Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization
Alaranta, J. M., Truong, K.-N., Matus, M. F., Malola, S. A., Rissanen, K. T., Shroff, S. S., Marjomäki, V. S., Häkkinen, H. J., & Lahtinen, T. M. (2022). Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization. Dyes and Pigments, 208, Article 110844. https://doi.org/10.1016/j.dyepig.2022.110844
Julkaistu sarjassa
Dyes and PigmentsTekijät
Päivämäärä
2022Oppiaine
Solu- ja molekyylibiologiaNanoscience CenterOrgaaninen kemiaCell and Molecular BiologyNanoscience CenterOrganic ChemistryTekijänoikeudet
© 2022 The Authors. Published by Elsevier Ltd.
In recent years, the studies of RNA and its use for the development of RNA based vaccines have increased drastically. Although cyanine dyes are commonly used probes for studying nucleic acids, in a wide range of applications, there is still a growing need for better and brighter dyes. To meet this demand, we have systematically studied the structure of SYBR green-related cyanine dyes to gain a deeper understanding of their interactions with biomolecules especially how they interact with nucleic acids and the structural components which makes them strongly fluorescent. Herein, five new dyes were synthesized, and their photophysical properties were evaluated. Observations of photophysical characteristics were compared to calculations by using density functional theory in its ground state and time-dependent form to model the optical absorption spectra and excited state properties of the selected molecules. Single crystal X-ray crystal structures of five cyanine dyes were determined and the interactions of the cyanine dye-DNA complex were studied by using molecular docking and molecular dynamics calculations. Three molecular structural features were discovered: a) removing the benzene ring from the thiazolium moiety of the dye lowers the fluorescence drastically, and that the quantum yield can be enhanced, therefore increasing the fluorescence, by b) incorporating methanethiol substituent at the quinoline moiety instead of dimethylamine or c) changing the thiazolium moiety to an oxazolium moiety.
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Julkaisija
Elsevier BVISSN Hae Julkaisufoorumista
0143-7208Asiasanat
Julkaisu tutkimustietojärjestelmässä
https://converis.jyu.fi/converis/portal/detail/Publication/159121444
Metadata
Näytä kaikki kuvailutiedotKokoelmat
Rahoittaja(t)
Suomen AkatemiaRahoitusohjelmat(t)
Akatemiaprofessorin tutkimuskulut, SA; Akatemiahanke, SALisätietoja rahoituksesta
This work was supported by the Academy of Finland [342251 to V.M. and S.S., and 319208 to H.H.] and the University of Jyväskylä.Lisenssi
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