Recent advances in bioprobes and biolabels based on cyanine dyes

Recent Advances in Organic Small-Molecule Fluorescent Probes Based on Dicyanoisophorone Derivatives

Fluorescent probe technology holds great promise in the fields of environmental monitoring and clinical diagnosis due to its inherent advantages, including easy operation, reliable detection signals, fast analysis speed, and in situ imaging capabilities. In recent years, a wide range of fluorescent probes based on diverse fluorophores have been developed for the analysis and detection of various analytes, yielding significant achievement. Among these fluorophores, the dicyanoisophorone-based fluorophores have garnered significant attention. Dicyanoisoporone exhibits minimal fluorescence, yet possesses a robust electron-withdrawing capability, rendering it suitable for constructing of D-π-A structured fluorophores. Leveraging the intramolecular charge transfer (ICT) effect, such fluorophores exhibit near-infrared (NIR) fluorescence emission with a large Stokes shift, thereby offering remarkable advantages in the design and development of NIR fluorescence probes. This review article primarily focus on small-molecule dicyanoisoporone-based probes from the past two years, elucidating their design strategies, detection performances, and applications. Additionally, we summarize current challenges while predicting future directions to provide valuable references for developing novel and advanced fluorescence probes based on dicyanoisoporone derivatives.

Role of Alkali Cations in DNA-Thioflavin T Interaction

This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg2+ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.

A supramolecular electrochemical probe based on a tetrazole derivative pillar[5]arene/methylene blue system

For the first time, an original synthetic approach has been developed that enables the introduce ten tetrazole fragments into the pillar[5]arene structure. A supramolecular electrochemical probe was assembled for the first time from the obtained macrocycles and an electrochemically active signal converter: methylene blue (MB) dye. The ability of pillar[5]arene containing tetrazole fragments to selectively bind MB was confirmed by UV-vis and 2D 1H-1H NOESY spectroscopy. The stoichiometry of the resulting pillar[5]arene/MB complex = 1 : 2. This new supramolecular probe pillar[5]arene/MB allowed the detection of changes in the electrochemical signals of MB implemented in the supramolecular complex depending on the presence or absence of some metal ions (Zn2+ and Co2+) that do not exert their own redox activity. This will find further applications for the enhancement of the range of analytes detected by their influence on host-guest complexation and for the design of biosensors based on specific DNA-MB interactions.

H-Aggregation of Squaraine Dye as Generic Colorimetric Molecules to Detect Cu2. APPLIED SPECTROSCOPY 2024:37028241254391. [PMID: 38772555 DOI: 10.1177/00037028241254391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

An infrared squaraine dye was utilized to detect Cu2+ in solvents based on H-aggregates of squaraine dye. H-aggregates are a type of aggregation with enhanced photophysical properties compared to monomers. In the presence of a Ca2+ solution, F-Cl offers exceptional H-aggregators that can be transformed into monomers by adding Cu2+. Furthermore, this mode successfully demonstrated fluorescence changes in HeLa cells cultured in vitro after the addition of Ca2+ or Cu2+. A highly specific detection of Cu2+ was achieved using this transformation mode.

Monitoring Hg2+ ions in food and environmental matrices using a novel ratiometric NIR fluorescent sensor via carbonothioate-deprotection reaction

Mercury toxicity and its environmental impact are significant concerns for public health and environmental protection. Therefore, the development of effective, rapid, and reliable detection methods for trace levels of Hg2+ is crucial. Herein, a cyanine dye bearing a carbonothioate group is reported as a potential NIR fluorescent probe for Hg2+ detection. The spectral properties of the free probe have been characterized by the presence and absence of a series of analytes. The addition of Hg2+ leads to significant changes in the fluorescence signal with distinct red coloration compared to other competing analytes, indicating that the probe is highly selective for Hg2+. The fluorescence quantum yield increases from 0.073 to 0.315. The detection limit is 0.10 μM, indicating the high sensitivity of the probe to low Hg2+ levels. The most prominent sensing features of the probe include NIR fluorescence, low cytotoxicity, ratiometric fluorescence response, and fast response compared to most of the currently available fluorescent probes. In addition, the probe can detect Hg2+ in actual samples such as foodstuff, soil, water, and live cells. Bioimaging studies have demonstrated that the present probe is highly efficient in targeting mitochondria and possesses good imaging abilities for detecting Hg2+ in cells. Therefore, these results suggest that it can be proposed as a powerful NIR fluorescent probe for the highly sensitive detection of Hg2+.

