Monomethine cyanine dyes (MCDs) are widely used as fluorescent probes for DNA. However, their potential for RNA detection has been studied only sparsely, and quantitative relationships between structure and analytical characteristics remain unclear. This work presents the results of a comprehensive comparative study of the properties of six monomethine cyanine dyes (MCDs), including unsymmetrical derivatives of thiazole orange and oxazole yellow with variable terminal groups, linkers, and side chains, within a single analytical protocol. Steady-state spectrophotometry and fluorescence titration, complemented by DFT and TD-DFT calculations, were used to study the solvatofluorochromism and aggregation of MCDs in aqueous solutions. Interaction with RNA was shown to be accompanied by a multiple (up to 1250-fold) enhancement of fluorescence (the "light-on" effect) due to the suppression of nonradiative deactivation and a shift in the aggregate-monomer equilibrium. Effective binding constants were determined (using the Benesi-Hildebrand, Hill, and Scatchard models), the interaction cooperativity was assessed, and key analytical parameters-the limit of detection (LOD), limit of quantification (LOQ), and linear range-were evaluated. Selectivity of MCDs for RNA with respect to DNA and human serum albumin (HSA) was analyzed. Molecular docking of MCDs with RNA was employed to explain the observed differences in the affinity and sensitivity of the dyes, and the method of spectral moments was used to quantify changes in the dye spectra. The intercalative interaction of the dyes with RNA was confirmed by fluorescent intercalator displacement (FID) method using ethidium bromide as a classical intercalator. Correlation between the structure of substituents, binding energy, and analytical characteristics was demonstrated, paving the way for the rational design of effective RNA sensors.

Cyanine dyes, characterized by a polymethine chain linking two nitrogen-containing heterocycles, are a versatile class of organic chromophores. Their absorption and fluorescence properties, in particular, their solvatochromism—the spectral shifts due to changes in solvent nature—make them the subjects of fundamental photophysical studies and create a basis for diverse applications. This article outlines the main origins, modeling, and studies of solvatochromism of cyanine dyes. The approach based on linear free energy relationships gives good correlations of solvatochromic shifts of symmetrical cyanine dyes with linear combinations of solvent polarizability and polarity functions, which creates a basis for the application of these dyes as micropolarity/polarizability probes. The article provides examples of the use of cyanines as probes for estimation of local dielectric constant and refractive index of molecular microenvironment of the dyes in their complexes with biomolecules. It is concluded that symmetrical cyanines constitute a new class of probes for polarity and polarizability of microenvironment in various studies, in particular, in biophysics and biochemistry.

The development of highly sensitive and selective turn-off fluorescence sensors for bilirubin (BR) is of significant clinical importance. This work explores the basis for such sensors using the noncovalent complexes of mesosubstituted anionic carbocyanine dyes with human serum albumin (HSA). The binding of these dyes to HSA is characterized by high association constants (of the order of 105-106 M-1) and induces a pronounced fluorescence increase due to the stabilization of monomeric trans-isomers. Subsequent introduction of BR, which itself binds strongly to HSA, results in efficient fluorescence quenching (super-quenching effect). Comprehensive spectral studies and molecular docking simulations indicate that the primary quenching mechanism is the competitive displacement of dye molecules from the complex with HSA into the weakly fluorescent free state. The quenching effect is somewhat enhanced in the presence of Cu2+ ions. The effective Stern-Volmer quenching constants were determined, and the analytical potential of these systems was evaluated, revealing low limits of detection (LOD) and quantification (LOQ) of BR. The dye-HSA and dye-HSA-Cu2+ complexes presented herein thus create promising and efficient platforms for the rational design of turn-off sensors for BR.

