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Pronkin PG, Tatikolov AS. Photonics of Some Monomethine Cyanine Dyes in Solutions and in Complexes with Biomolecules. Int J Mol Sci 2023; 24:13954. [PMID: 37762255 PMCID: PMC10531095 DOI: 10.3390/ijms241813954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/03/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
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.
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Affiliation(s)
| | - Alexander S. Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia;
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Pronkin PG, Tatikolov AS. Spectral-fluorescent and photochemical study of 6,6'-di(benzoylamino)trimethine cyanine dyes in solutions as possible probes for DNA. Spectrochim Acta A Mol Biomol Spectrosc 2023; 292:122416. [PMID: 36746042 DOI: 10.1016/j.saa.2023.122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
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.
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Affiliation(s)
- P G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia.
| | - A S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia
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Pronkin PG, Tatikolov AS. Meso-aryl-substituted thiacarbocyanine dyes as spectral-fluorescent probes for DNA. Spectrochim Acta A Mol Biomol Spectrosc 2022; 269:120744. [PMID: 34929626 DOI: 10.1016/j.saa.2021.120744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
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.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
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Pronkin PG, Tatikolov AS. Photonics of meso-substituted carbocyanine dyes in solutions and in complexes with DNA. Spectrochim Acta A Mol Biomol Spectrosc 2021; 263:120171. [PMID: 34280796 DOI: 10.1016/j.saa.2021.120171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Spectral-fluorescent and photochemical properties (photoisomerization and generation of the triplet state) of meso-substituted cationic carbocyanine dyes, 3,3'-di-(β-hydroxyethyl)-5,5'-dimethoxy-9-ethylthiacarbocyanine iodide (K1) and 3,3'-di-(β-hydroxyethyl)-9-methylthiacarbocyanine iodide (K2), have been studied in solutions and in the presence of DNA. In solutions, on passing from acetonitrile to dioxane, a growth of fluorescence of the dyes is observed due to a shift of the equilibrium of cis/trans isomers toward the fluorescent trans-isomer. Upon flash photolysis of dye solutions in dioxane, the formation and subsequent decay of the cis-photoisomers of the dyes are observed. In aqueous solutions, the interaction with DNA leads to the formation of noncovalent complexes of K1 and K2 with DNA, which is accompanied by a significant increase in the fluorescence intensity. The results of the molecular docking experiments showed the possibility of several types of binding, which was confirmed by the data obtained from other experiments. The effects of temperature and additions of NaCl on the stability of the dye-DNA complexes were studied. The spectral-fluorescent data were used to estimate the binding constants of the dyes with DNA and other characteristics of the dyes that are important for their use as probes. Upon flash photolysis of the dyes in complexes with DNA, photoisomerization is not observed, but the quantum yield of intersystem crossing to the triplet state increases. The decay of the triplet states occurs by a two-exponential law. The rate constants for quenching of the triplet states of the dyes complexed with DNA by oxygen were found to be lower than the expected values for diffusion-controlled quenching (taking into account the spin statistical factor 1/9), which is explained by the steric factor of complexation.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
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Pronkin PG, Shvedova LA, Tatikolov AS. Hydrophilic meso-substituted cyanine dyes in solution and in complexes with serum albumins: spectral properties and molecular docking study. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01858-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bychkova AV, Lopukhova MV, Wasserman LA, Pronkin PG, Degtyarev YN, Shalupov AI, Vasilyeva AD, Yurina LV, Kovarski AL, Kononikhin AS, Nikolaev EN. Interaction between immunoglobulin G and peroxidase-like iron oxide nanoparticles: Physicochemical and structural features of the protein. Biochim Biophys Acta Proteins Proteom 2019; 1868:140300. [PMID: 31676449 DOI: 10.1016/j.bbapap.2019.140300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/26/2019] [Accepted: 09/28/2019] [Indexed: 10/25/2022]
Abstract
The study is devoted to the oxidative modification of immunoglobulin G (IgG) on the surface of peroxidase-like iron oxide magnetic nanoparticles (MNPs) under conditions of induced reactive oxygen species (ROS) generation and without them. A pronounced change of thermodynamic parameters of denaturation has been detected for IgG in solutions containing MNPs under hydrogen peroxide action during 24 h of incubation. Dynamic light scattering measurements and UV-Visible spectrophotometry have been used to show aggregation in these solutions. Ferromagnetic resonance (FMR) was used to compare IgG coating thickness on individual MNPs under conditions of induced ROS generation and without them. The similarity between IgG adsorption on MNPs under these conditions after 24 h of incubation has been confirmed by the fluorescence measurements. The sites of IgG oxidative modifications that take place on MNPs surface and some evidences of the influence of oxidative modification and adsorption on the chemical structure of IgG were revealed by HPLC MS/MS analysis.
