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Aristova D, Selin R, Heil HS, Kosach V, Slominsky Y, Yarmoluk S, Pekhnyo V, Kovalska V, Henriques R, Mokhir A, Chernii S. Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy. ACS OMEGA 2022; 7:47734-47746. [PMID: 36591208 PMCID: PMC9798395 DOI: 10.1021/acsomega.2c05231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
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.
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Affiliation(s)
- Daria Aristova
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
- Instituto
Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Roman Selin
- V.I.
Vernadsky Institute of General and Inorganic Chemistry NASU, 32/34 Palladin Ave, 03142 Kyiv, Ukraine
- Organic
Chemistry II, Friedrich-Alexander-University
of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Hannah Sophie Heil
- Instituto
Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Viktoriia Kosach
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Yuriy Slominsky
- Institute
of Organic Chemistry NASU, 5 Murmans’ka St., 02094 Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Vasyl Pekhnyo
- V.I.
Vernadsky Institute of General and Inorganic Chemistry NASU, 32/34 Palladin Ave, 03142 Kyiv, Ukraine
| | - Vladyslava Kovalska
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Ricardo Henriques
- Instituto
Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Andriy Mokhir
- Organic
Chemistry II, Friedrich-Alexander-University
of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Svitlana Chernii
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
- V.I.
Vernadsky Institute of General and Inorganic Chemistry NASU, 32/34 Palladin Ave, 03142 Kyiv, Ukraine
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Aristova D, Kosach V, Chernii S, Slominsky Y, Balanda A, Filonenko V, Yarmoluk S, Rotaru A, Özkan HG, Mokhir A, Kovalska V. Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy. Methods Appl Fluoresc 2021; 9. [PMID: 34198271 DOI: 10.1088/2050-6120/ac10ad] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022]
Abstract
We have studied spectral-luminescent properties of the monomethine cyanine dyes both in their free states and in the presence of either double-stranded deoxyribonucleic acids (dsDNAs) or single-stranded ribonucleic acids (RNAs). The dyes possess low fluorescence intensity in an unbound state, which is increased up to 479 times in the presence of the nucleic acids. In the presence of RNAs, the fluorescence intensity increase was stronger than that observed in the presence of dsDNA. Next, we have performed staining of live and fixed cells by all prepared dyes. The dyes proved to be cell and nuclear membrane permeant. They are photostable and brightly stain RNA-containing organelles in both live and fixed cells. The colocalization confirmed the specific nucleoli staining with anti-Ki-67 antibodies. The RNA digestion experiment has confirmed the selectivity of the dyes toward intracellular RNA. Based on the obtained results, we can conclude that the investigated monomethine cyanine dyes are useful fluorescent probes for the visualization of intracellular RNA and RNA-containing organelles such as nucleoli by using fluorescence microscopy.
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Affiliation(s)
- Daria Aristova
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Viktoriia Kosach
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Svitlana Chernii
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Yuriy Slominsky
- Institute of Organic Chemistry NASU, 5 Murmans'ka St., 02094 Kyiv, Ukraine
| | - Anatoliy Balanda
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Valeriy Filonenko
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Alexandru Rotaru
- 'Petru Poni' Institute of Macromolecular Chemistry, Romanian Academy, Grigore Ghica Voda Alley 41A, 700487 Iasi, Romania
| | - Hülya Gizem Özkan
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Andriy Mokhir
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Vladyslava Kovalska
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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Kovalska VB, Losytskyy MY, Yarmoluk SM, Lubitz I, Kotlyar AB. Mono and trimethine cyanines Cyan 40 and Cyan 2 as probes for highly selective fluorescent detection of non-canonical DNA structures. J Fluoresc 2010; 21:223-30. [PMID: 20809136 DOI: 10.1007/s10895-010-0709-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/11/2010] [Indexed: 01/14/2023]
Abstract
Two of earlier reported dsDNA sensitive cyanine dyes-monomethine Cyan 40 and meso-substituted trimethine Cyan 2 were studied for their ability to interact with non-canonical DNA conformations. These dyes were characterized by spectral-luminescent methods in the presence of G-quadruplex, triplex and dsDNA motifs. We have demonstrated that Cyan 2 binds strongly and preferentially to triple- and quadruple-stranded DNA forms that results in a strong enhancement of the dye fluorescence, as compared to dsDNA, while Cyan 40 form fluorescent complexes preferentially only with the triplex form. Highly fluorescent complexes of Cyan 2 with DNA triplexes and G-quadruplexes and Cyan 40 with DNA triplexes are very stable and do not dissociate during gel electrophoresis, leading to preferential staining of the above DNA forms in gels. The data presented point to the intercalation mechanism of the Cyan 2 binding to G4-DNA, while the complexes of Cyan 40 and Cyan 2 with triplex DNA are believed to be formed via groove binding mode. The Cyan dyes can provide a highly sensitive method for detection and quantification of non-canonical structures in genome.
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Affiliation(s)
- Vladyslava B Kovalska
- Department of Combinatorial Chemistry, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine.
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Yarmoluk SM, Losytskyy MY, Yashchuk VM. Nonradiative deactivation of the electronic excitation energy in cyanine dyes: influence of binding to DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2002; 67:57-63. [PMID: 12007468 DOI: 10.1016/s1011-1344(02)00281-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The processes of nonradiative deactivation of electronic excitation energy in cyanine dyes determine their quantum yield. Because of that, the study of the influence of cyanines binding to DNA on these processes can provide information on the causes leading to the cyanines fluorescence intensity enhancement in the presence of DNA. In the presented paper, the activation energies of nonradiative degradation of electronic excitation, quantum yields and rate constants of nonradiative transitions of several cyanines in free state and in the presence of DNA were established and compared. The mechanisms of nonradiative deactivation of dye excitation energy were discussed.
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Affiliation(s)
- S M Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo Str. 150, 03143, Kyiv, Ukraine.
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