Bilirubin, a yellow bile pigment, plays an important role in the body, being a potent antioxidant and having anti-inflammatory, immunomodulatory, cytoprotective, and neuroprotective functions. This makes bilirubin promising as a therapeutic and diagnostic agent in biomedicine. However, excess bilirubin is toxic and should be removed from the body. Bilirubin exhibits photochemical activity, which has been the subject of numerous studies up to now. Such studies are relevant because the bilirubin photochemistry provides the basis for bilirubin removing in phototherapy of neonatal jaundice (neonatal hyperbilirubinemia) and for some therapeutic applications. Furthermore, it can model several elementary processes of molecular photonics. In particular, the bilirubin molecule is capable of ultrafast Z-E photoisomerization and contains two almost identical dipyrromethenone chromophores capable of exciton coupling. The present review considers the data on the photophysical and photochemical properties of bilirubin and ultrafast routes of its phototransformations, as well as its photochemical reactions in phototherapy of neonatal hyperbilirubinemia and the ways to decrease the possible adverse effects of the phototherapy. The main analytical methods of bilirubin measurement in biological systems are also viewed.

Bilirubin, a product of heme catabolism, is toxic at elevated concentrations (>250-300 mu M in blood serum), whereas at therapeutic concentrations (similar to 20-200 mu M) exerts potent antioxidant, anti-inflammatory, immunomodulatory, cytoprotective and neuroprotective effects. Despite the therapeutic potential, its use in clinical practice is hampered by poor aqueous solubility, instability, and rapid metabolism. Nanotechnology overcomes these limitations and additionally imparts to bilirubin the advantages characteristic of nanopreparations: targeted action on the desired organ/tissue, increased therapeutic efficacy by delaying drug elimination from the body, improved transportation over biological barriers, the ability to combine therapeutic and diagnostic properties in a single agent. The review analyses the chemical synthesis, therapeutic mechanisms, and preclinical applications of nanosystems comprising bilirubin. In particular, nanostructures obtained by the covalent binding of bilirubin to macromolecules, bilirubin encapsulation in nanocarriers, bilirubin conjugation with metal nanoparticles and nanofunctionalization of inorganic compounds are considered; the data on the therapeutic trials of nanobilirubin are summarized. While studies on animal models and in vitro systems demonstrate improved biodistribution, reduced toxicity, and enhanced efficacy, no clinical trials to date have validated nanobilirubin formulations. Key barriers may include unresolved challenges in scalable synthesis, long-term biocompatibility, reproducible dosing of nanoformulations. Hence, further development of nanotherapeutic bilirubin agents for clinical practice is urgent.

The structures of the developing eye may be damaged as a result of the impact of reactive oxygen species (ROS) interacting with different cellular components. The antioxidant molecules found in the eye, especially in the vitreous body—the largest component of the eye, playing a crucial role in the formation of structures and functions of the developing eye—provide protection to the eye tissues from ROS. This review considers various antioxidant molecules (ascorbic acid, lutein, bilirubin, uric acid, catecholamines, erythropoietin, albumin, and alpha-fetoprotein) that have been found in the human vitreous body during the early stages of pregnancy (10–31 weeks of gestation) and their functions in the development of the eye. The presence of some molecules is transient (lutein, AFP), whereas a temporal decrease (albumin, bilirubin) or increase (ascorbic acid, erythropoietin) in the concentrations of other antioxidants is observed. Since the actual overall content of antioxidants in the developing vitreous body is probably much higher than that found to date, further research is needed to study antioxidants there. It is especially important to study the antioxidant status of the vitreous body at the earliest stages of its development. Antioxidants found suggest their use for the prophylactic of ocular diseases during pregnancy and finding new antioxidants could create an additional opportunity in this regard.

Bilirubin (BR), a bile pigment with photochemical activity, plays an important role in the body. The photonics (photophysics and photochemistry) of BR continues to attract scientific and practical interest from researchers to this day. This is due to the fact that its molecule is capable of ultrafast photoisomerization processes and also contains two interacting dipyrromethenone chromophores. Furthermore, the photochemical reactions of BR are used in the widespread phototherapy method of neonatal jaundice (neonatal hyperbilirubinemia (NHB)), carried out to reduce the level of BR in the body. This review briefly discusses the photonics of BR and its main photochemical reactions in the phototherapy of NHB.

