modifying reagents in biochemistry and medicine.

Substituent Effects on the Solubility and Electronic Properties of the Cyanine Dye Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations.

The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of withdrawing substituents (W-W pairs) exhibiting the most negative solvation energies, suggesting dyes with W-W pairs are more soluble than others. With respect to pristine Cy5, the transition dipole moment was relatively unaffected upon substitution while numerous W-W pairs and pairs of donating and withdrawing substituents (D-W pairs) enhanced the static dipole difference. The increase in static dipole difference was correlated with an increase in the magnitude of the sum of the Hammett constants of the substituents on the dye. The results of this study provide insight into how specific substituents affect Cy5 monomers and which pairs can be used to engineer dyes with desired properties.

Metallothionein dimerization evidenced by QD-based Förster resonance energy transfer and capillary electrophoresis

Herein, we report a new simple and easy-to-use approach for the characterization of protein oligomerization based on fluorescence resonance energy transfer (FRET) and capillary electrophoresis with LED-induced detection. The FRET pair consisted of quantum dots (QDs) used as an emission tunable donor (emission wavelength of 450 nm) and a cyanine dye (Cy3), providing optimal optical properties as an acceptor. Nonoxidative dimerization of mammalian metallothionein (MT) was investigated using the donor and acceptor covalently conjugated to MT. The main functions of MTs within an organism include the transport and storage of essential metal ions and detoxification of toxic ions. Upon storage under aerobic conditions, MTs form dimers (as well as higher oligomers), which may play an essential role as mediators in oxidoreduction signaling pathways. Due to metal bridging by Cd2+ ions between molecules of metallothionein, the QDs and Cy3 were close enough, enabling a FRET signal. The FRET efficiency was calculated to be in the range of 11–77%. The formation of MT dimers in the presence of Cd2+ ions was confirmed by MALDI-MS analyses. Finally, the process of oligomerization resulting in FRET was monitored by CE, and oligomerization of MT was confirmed.

Ratiometric electrogenerated chemiluminescence sensor based on a designed anti-fouling peptide for the detection of carcinoembryonic antigen

In this paper, an effective and accurate ratiometric electrochemiluminescence (ECL) system based on Au-luminol and CdS quantum dots (CdS QDs) as signal probes was constructed for detecting carcinoembryonic antigen (CEA). Polyaniline (PANI) and gold nanoparticles (AuNPs) strongly enhanced the electronic transfer efficiency and the specific area of the modified sensing surface, and improved the detection sensitivity. CdS QDs functionalized DNA strands functioned as cathode ECL emitters, and the aptamer of CEA modified with Au-luminol and quencher cyanine dye (Cy5) fluorophore functioned as anode ECL emitters. After the DNA capture probe combined with CEA aptamer, the negative potential ECL response of the CdS QDs was quenched because of electrochemiluminescence resonance energy transfer (ERET) between the Cy5 fluorophore and CdS QDs. However, the positive potential ECL response of Au-luminol can still be detected. The negative potential ECL response of CdS QDs was recovered, and the positive potential ECL response of Au-luminol decreased after CEA combined with its aptamer to take Cy5 and Au-luminol off the sensing interface. Additionally, the peptide provided effective anti-fouling performance in the detection of complex samples. The ratiometric ECL sensor with anti-fouling ability can sensitively determine the concentration of CEA in human serum.