Design and Screening of Fluorescent Probes Based upon Hemicyanine Dyes for Monitoring Mitochondrial Viscosity in Living Cells

Viscosity, at the subcellular level, plays a crucial role as a physicochemical factor affecting microenvironment homeostasis. Abnormal changes in mitochondrial viscosity often lead to various diseases in the organism. Based on the twisted intramolecular charge transfer mechanism, four hemicyanine dye fluorescent probes (HT-SA, HT-SA-S, HT-Bzh, and HT-NA) were designed and synthesized for viscosity response. The single bond between the nitrogen-containing heterocycle and the carbon-carbon double in the structure of the probe bond served as the viscosity response site. Finally, the probe HT-Bzh was screened as the optimal mitochondrial viscosity probe according to its responsiveness, targeting, and interference resistance. The fluorescence intensity of the probe HT-Bzh increased 22-fold when the viscosity was increased from 13.75 to 811.2 cP. In summary, all four viscosity probes we have developed can be used in different applications depending on the external environment, providing a valuable reference for the design of potential tools to address viscosity monitoring in biological systems.

Aminoguanidine-based bioactive proligand as AIEE probe for anticancer and anticovid studies

The emission features of a novel bioactive compound, 1,3-bis(2-hydroxy-3,5-diiodophenyl-methylideneamino)guanidine is found impressive with aggregation induced emission enhancement. The nitrogen and iodine rich multidentate proligand was characterized physicochemically. SCXRD and Hirshfeld surface investigation have revealed the presence of significant triangular iodine bonding apart from hydrogen bonding, weak C-H⋯π and π⋯π intermolecular interactions. These interactions collectively contribute to the solid-state packing arrangement of the molecules within the crystal lattice. The band gap of the compound was estimated experimentally and is supported with theoretical calculations. The solid-state fluorescence quantum yield of Φ = 0.36 emphasizes the utility of the proligand and the AIEE characteristics is attributed to restricted intramolecular motions as indicated by fluorescence lifetime decay studies. Strong interaction of the compound with calf thymus DNA was explored experimentally and found to align with in silico docking results. Notably, in vitro anticancer assessment on MCF-7 breast cancer cells show an IC50 value of 181.05 μg mL-1 and signifying its potent cytotoxic properties. Also, the compound is found to have lesser cytotoxicity against L929 normal cell line with an IC50 value of 356.54 μg mL-1. Computational studies further underscore the exceptional binding affinity with active sites in the SARS-CoV-2 main protease 3CLpro, surpassing established repurposed drugs. Furthermore, the proligand demonstrates excellent putative affinity towards the SARS-CoV-2 spike glycoprotein, accompanied by its distinctive AIEE attributes, drug likeness and DNA binding capability rendering it a valuable tool for prospective research investigations.

Rational Design and Biological Application of Hybrid Fluorophores

Fluorophores are considered powerful tools for not only enabling the visualization of cell structures, substructures, and biological processes, but also making for the quantitative and qualitative measurement of various analytes in living systems. However, most fluorophores do not meet the diverse requirements for biological applications in terms of their photophysical and biological properties. Hybridization is an important strategy in molecular engineering that provides fluorophores with complementarity and multifunctionality. This review summarizes the basic strategies of hybridization with four classes of fluorophores, including xanthene, cyanine, coumarin, and BODIPY with a focus on their structure-property relationship (SPR) and biological applications. This review aims to provide rational hybrid ideas for expanding the reservoir of knowledge regarding fluorophores and promoting the development of newly produced fluorophores for applications in the field of life sciences.

