Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy

Aristova, Daria; Kosach, V. R.; Chernii, Svitlana; Slominsky, Yuriy L.; Balanda, A.O.; Filonenko, Valeriy; Yarmoluk, S. M.; Rotaru, Alexandru; Özkan, Hülya Gizem; Mokhir, Andriy; Kovalska, Vladyslava

doi:10.1088/2050-6120/ac10ad

Cited by 18 publications

(24 citation statements)

References 46 publications

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“…To identify the most promising fluorescent probe for RNA imaging, newly synthesized compounds were screened for fluorescence performance with a focus on their detection limits and selectivity for RNA. Two representative nucleic acids, including baker’s yeast RNA and salmon testes DNA, were employed in the assays, as these nucleic acids from biological species are often utilized in studies for RNA-targeting fluorescent probes [ 13 , 15 , 31 ]. As shown in Table 1 , these candidate probes alone in buffer displayed extremely weak emission, even in the presence of DNA samples.…”

Section: Resultsmentioning

confidence: 99%

Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells

et al. 2022

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RNA imaging is of great importance for understanding its complex spatiotemporal dynamics and cellular functions. Considerable effort has been devoted to the development of small-molecule fluorescent probes for RNA imaging. However, most of the reported studies have mainly focused on improving the photostability, permeability, long emission wavelength, and compatibility with live-cell imaging of RNA probes. Less attention has been paid to the selectivity and detection limit of this class of probes. Highly selective and sensitive RNA probes are still rarely available. In this study, a new set of styryl probes were designed and synthesized, with the aim of upgrading the detection limit and maintaining the selectivity of a lead probe QUID−1 for RNA. Among these newly synthesized compounds, QUID−2 was the most promising candidate. The limit of detection (LOD) value of QUID−2 for the RNA was up to 1.8 ng/mL in solution. This property was significantly improved in comparison with that of QUID−1. Further spectroscopy and cell imaging studies demonstrated the advantages of QUID−2 over a commercially available RNA staining probe, SYTO RNASelect, for highly selective and sensitive RNA imaging. In addition, QUID−2 exhibited excellent photostability and low cytotoxicity. Using QUID−2, the global dynamics of RNA were revealed in live cells. More importantly, QUID−2 was found to be potentially applicable for detecting RNA granules in live cells. Collectively, our work provides an ideal probe for RNA imaging. We anticipate that this powerful tool may create new opportunities to investigate the underlying roles of RNA and RNA granules in live cells.

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Section: Resultsmentioning

confidence: 99%

Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells

et al. 2022

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“…However, a lower concentration of T-3 (0.1 μM) had to be used in cancer cells due to the signal’s overbrightness. Similar results were previously shown on monomethine cyanine dyes, where benzoxazole derivative was ∼5 times more photostable than benzothiazoles . We suggest that a heavy atom in the heterocycle of benzoxazole reduces the effective length of the π-electron system (thus, the length of the polymethine chain), positively affecting the stability of T-4 and T-5 dyes.…”

Section: Resultsmentioning

confidence: 99%

“…Similar results were previously shown on monomethine cyanine dyes, where benzoxazole derivative was ∼5 times more photostable than benzothiazoles. 19 We suggest that a heavy atom in the heterocycle of benzoxazole reduces the effective length of the π-electron system (thus, the length of the polymethine chain), positively affecting the stability of T-4 and T-5 dyes. The obtained photostability results are consistent with the location of the absorption maximums and the relation between the polymethine chain length and photostability.…”

Section: The Fluorescence Microscopy Study Of Staining Properties Of ...mentioning

confidence: 99%

“…18 We have also shown that this dye in low concentration could stain RNA-rich nucleoli without a background in the cytoplasm and have reported highly specific green-emitted monomethine cyanine dyes to stain RNAcontaining structures in cells. 19 Besides this, our research group proposed near-infrared fluorescent probes among pentamethine cyanines and merocyanines as powerful far-red fluorescent probes applicable for the highly sensitive detection of albumins. 20,21 Here we present our research of symmetrical cationic trimethine cyanine dyes with β-substituents in the polymethine chain based on substituted benzothiazole and benzoxazole heterocycles (ethyl group at the 3 positions and ethoxy group at the 6 positions for dye T-1, methyl group at the 3 positions for dyes T-2−T-5 with additional chloro-group at the 5 positions for dye T-5) as probes for nucleic acids detection and visualization by fluorescence microscopy (Figure 1).…”

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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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Target‐mediated suppression of rolling circle amplification for label‐free detection of aflatoxin B₁

et al. 2023

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Background Aflatoxin B1 (AFB1) has been considered as a prevailing natural carcinogenic mycotoxin in various food and feedstuff products, posing serious endangers to human health. The quantitative and selective detection of AFB1 was significantly essential for food safety control. Results We developed a label‐free fluorescent aptasensor using a target‐binding aptamer probe as the rolling circle amplification (RCA) primer for AFB1 detection. In the presence of AFB1, the probe preferentially combined with AFB1 rather than binding to the circular template, inhibiting the initiation of RCA process. The detection limit of the proposed method was as low as 6.6 nM, and the linear dynamic response range was four orders of magnitude wide. Besides, it revealed excellent specificity for AFB1 and high‐quality detection performance in food samples. Conclusion The presented detection method was simple, rapid, and economical, which indicated a promising application in food safety monitoring.

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Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy

Cited by 18 publications

References 46 publications

Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells

Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells

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

Target‐mediated suppression of rolling circle amplification for label‐free detection of aflatoxin B₁

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Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy

Cited by 18 publications

References 46 publications

Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells

Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells

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

Target‐mediated suppression of rolling circle amplification for label‐free detection of aflatoxin B1

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Target‐mediated suppression of rolling circle amplification for label‐free detection of aflatoxin B₁