The aggregation properties of a number of 6,6'-disubstituted thiacarbocyanine dyes are studied by spectral-fluorescent methods: T-304, T-306, T-307, T-336 and, for comparison, thiacarbocyanine Cyan 2, which has no substituents in the 6,6'-positions, in aqueous buffer solutions, or in the presence of various types of surfactants. The method of moments is used to characterize the absorption spectra (band positions, width, shape). Substituents in the 6,6'-positions significantly increase the ability of dyes T-304, T-306, T-307, and T-336 to aggregate (dimerization and the formation of disordered aggregates with broad low-intensity absorption spectra). The introduction of surfactants leads to the rearrangement of the spectra associated with the complex nature of the equilibria between monomers and aggregates of various structures (including surfactant molecules, if present), and in particular, with a decrease in the contribution of disordered aggregates. However, the decomposition of dimeric aggregates of 6,6'-disubstituted cyanines is observed only at very high surfactant concentrations ( 20 CMC or higher, where CMC is the critical micelle concentration). At the same time, the passing of surfactant concentrations through CMC does not significantly affect the spectral-fluorescent properties of the dyes, which is probably due to the rather strong interactions of the dyes with individual surfactant molecules and premicellar associates of the surfactants.

Trimethine cyanine dyes are widely used as probes for the detection, study and quantification of biomolecules. In particular, cationic trimethine cyanines noncovalently interact with DNA with growing fluorescence. However, their use is often limited by the tendency to self -association - to the formation of aggregates. Disubstituted trimethine cyanines with hydrophobic substituents are especially prone to aggregation. In this work, we studied the interaction of a number of substituted trimethine cyanines with DNA (in aqueous buffer solutions) and showed that their aggregation strongly interfered with their use as fluorescent probes for DNA. To eliminate this drawback, preliminary heating of dye solutions with DNA to 60 - 70 degrees C was used, followed by cooling to room temperature. Compared to the experiments without heating, an increase in the dye fluorescence intensity was observed due to the partial thermal decomposition of the aggregates and the interaction of the resulting monomers with DNA. To decompose aggregates, another method was also used - protonation of the dyes with amino substituents in buffer solutions with pH 5.0, which also led to growing the dye fluorescence intensity in the presence of DNA. Complexes of the dyes with DNA were modeled using molecular docking. Effective binding constants of the dyes to DNA and detection limits when using the dyes as probes for DNA (LOD and LOQ) were determined. It is shown that dye 3 with heating in neutral buffer and dye 1 in acidic buffer may be recommended as sensitive probes for DNA. It is concluded that the method of preliminary heating may be applied to dyes prone to aggregation, for improving their properties as biomolecular probes. Another possible means to reduce the interfering effects of dye aggregates is to use easily protonated dyes (with amino substituents) in slightly acidic media.

The spectral and luminescent properties of solutions of bis(hydroxyphenylazomethine)s (I and II) and bis(hydroxynaphthylazomethine)s (III and IV) of the benzene and pyridine series in toluene and ethanol have been studied. The keto–enol equilibrium in pyridine azomethine II in the ground state weakly depends on the presence of the pyridine N atom, whereas the influence of pyridine is significant for pyridine azomethine IV. In solutions of I and II in both solvents, two luminescence bands are observed from the enol (E*) and (K*) keto forms, the ratio of which depends on the excitation wavelength. Luminescence in solutions of III and IV is determined by the formation of K*, and predominant short-wavelength luminescence from E* is added to the luminescence spectrum only in a solution of III in toluene in the case of short-wavelength excitation. The solvent and the pyridine atom were found to affect the position of the emission bands, with the influence being more pronounced for compound II than for IV. For all compounds I–IV, luminescence in alcohol is an order of magnitude more intense than in toluene.