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

The photoreactions of selected styrylpyridine derivatives to the corresponding benzo[c]quinolizinium ions are described. It is shown that these reactions are more efficient in aqueous solution (97-44%) than in organic solvents (78-20% in MeCN). The quinolizinium derivatives bind to DNA by intercalation with binding constants of 6-11 × 104 M-1, as shown by photometric and fluorimetric titrations as well as by CD- and LD-spectroscopic analyses. These ligand-DNA complexes can also be established in situ upon irradiation of the styrylpyridines and formation of the intercalator directly in the presence of DNA. In addition to the DNA-binding properties, the tested benzo[c]quinolizinium derivatives also operate as photosensitizers, which induce DNA damage at relative low concentrations and short irradiation times, even under anaerobic conditions. Investigations of the mechanism of the DNA damage revealed the involvement of intermediate hydroxyl radicals and C-centered radicals. Under aerobic conditions, singlet oxygen only contributes to marginal extent to the DNA damage.

Dual-responsive fluorescence probe for measuring HSO3- and viscosity and its application in living cells and real foods

Microenvironmental indicators in organisms drive the operation of different physiological functions. In contrast, disruption of microenvironmental homeostasis is often closely associated with various pathological processes. A novel dual-response fluorescent probe based on hemicyanine dye (HT-Bzh) was designed and synthesized for the detection of HSO3- and viscosity changes. The probe not only provides high sensitivity (limit of detection = 0.2526 μM) for the detection of HSO3- using the Michael addition reaction, but also allows the observation of fluorescence emission at 528 nm and thus the monitoring of viscosity changes through hindering of the twisted intramolecular charge transfer (TICT) mechanism. Additionally, dual-response probe has been successfully used to image living cells and detect real food samples. As a new designed tool, HT-Bzh shows excellent anti-interference capability and biocompatibility, which makes it have application potential in other biological systems and in-vivo imaging.

A new fluorescent probe for the visualization of progerin

Hutchinson-Gilford progeria syndrome (HGPS) or progeria is a rare genetic disease that causes premature aging, leading to a drastic reduction in the life expectancy of patients. Progeria is mainly caused by the intracellular accumulation of a defective protein called progerin, generated from a mutation in the LMNA gene. Currently, there is only one approved drug for the treatment of progeria, which has limited efficacy. It is believed that progerin levels are the most important biomarker related to the severity of the disease. However, there is a lack of effective tools to directly visualize progerin in the native cellular models, since the commercially available antibodies are not well suited for the direct visualization of progerin in cells from the mouse model of the disease. In this context, an alternative option for the visualization of a protein relies on the use of fluorescent chemical probes, molecules with affinity and specificity towards a protein. In this work we report the synthesis and characterization of a new fluorescent probe (UCM-23079) that allows for the direct visualization of progerin in cells from the most widely used progeroid mouse model. Thus, UCM-23079 is a new tool compound that could help prioritize potential preclinical therapies towards the final goal of finding a definitive cure for progeria.

Water-soluble chromenylium dyes for shortwave infrared imaging in mice

In vivo imaging using shortwave infrared light (SWIR, 1000-2000 nm) benefits from deeper penetration and higher resolution compared to using visible and near-infrared wavelengths. However, the development of biocompatible SWIR contrast agents remains challenging. Despite recent advancements, small molecule SWIR fluorophores are often hindered by their significant hydrophobicity. We report a platform for generating a panel of soluble and functional dyes for SWIR imaging by late-stage functionalization of a versatile fluorophore intermediate, affording water-soluble dyes with bright SWIR fluorescence in serum. Specifically, a tetra-sulfonate derivative enables clear video-rate imaging of vasculature with only 0.05 nmol dye, and a tetra-ammonium dye shows strong cellular retention for tracking of tumor growth. Additionally, incorporation of phosphonate functionality enables imaging of bone in awake mice. This modular design provides insights for facile derivatization of existing SWIR fluorophores to introduce both solubility and bioactivity towards in vivo bioimaging.

