Development of functionalized SYBR green II related cyanine dyes for viral RNA detection
Saarnio, V. K., Salorinne, K., Ruokolainen, V. P., Nilsson, J. R., Tero, T.-R., Oikarinen, S., Wilhelmsson, L. M., Lahtinen, T. M., & Marjomäki, V. S. (2020). Development of functionalized SYBR green II related cyanine dyes for viral RNA detection. Dyes and Pigments, 177, Article 108282. https://doi.org/10.1016/j.dyepig.2020.108282
Published inDyes and Pigments
DisciplineOrgaaninen kemiaNanoscience CenterFysikaalinen kemiaSolu- ja molekyylibiologiaOrganic ChemistryNanoscience CenterPhysical ChemistryCell and Molecular Biology
Embargoed until: 2022-06-01Request copy from author
© 2020 Elsevier Ltd. All rights reserved.
Fluorescent probes for sensing nucleic acids have found widespread use in the field of cell and molecular biology. However, probes combined with potential for post-synthetic conjugation, e.g. for intra-endosomal measurements of RNA, are unavailable. Herein we developed cyanine dyes that can be conjugated to viral capsid or other targets. First, we solved the crystal structure of SYBR Green II. The structural elucidation of this commonly used RNA probe provided the basis for synthesizing similar molecules with much desired function for post-synthetic conjugation. To address this need, cyanine dyes were prepared using an alternative synthesis protocol. All studied compounds showed considerable brightness upon binding to nucleic acids. However, regardless of the common chromophore on the dyes, the observed fluorescence emission intensities varied significantly, where methyl-substituted dye 1 gave values higher than SYBR Green II, whereas compounds 2–5 containing undecyl spacers had lower values. Studying the structure-activity relationship revealed the longer alkyl chains to induce slight perturbation in dye intercalation, as well as demanding larger binding area on the nucleic acid lattice, explaining these differences. To study the potential biological use of the dyes, the RNA genome of enterovirus echovirus 1 was studied in vitro with the probes. A novel method employing the low binding space requirement of 1 was developed to determine the single-to-double-stranded RNA ratio of a sample, whereas compound 4 was covalently bound to the viral capsid and used successfully to monitor the viral RNA release from within the capsid. The presented results open new possibilities for preparation and use of SYBR Green-based nucleic acid probes to further apply these compounds for increasingly demanding targeting in biological contexts. ...
Publication in research information system
MetadataShow full item record
Related funder(s)Academy of Finland; Jane and Aatos Erkko Foundation
Funding program(s)Academy Project, AoF; Foundation
Additional information about fundingThis work was supported by the Academy of Finland [266492 to T.-R.T and V.S., and 257125 to V.M.]; Jane and Aatos Erkko Foundation [Novel probes for discovering anti-virals to V.S., T.L., and V.M.]; and the Swedish Foundation for Strategic Research [IRC15-0065 for J.R.N., and L.M.W.]. GLP-GPI plasmid was obtained as a kind gift from Lucas Pelkmans from ETH Zurich.
Showing items with similar title or keywords.
The effect of PLC-inhibitor on echovirus 1 internalization probed with fluorescently labeled echovirus 1 Myllynen, Mira (2014)Echovirus 1 (EV1) kuuluu Pikornavirusperheeseen ja tarkemmin luokiteltuna Enterovirusten sukuun. EV1 on pieni ja vaipaton RNA-virus, jonka proteiinikuori koostuu neljästä proteiinista VP1-VP4. Infektion on osoitettu alkavan, ...
Schoder, Stefan; Schröder, Hendrik V.; Cera, Luca; Puttreddy, Rakesh; Güttler, Arne; Resch-Genger, Ute; Rissanen, Kari; Schalley, Christoph A. (Wiley - VCH Verlag GmbH & Co. KGaA, 2019)Organic fluorophores, particularly stimuli-responsive molecules, are very interesting for biological and material sciences applications, but frequently limited by aggregation- and rotation-caused photoluminescence quenching. ...
Fabrication techniques for developing a functional microfluidic glass device suitable for detection in optical spectroscopy system Rojas Rojas, Laura (2012)Microfluidic devices offer the chance to manipulate and analyze fluids including bioassays and chemical reactions. In this study, a method to develop a microfluidic analysis system is proposed for detection of nanotubes ...
Selective recognition of aromatic hydrocarbons by endo-functionalized molecular tubes via C/N-H⋅⋅⋅π interactions Huang, Guo-bao; Liu, Wei-Er; Valkonen, Arto; Yao, Huan; Rissanen, Kari; Jiang, Wei (Elsevier Ltd; Chinese Chemical Society, 2018)Molecular recognition of aromatic hydrocarbons by four endo-functionalized molecular tubes has been studied by 1H NMR spectroscopy, computational methods, and single crystal X-ray crystallography. The binding selectivity ...
Borovský, Ján (University of Jyväskylä, 2018)Sorting of carbon nanotubes by their chirality is the current bottleneck in the way to their broad employment based on their exceptional electronic and optical properties. Despite the extensive effort, there is no known ...