Spectral-fluorescent and photochemical properties of trimethine cyanine dyes T-304, T-306, and T-307, having substituents in 6,6'-positions, in various organic solvents, in aqueous buffer solutions, in the presence of surfactants and ethanol additives, and the effect on these properties of addition of DNA have been studied. Strong aggregation of the dyes in aqueous and aqueous buffer solutions has been shown. This is due to increased hydrophobicity of the dyes, which makes it difficult to use them as spectral-fluorescent probes for DNA. In the presence of DNA, trimethine cyanines partially form highly fluorescent complexes of dye monomers with the biomolecule, with slight decomposition of the initial aggregates and the formation of aggregates on DNA molecules. The formation of different types of dye-DNA complexes, i.e., intercalation and binding in the DNA grooves, was modeled by molecular docking. Dye-DNA complexes were also studied by circular dichroism spectroscopy and by thermal dissociation of DNA. To reveal selectivity of the dyes, their interaction with human serum albumin was briefly studied. The presence of moderate concentrations of nonionic surfactants does not lead to a significant decomposition of aggregates, but leads to a biphasic dependence of the fluorescence intensity on the DNA concentration. At the same time, ethanol additives (15%) lead to a more or less linear concentration dependence of the fluorescence intensity, which makes it possible to use these dyes as fluorescent probes for DNA. The effective binding constants of the dyes to DNA and the limits of DNA detection using the dyes in the presence of 15% ethanol were estimated. Photoisomerization and generation of the triplet states of T-304, T-306, and T-307 have been also studied. Along with the fluorescence growth, complexation with DNA leads to an increase in the yield of the triplet states of the dyes. This creates a prerequisite for using the dyes in targeted PDT. In the presence of DNA, the decay kinetics of the triplet states are biexponential, which indicates different types of dye complexes with DNA. The rate constants of oxygen quenching of the triplet states of the dyes bound to DNA are significantly lower than the diffusion-controlled values (taking into account the spin-statistical factor), which is explained by the shielding effect on the triplet molecules in complexes with DNA. The data obtained show that dyes T-304, T-306 and T-307, with addition of 15% ethanol, can be used as possible fluorescent probes for DNA.

The vitreous body of the eye of human fetuses contains serum albumin (SA) and alpha-fetoprotein (AFP), which is normally characteristic of human embryos and fetuses. In the second trimester, both proteins are found in the vitreous body at a concentration comparable to that in the blood serum, after which their content decreases sharply. In this analytical review, taking into account the biological properties of SA and AFP, the role of these proteins in the processes of growth and differentiation of the structures of the developing eye is discussed.

In search of new probes for biomolecules, the spectral fluorescent study of four monomethine cyanine dyes (MCD), both unsymmetrical and symmetrical, has been carried out in different organic solvents, in aqueous buffer solutions, and in the presence of DNA and HSA. The complexation of MCD with biomacromolecules leads to a steep growth of the fluorescence intensity. Complexes of MCD with dsDNA and HSA of various types were modeled in silico by molecular docking. Experiments on thermal dissociation of dsDNA in the presence of MCD showed the formation of intercalative complexes of MCD with DNA. Quenching of intrinsic fluorescence of HSA by MCD occurred with rate constants much higher than the diffusion limit, that is, in dye–HSA complexes. Effective constants of MCD complexation with the biomacromolecules were estimated. MCD 1 has the best characteristics as a possible fluorescent probe for dsDNA and can serve as a sensitive and selective probe for dsDNA in the presence of HSA. Photochemical properties of MCD complexed with DNA have been also studied. An increase in the quantum yield of the triplet states of MCD in complexes with DNA has been found, which may be important for using these dyes as potential candidates in photodynamic therapy.

Monomethine cyanine dyes (MCDs) are widely applied as biomolecular probes and stains in biochemical and biomedical research. This is based on the ability of MCDs to associate with biomolecules (mostly nucleic acids) with significant fluorescent growth. The present review considers the works devoted to the properties of MCDs and the influence of noncovalent interactions with biomacromolecules on their properties, as well as their use as noncovalent probes and stains for various biomacromolecules. The synthesis and photonics (photophysics and photochemistry; in particular, the generation of the triplet state) of MCDs are also considered. Areas and prospects of the practical applications of MCDs in biochemistry and biomedicine are discussed.