Supra-Cyanines: Ultrabright Cyanine-Based Fluorescent Supramolecular Materials in Solution and in the Solid State

Fluorescent materials with high brightness play a crucial role in the advancement of various technologies such as bioimaging, photonics, and OLEDs. While significant efforts are dedicated to designing new organic dyes with improved performance, enhancing the brightness of existing dyes holds equal importance. In this study, we present a simple supramolecular strategy to develop ultrabright cyanine-based fluorescent materials by addressing long-standing challenges associated with cyanine dyes, including undesired cis-trans photoisomerization and aggregation-caused quenching. Supra-cyanines are obtained by incorporating cyanine moieties in a cyclic peptide-based supramolecular scaffold, and exhibit high fluorescence quantum yields (up to 50 %) in both solution and in the solid state. These findings offer a versatile approach for constructing highly emissive cyanine-based supramolecular materials.

A new twist on PIFE: photoisomerisation-related fluorescence enhancement

PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule. In this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turning PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.

Julolidine-based small molecular probes for fluorescence imaging of RNA in live cells

Intracellular RNA imaging with organic small molecular probes has been an intense topic, although the number of such reported dyes, particularly dyes with high quantum yields and long wavelength excitation/emission, is quite limited. The present work reports the design and synthesis of three cationic julolidine-azolium conjugates (OX-JLD, BTZ-JLD and SEZ-JLD) as turn-on fluorescent probes with appreciably high quantum yields and brightness upon interaction with RNA. A structure-efficiency relationship has been established for their potential for the interaction and imaging of intracellular RNA. Given their chemical structure, the free rotation between the donor and the acceptor gets restricted when the probes bind with RNA resulting in strong fluorescence emission towards a higher wavelength upon photoexcitation. A detailed investigation revealed that the photophysical properties and the optical responses of two probes, viz. BTZ-JLD and SEZ-JLD, towards RNA are very promising and qualify them to be suitable candidates for biological studies, particularly for cellular imaging applications. The probes allow imaging of intracellular RNA with prominent staining of nucleoli in live cells under a range of physiological conditions. The results of the cellular digest test established the appreciable RNA selectivity of BTZ-JLD and SEZ-JLD inside the cellular environment. Moreover, a comparison between the relative intensity profile of SEZ-JLD before and after the RNA-digestion test inside the cellular environment indicated that the interference of cellular viscosity in fluorescence enhancement is insignificant, and hence, SEZ-JLD can be used as a cell membrane permeable cationic molecular probe for deep-red imaging of intracellular RNA with a good degree of selectivity.

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.

"One stone, two birds": a mitochondria-targeted fluorescent probe for the detection of viscosity and HSO3- in living cells

The material transport and physiological events of mitochondria need to be supported by a suitable microenvironment. For example, high viscosity will seriously hinder material exchange, and SO2, as the precursor of HSO3-, is an endogenous signal molecule that plays a key role in information transmission. It is very important to detect viscosity and HSO3- in mitochondria. Here, we developed a dual-responsive fluorescent probe (named Hcy-NT) to image the changes in mitochondrial viscosity and HSO3- in a "killing two birds with one stone" manner. Hcy-NT showed an OFF-ON fluorescence signal for the increase in cell viscosity induced by nystatin, while an ON-OFF fluorescence signal for intracellular and endogenous HSO3-. Its limits of detection for HSO3- were calculated by both absorption and fluorescence methods, which were 1.200 and 1.291 μM, respectively. This work provides a valuable tool for the study of viscosity and HSO3- related physiological processes and the diagnosis of potential diseases.

