Benzothiazole-based cyanines as fluorescent “light-up” probes for duplex and quadruplex DNA

Turaev, Anton V.; Цветков, В. Б.; Танкевич, М. В.; Smirnov, Igor P.; Aralov, Andrey V.; Pozmogova, Galina E.; Varizhuk, Anna M.

doi:10.1016/j.biochi.2019.04.018

Cited by 18 publications

(9 citation statements)

References 102 publications

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“…Thermal stabilities increased from ON15 to ON31, supporting the positive effects of the duplex modules in the series ( Figure 2E, Table 1). The binding of BO with ribo-analogues led to a fluorescence intensity enhancement (Table S1), comparable to those previously obtained for the deoxyribo-variants [32]. These results indirectly confirm that ON31 structure also contains a junction, which can enhance the light-up effect upon dye binding.…”

Section: Interaction Of Gfp Chromorophore Analogues With Ribo-variantsupporting

confidence: 86%

“…The relationship between the structure and the ability of fluorophores to light up remains unclear, although leader compounds 1a-e, 2 and 3 share a common 4-(4-hydroxybenzylidene)-1-methyl-1H-imidazol-5(4H)-one fragment typical for the parent GFP chromophore. In addition, derivative 6 with the highest light-up effect consists of conjugated bicyclic and monocyclic aromatic rings -a structure that has much in common with the BO structure [32]. It should be noted that developed compounds have emission maxima in a wide wavelength range (450-616 nm), which allows multiplex detection together with alternative approaches.…”

Section: Interaction Of Gfp Chromophore Analogues With Tba15 and Tba31mentioning

confidence: 99%

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Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues

Zaitseva

Балеева

Zatsepin

et al. 2020

Sensors

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Aptasensors became popular instruments in bioanalytical chemistry and molecular biology. To increase specificity, perspective signaling elements in aptasensors can be separated into a G-quadruplex (G4) part and a free fluorescent dye that lights up upon binding to the G4 part. However, current systems are limited by relatively low enhancement of fluorescence upon dye binding. Here, we added duplex modules to G4 structures, which supposedly cause the formation of a dye-binding cavity between two modules. Screening of multiple synthetic GFP chromophore analogues and variation of the duplex module resulted in the selection of dyes that light up after complex formation with two-module structures and their RNA analogues by up to 20 times compared to parent G4s. We demonstrated that the short duplex part in TBA25 is preferable for fluorescence light up in comparison to parent TBA15 molecule as well as TBA31 and TBA63 stabilized by longer duplexes. Duplex part of TBA25 may be partially unfolded and has reduced rigidity, which might facilitate optimal dye positioning in the joint between G4 and the duplex. We demonstrated dye enhancement after binding to modified TBA, LTR-III, and Tel23a G4 structures and propose that such architecture of short duplex-G4 signaling elements will enforce the development of improved aptasensors.

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Section: Interaction Of Gfp Chromorophore Analogues With Ribo-variantsupporting

confidence: 86%

Section: Interaction Of Gfp Chromophore Analogues With Tba15 and Tba31mentioning

confidence: 99%

Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues

Zaitseva

Балеева

Zatsepin

et al. 2020

Sensors

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“…The development of label-free assays is highly desired for detecting small molecules [ 38 , 39 ]. Label-free detection provides several advantages over covalent modification of ssDNA aptamers with fluorophores.…”

Section: Resultsmentioning

confidence: 99%

Novel DNA Aptameric Sensors to Detect the Toxic Insecticide Fenitrothion

Trinh

Kadam

Song

et al. 2021

IJMS

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Fenitrothion is an insecticide belonging to the organophosphate family of pesticides that is widely used around the world in agriculture and living environments. Today, it is one of the most hazardous chemicals that causes severe environmental pollution. However, detection of fenitrothion residues in the environment is considered a significant challenge due to the small molecule nature of the insecticide and lack of molecular recognition elements that can detect it with high specificity. We performed in vitro selection experiments using the SELEX process to isolate the DNA aptamers that can bind to fenitrothion. We found that newly discovered DNA aptamers have a strong ability to distinguish fenitrothion from other organophosphate insecticides (non-specific targets). Furthermore, we identified a fenitrothion-specific aptamer; FenA2, that can interact with Thioflavin T (ThT) to produce a label-free detection mode with a Kd of 33.57 nM (9.30 ppb) and LOD of 14 nM (3.88 ppb). Additionally, the FenA2 aptamer exhibited very low cross-reactivity with non-specific targets. This is the first report showing an aptamer sensor with a G4-quadruplex-like structure to detect fenitrothion. Moreover, these aptamers have the potential to be further developed into analytical tools for real-time detection of fenitrothion from a wide range of samples.

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“…Обнаружено, что еще один флуоресцентный краситель, тиофлавин Т (ThT), широко применяющийся для специфического окрашивания амилоидов, также связывается с различными структурами ДНК, при этом усиление флуоресценции при связывании с G-квадруплексами особенно велико (в ~2100 раз в видимой области) [31,32]. За последние годы разработан и изучен ряд новых соединений для использования в качестве флуоресцентных зондов на G-квадруплексы и i-мотивы [33], в частности, производные бензотиазола [34,35].…”

Section: флуоресцентная микроскопия неканонических структур днкunclassified

Visualization of G-Quadruplexes, i-Motifs and Their Associates

2022

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The non-canonical structures formed by G- or C-rich DNA regions, such as quadruplexes and i-motifs, as well as their associates, have recently been attracting increasing attention both because of the arguments in favor of their existence in vivo and their potential application in nanobiotechnology. When studying the structure and properties of non-canonical forms of DNA, as well as when controlling the artificially created architectures based on them, visualization plays an important role. This review analyzes the methods used to visualize quadruplexes, i-motifs, and their associates with high spatial resolution: fluorescence microscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). The key approaches to preparing specimens for the visualization of this type of structures are presented. Examples of visualization of non-canonical DNA structures having various morphologies, such as G-wires, G-loops, as well as individual quadruplexes, i-motifs and their associates, are considered. The potential for using AFM for visualizing non-canonical DNA structures is demonstrated.

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Benzothiazole-based cyanines as fluorescent “light-up” probes for duplex and quadruplex DNA

Cited by 18 publications

References 102 publications

Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues

Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues

Novel DNA Aptameric Sensors to Detect the Toxic Insecticide Fenitrothion

Visualization of G-Quadruplexes, i-Motifs and Their Associates

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