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.

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.

One of the important features of polymethine (cyanine) dyes is isomerization about one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomer-ization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocy-anine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be ex-plained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric ef-fect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes com-plexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cya-nine dyes can be used in various systems of information storage and deserves further investiga-tion using modern research methods.

The noncovalent interaction of the cyanine dyes Cyan 2 and Cyan 45 with DNA (in a pH 7 phosphate buffer) was studied by spectral and fluorescent methods. Upon titration of dye solutions with a concentrated DNA solution, a drop in the absorption band of the initial dye, a long-wavelength shift, and a rise of the absorption of the dye bound to DNA occur. Simultaneously, a growth of dye fluorescence is observed. Mathematical modeling of the fluorescence growth has been performed on the basis of the formation of one or two types of dye complexes with DNA. The experimental results are adequately described by the model involving one type of the dye-DNA complex. It is shown that Cyan 2 binds to DNA probably as the cis-isomer, whereas Cyan 45 as the trans-isomer.

The processes of cis-trans photoisomerization and thermal back isomerization as well as the effect of DNA on the spectral and kinetic characteristics of the triplet state of a number of meso-substituted thiacarbocyanine dyes: 3,3’-diethyl-9-methoxythiacarbocyanine iodide (K1), 3,3’,9-triethylthiacarbocyanine iodide (K2), 3,3’-diethyl-9-methylthiacarbocyanine iodide (K3), and 3,3’-diethyl-9-chlorothiacarbocyanine perchlorate (K4), were studied by the flash photolysis method. Upon flash photoexcitation, the processes of trans-cis and cis-trans photoisomerization were observed for dye K1; the data on the structure of the absorption bands of the photoisomers were obtained. Complexation with DNA leads to an increase in the quantum yield of the triplet state of the dyes, which is explained by growing rigidity of the bound molecules. In the presence of DNA, triplet state deactivation follows the two-exponential law, thus showing that the dyes form complexes of two different types. The processes of quenching of the dye triplet state by oxygen were studied in solutions and in complexes with DNA. The rate constants for oxygen quenching of the triplet state of the dyes in complexes with DNA were found to be much lower than the values expected for the diffusion-controlled reactions (with allowance for the spin statistical factor, $k_{qO_2 } < 1/9k_{dif} $ ), which is explained by the steric factor of the complexation.

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.