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Affiliation(s)
- Anna V Bychkova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia.
| | - Mariia V Lopukhova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Luybov A Wasserman
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Yevgeniy N Degtyarev
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexander I Shalupov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Alexandra D Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Lyubov' V Yurina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Alexander L Kovarski
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Alexey S Kononikhin
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Center of Chemical Physic, Russian Academy of Sciences, Moscow, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Evgene N Nikolaev
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Center of Chemical Physic, Russian Academy of Sciences, Moscow, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia
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Tatikolov AS, Pronkin PG, Panova IG. Spectral-fluorescent study of the interaction of polymethine dye probes with biological surfactants - bile salts. Spectrochim Acta A Mol Biomol Spectrosc 2019; 216:190-201. [PMID: 30901704 DOI: 10.1016/j.saa.2019.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Spectral-fluorescent properties of polymethine dye probes anionic 3,3'-di(sulfopropyl)-4,5,4',5'-dibenzo-9-ethylthiacarbocyanine-betaine (DEC) and cationic 3,3',9-trimethylthiacarbocyanine iodide (Cyan 2) in the presence of biological surfactants, bile salts sodium cholate (NaC), sodium deoxycholate (NaDC) and sodium taurocholate (NaTC), as well as sodium dodecyl sulfate (SDS), have been studied in a wide range of surfactant concentrations. When a surfactant is introduced into a solution of DEC, changes of the spectral-fluorescent properties are observed due to decomposition of dye dimers into cis-monomers and cis-trans conversion of the resulting monomers. In the presence of SDS, both processes occur in parallel, caused by noncovalent interaction of dye monomers with micelles, and mainly occur near the critical micelle concentration (CMC). In contrast, upon the introduction of increasing concentrations of bile salts, decomposition of dye dimers into the monomers begins at lower concentrations than cis-trans conversion. The former process is almost completed at concentrations close to CMC of secondary micelles (CMC2), while the latter process occurs even at concentrations of bile salts much higher than CMC2. Hence, DEC can serve as a probe that permits estimating the value of CMC2 and is indicative of reorganization of secondary micelles upon an increase in bile salt concentration. Aggregation of DEC and Cyan 2 on bile salts is also observed. Since it is observed at relatively low concentrations of bile salts (<CMC2), the aggregation probably occurs on monomeric molecules of bile salts and their small associates and primary micelles. Decomposition of the aggregates formed begins at concentrations of bile salts above CMC2 (that is, upon the interaction with secondary micelles).
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Affiliation(s)
- Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
| | - Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia
| | - Ina G Panova
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilov St. 26, Moscow 119334, Russia
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Pronkin PG, Tatikolov AS. Influence of the interaction with DNA on the spectral-fluorescent and photochemical properties of some meso-substituted polymethine dyes. Spectrochim Acta A Mol Biomol Spectrosc 2018; 202:269-275. [PMID: 29800889 DOI: 10.1016/j.saa.2018.05.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Spectral-fluorescent and photochemical properties of meso-substituted thiacarbocyanine dyes 3,3'-dimethyl-9-phenylthiacarbocyanine and 3,3'-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine in solutions and their interaction with DNA were studied. The dyes form noncovalent complexes with DNA, which is accompanied by changes in the absorption spectra and an increase in the fluorescence intensity of the dyes. The data obtained suggest that the dyes are in the form of trans-isomers both in solvents of different polarity and in complexes with DNA. It was shown that the interaction of the dyes with DNA is a complex process involving monomeric dye molecules and aggregates of the dyes. The primary photochemical processes of the dyes in solutions and in complexes with DNA were studied by flash photolysis technique. Upon flash photoexcitation in solutions, the formation and decay of the photoisomers of the dyes were observed, with no generation of the triplet states. In the complex with DNA, no signal of photoisomers was detected; in the absence of oxygen, the formation of the triplet state of the dyes was observed. The decay kinetics of the triplet state of the dyes were two-exponential. The process of quenching of the triplet state of the dyes by oxygen in a complex with DNA was studied, the respective quenching rate constants were estimated, being lower than the diffusion-controlled value.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia
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