Development of functionalized SYBR green II related cyanine dyes for viral RNA detection

Saarnio, Ville; Salorinne, Kirsi; Ruokolainen, Visa; Nilsson, Jesper; Tero, Tiia‐Riikka; Oikarinen, Sami; Wilhelmsson, L. Marcus; Lahtinen, Tanja; Marjomäki, Varpu

doi:10.1016/j.dyepig.2020.108282

Cited by 15 publications

(26 citation statements)

References 25 publications

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“…In the assay, gradual heating of the virus up to 90 °C induces the uncoating and release of the viral RNA to the solution, typically between 40 and 50 °C for enteroviruses [ 22 ]. Non-fluorescent SGII in the medium intercalates within the double-stranded regions in the viral RNA and emits fluorescence upon binding [ 33 ]. Increase in capsid stability would lead to a higher melting temperature, whereas lower melting temperature would suggest destabilization.…”

Section: Resultsmentioning

confidence: 99%

Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses

et al. 2021

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To efficiently lower virus infectivity and combat virus epidemics or pandemics, it is important to discover broadly acting antivirals. Here, we investigated two naturally occurring polyphenols, Epigallocatechin gallate (EGCG) and Resveratrol (RES), and polyphenol-functionalized nanoparticles for their antiviral efficacy. Concentrations in the low micromolar range permanently inhibited the infectivity of high doses of enteroviruses (107 PFU/mL). Sucrose gradient separation of radiolabeled viruses, dynamic light scattering, transmission electron microscopic imaging and an in-house developed real-time fluorescence assay revealed that polyphenols prevented infection mainly through clustering of the virions into very stable assemblies. Clustering and stabilization were not compromised even in dilute virus solutions or after diluting the polyphenols-clustered virions by 50-fold. In addition, the polyphenols lowered virus binding on cells. In silico docking experiments of these molecules against 2- and 3-fold symmetry axes of the capsid, using an algorithm developed for this study, discovered five binding sites for polyphenols, out of which three were novel binding sites. Our results altogether suggest that polyphenols exert their antiviral effect through binding to multiple sites on the virion surface, leading to aggregation of the virions and preventing RNA release and reducing cell surface binding.

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Section: Resultsmentioning

confidence: 99%

Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses

et al. 2021

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“…15,16 In order to meet this demand, we have synthesized five new cyanine dyes and evaluated their photophysical properties (Chart 1). The synthesis of the compounds was conducted using previously published protocols, 17,18 combined with an additional nucleophilic substitution step, as shown in the ESI † Scheme S2. Our previous results indicated significant differences in the dye properties of the heteroatoms in the chromophore; 18 in this study, we set out to evaluate those differences.…”

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confidence: 99%

“…The synthesis of the compounds was conducted using previously published protocols, 17,18 combined with an additional nucleophilic substitution step, as shown in the ESI † Scheme S2. Our previous results indicated significant differences in the dye properties of the heteroatoms in the chromophore; 18 in this study, we set out to evaluate those differences. The examined dyes were varied in structure by changing between an oxazole and thiazole moiety and varying the 2-substituent between a mercaptomethyl, dimethylamine or chloride.…”

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confidence: 99%

“…This was made possible by employing the theoretical model of DNAprotein interactions developed by von Hippel and McGhee elucidated in more detail in our previous work. 18,22 The processing of the obtained data produced a Scatchard plot (Fig. S24c, ESI †) that enabled the fitting of the McGhee and von Hippel equation for non-cooperative binding to obtain values for K a , n and subsequent determination of the Gibbs free energy of binding involved (DG 0 , Table 2).…”

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Systematic study of SYBR green chromophore reveals major improvement with one heteroatom difference

2021

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“…Fluorescent dyes are widely used for the detection and quantification of nucleic acids (NA) and proteins and are applied in real-time PCR, gel electrophoresis, flow cytometry, microscopy, etc. [1][2][3]. This is due to the ability of specific fluorescent dyes to bind to various target biomolecules in a mostly noncovalent mode, leading to changes in the fluorescent properties of the respective dye.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Modeling of Absorption and Fluorescent Characteristics of Cyanine Dyes

et al. 2022

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The rational design of cyanine dyes for the fine-tuning of their photophysical properties undoubtedly requires theoretical considerations for understanding and predicting their absorption and fluorescence characteristics. The present study aims to assess the applicability and accuracy of several DFT functionals for calculating the absorption and fluorescence maxima of monomethine cyanine dyes. Ten DFT functionals and different basis sets were examined to select the proper theoretical model for calculating the electronic transitions of eight representative molecules from this class of compounds. The self-aggregation of the dyes was also considered. The pure exchange functionals (M06L, HFS, HFB, B97D) combined with the triple-zeta basis set 6-311+G(2d,p) showed the best performance during the theoretical estimation of the absorption and fluorescent characteristics of cyanine dyes.

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Development of functionalized SYBR green II related cyanine dyes for viral RNA detection

Cited by 15 publications

References 25 publications

Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses

Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses

Systematic study of SYBR green chromophore reveals major improvement with one heteroatom difference

Theoretical Modeling of Absorption and Fluorescent Characteristics of Cyanine Dyes

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