The use of conventional contrast media for diagnostic purposes (in particular, Gd-containing and iodinated agents) causes a large number of complications, the most common of which is contrast-induced nephropathy. It has been shown that after exposure to contrast agents, oxidative stress often occurs in patients, especially in people suffering from various diseases. Antioxidants in the human body can diminish the pathological consequences of the use of contrast media by suppressing oxidative stress. This review considers the research studies on the role of antioxidants in preventing the negative consequences of the use of contrast agents in diagnostics (mainly contrast-induced nephropathy) and the clinical trials of different antioxidant drugs against contrast-induced nephropathy. Composite antioxidant/contrast systems as theranostic agents are also considered.

The ongoing spread of the COVID-19 coronavirus infection requires us to find new tools and methods for detecting and studying the infection and preventing morbidity (new analytical procedures and tests). With the aim of developing probes for the detection of SARS-CoV-2 coronavirus by modeling in silico (molecular docking), the noncovalent binding of cyanine and squarylium dyes with different molecular charges and different types of heterocyclic residues and substituents (42 compounds in total) with different variants of the NSP15 endoribonuclease of the SARS-CoV-2 coronavirus (COVID-19) of the original (wild) type and mutant types is studied. The interaction energies and spatial configurations of the dye molecules in complexes with NSP15 are determined. Some dyes with negative values of the total energy of the complex Etot are promising for further practical study as probes for coronavirus.

The noncovalent interaction of meso-aryl-substituted thiacarbocyanine dyes I and II with dsDNA and ssDNA in aqueous solutions has been studied by spectral-fluorescent methods. Complexation with DNA is accompanied by both aggregation of the dyes and the formation of monomeric strongly fluorescent complexes. Experiments on molecular docking of dyes I and II with dsDNA confirm the previous assumption about the possibility of the formation of complexes of different types: intercalation between base pairs and in the grooves of the double helix of the biopolymer. The possibility of intercalation of the dyes in the complex is confirmed by experiments on thermal dissociation of dsDNA in the presence of dyes I and II, as well as experiments on the interaction of the dyes with ssDNA. An increase in the melting temperatures Tm of dsDNA is obtained in the presence of I and II, similar to that observed for the classical intercalator ethidium bromide. The limits of detection and quantification of DNA, which are important for the use of the dyes as probes for DNA, have been determined. The primary photochemical processes of the dyes in complexes with ssDNA were studied by flash photolysis technique. Complexation with ssDNA hinders photoisomerization and creates favorable conditions for the dye triplet state formation. The decay kinetics of the triplet state of the dyes were monoexponential. The rate constant of quenching of the triplet state by air oxygen was estimated for dye I complexed with ssDNA and was found to be less than the diffusion-controlled limit. This is probably a consequence of the shielding effect of the complex on the triplet quenching process.

The paper presents the results of developing the method of obtaining magnetic liposomes (MLP) and magneto-liposomal (MLP) form of aminoalkylamide derivative of chlorine e6: 13(1)-N-(2 aminoethyl)amid-15(2),17(3)-dimethyl ether (I) on the basis of magnetite nanoparticles (MNP). Photosensitizer (PS) of chlorine e6 series (I) was obtained by chemical modification of chlorophyll a, isolated from Spirulina platensis by ethanol extraction. MNP were synthesized by thermal decomposing of iron (III) acetylacetonate in triethylene glycol. The MLP form of PS (I) was obtained by the rehydration method of thin lipid films. Inclusion of PS (I) into MLP was shown to be 50-60 %. The structure and size of the MNP, MLP and MLP form (I) were studied by the methods of transmission electron microscopy (TEM) and dynamic light scattering (DLS). The average sizes of MLP and MLP form (I), according to methods of DLS and TEM, were 173.0±67.4 nm and 204.6±84.5 nm, respectively.

Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.