12.3.2021New probes for virus research from the combination of fluorescent dyes and nanoparticles (Saarnio)

Fluorescent, light emitting dyes are a remarkable group of molecules employed by biologists world-wide in their experimental work. A wide selection of products is available with labelling targets varying from cellular proteins and membranes to their genetic material in all colours. The development of these probes continues, motivated by the desire for brighter and better compounds. In his doctoral thesis, Ville Saarnio was studying nucleic acid targeting cyanine dyes and combining fluorescent dyes with noble metal nanoparticles, developing improved probes for the specific needs of virus researchers.
Published
12.3.2021

Cyanine dyes have acquired a position of importance as fluorescent markers commonly used for sensing nucleic acids. Particularly the products of the SYBR family are widely employed for this purpose. This is due to the characteristic binding of these compounds to the DNA through intercalation i.e. by inserting between the basepairs of the nucleic acid. This leads to major increase in the fluorescence exhibited by these dyes.

Every atom matters

In the thesis, the previously unknown structure of the SYBR Green II probe was elucidated and used as a foundation for improving the characteristics of cyanine dyes. With systematic changes to the structure of the chromophore, it was found that the photophysical properties of the dyes could be greatly improved through changes of a single atom.

“We were able to improve the brightness of the dye by over a two-fold, while the stability of the compound with minor structural changes”, Saarnio explains.

Additionally the possibility of covalently binding these dyes to different targets was explored, enabling better localization of the dyes to its desired destination. As an example, a dye was bound on the surface of a viral particle and the release of the viral genome from within its capsid was observed successfully in vitro.

Gold nanoclusters as carrier molecules

The thesis involved studying the potential of using gold nanoclusters as nanosized carrier molecules. The strength of using gold nanoclusters in biological research is based on their small, atomically exact structure and nontoxicity towards cells. In the study, new structures of gold nanoclusters were synthesized, characterized and employed as support molecules for binding fluorescent dyes on their surface, using previously developed methods. Such system employing a fluorophore bound to the surface of the nanocluster was then used to monitor the pH within cells. Low pH in the local environment of the cell led to the detachment of the fluorescent dye off the nanocluster surface, leading to increase in its brightness.

“The use of nanoparticles as carriers prohibits the spreading of the dye all over within the cell. At the same time, major opportunities to take advantage of completely new interactions between fluorophores and nanoparticles are presented to the biological research”, Saarnio expands.

The dissertation is published in JYU Dissertations series, number 361. ISBN 978-951-39-8559-2 (PDF) URN:ISBN:978-951-39-8559-2 ISSN 2489-9003.
Link to publication:

M.Sc. Ville Saarnio defends his doctoral dissertation "Fluorescent probes, noble metal nanoparticles and their nanocomposites: Detection of nucleic acids and other biological targets" on Friday 12th of March 2021 starting at 12. Opponent Associate Professor Nonappa (Tampere University) and Custos Senior Lecturer, Docent Tanja Lahtinen (Ģֱ). The doctoral dissertation is held in English.

The audience can follow the dissertation online.
Link to the online event:

Phone number to which the audience can present possible additional questions at the end of the event (to the custos): +358408053697