ON-OFF Fluorescent Cyanine Dye Based on a Benzothiophenyl Rotor Enables Selective Illumination of G-Quadruplexes in Mitochondria

Conventional cyanine dyes exist as "always-on" fluorescent probes leading to inevitable background signals which often limit their performance and scope of applications. To develop specific fluorescent probes with high sensitivity and robust OFF/ON switching for targeting G4s, we introduced aromatic heterocycles through conjugation with polymethine chains to construct a rotor-π system. Here, a universal strategy is presented to synthesize pentamethine cyanines with different aromatic heterocycle substituents on the meso-polymethine chain. In these probes, SN-Cy5-S is self-quenched in aqueous solution due to H-aggregation. The structure indicates that SN-Cy5-S with a flexible meso-benzothiophenyl rotor conjugated to the cyanine backbone matches adaptively with G-tetrad planes, enhancing π-π stacking and resulting in triggered fluorescence. This allows recognition of G-quadruplexes due to the synergy of disaggregation-induced emission (DIE) and inhibited twisted intramolecular charge-transfer effects. This combination leads to a robust lighting-up fluorescence response for c-myc G4 with superior fluorescence enhancement (98-fold), allowing for a low detection limit of 1.51 nM, which is much more sensitive than the previously reported DIE-based G4 probes (22-83.5 nM). In addition, the superior imaging properties and rapid internalization time (5 min) in mitochondria allow SN-Cy5-S to also have a high potential for mitochondrially targeting anti-cancer therapy.

2-[2,6-Diisopropylphenyl]-4-phenyl-5H-5,9b[1′,2′]-benzonaphtho[1,2-b]pyrrol-2-ium Tetrafluoroborate

A novel α,β-unsaturated iminium salt (3) incorporated into a rigid dibenzobarrelene backbone was synthesized by heating N-(anthracen-9-ylmethyl)-2,6-diisopropylaniline (2) and 3-phenyl-2-propynal in THF in the presence of excess amounts of magnesium sulfate and 0.5 equivalents of an HBF4-Et2O complex. The molecular structure of 3 was characterized unambiguously by NMR spectroscopy and single-crystal X-ray diffraction (SCXRD) analyses. Compound 3 exhibits yellow luminescence in CH2Cl2 (λem = 516 nm) and in the solid state (λem = 517 nm) with relatively high to moderate quantum yields (ΦF(CH2Cl2) = 0.63; ΦF(solid) = 0.34).

Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy

We propose symmetrical cationic trimethine cyanine dyes with β-substituents in the polymethine chain based on modified benzothiazole and benzoxazole heterocycles as probes for the detection and visualization of live and fixed cells by fluorescence microscopy. The spectral-luminescent properties of trimethine cyanines have been characterized for free dyes and in the presence of nucleic acids (NA) and globular proteins. The studied cyanines are low to moderate fluorescent when free, but in the presence of NA, they show an increase in emission intensity up to 111 times; the most pronounced emission increase was observed for the dyes T-2 in the presence of dsDNA and T-1 with RNA. Spectral methods showed the binding of all dyes to nucleic acids, and different interaction mechanisms have been proposed. The ability to visualize cell components of the studied dyes has been evaluated using different human cell lines (MCF-7, A2780, HeLa, and Hs27). We have shown that all dyes are cell-permeant staining nucleus components, probably RNA-rich nucleoli with background fluorescence in the cytoplasm, except for the dye T-5. The dye T-5 selectively stains some structures in the cytoplasm of MCF-7 and A2780 cells associated with mitochondria or lysosomes. This effect has also been confirmed for the normal type of cell line-human foreskin fibroblasts (Hs27). The costaining of dye T-5 with MitoTracker CMXRos Red demonstrates specificity to mitochondria at a concentration of 0.1 μM. Colocalization analysis has shown signals overlapping of dye T-5 and MitoTracker CMXRos Red (Pearson's Coefficient value = 0.92 ± 0.04). The photostability study shows benzoxazole dyes to be up to ∼7 times more photostable than benzothiazole ones. Moreover, studied benzoxazoles are less cytotoxic at working concentrations than benzothiazoles (67% of cell viability for T-4, T-5 compared to 12% for T-1, and ∼30% for T-2, T-3 after 24 h). Therefore, the benzoxazole T-4 dye is proposed for nucleic acid detection in vitro and intracellular fluorescence imaging of live and fixed cells. In contrast, the benzoxazole dye T-5 is proposed as a good alternative to commercial dyes for mitochondria staining in the green-yellow region of the spectrum.