G-quadruplex-forming aptamers: Rhodamine 6G interaction

G-quadruplex-forming aptamers: Rhodamine 6G interaction

Year:
2021

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Mgr. Martin Russin100%100%-
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Mgr. Michaela Harmošová100%100%100%
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ISBN: ISBN 978-80-972360-7-6

G-quadruplex-forming aptamers: Rhodamine 6G interaction

Lukáš Trizna1 , Viktor Víglaský ,
1 Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University, Moyzesova 11, 040 01 Košice, Slovakia
lukas.trizna@yahoo.com

G-quadruplexes (G4) are non-canonical DNA or RNA structures formed from G-rich sequences. Aptamers are short oligonucleotides, which can adopt  the three-dimensional structures able to bind any biomacromolecules (enzymes, proteins). Some aptamers contain G-quadruplex motif. Synthetically prepared DNA aptamers have the potential to be as electrochemical biosensors, they are frequently used in some microarrays, nano-devices. Aptamers are frequently used in therapeutics for treatment of various types of diseases [1]. They are also used for labeling of small organic molecules and biomacromolecules and for funcioning of nanoparticles and fluorescent probes with high quantum yield [2].

There is a possibility to use fluorescent probe Rhodamine 6G as G4 ligand. For this purpose the spectroscopic and electrophoretic methods are used in our work. Circular dichroism (CD) is a suitable biophysical method to analyse various G4-ligand interactions [3]. All the studied parallel G4s show characteristic induced CD signals in presence of Rhodamine 6G at 570 nm, 540 nm and 510 nm. UV-Vis spectra titrations, hypochromic and batochromic shifts, confirmed the G4-Rhodamine 6G interaction. The results of the effect of Rhodamine 6G fluorescent probe on stability and topology of applicable G-quadruplex aptamers are presented. Electrophroretic analysis also shows the effect of multimerisation. According to previous results, Rhodamine 6G appears to be highly selective ligand for parallel G4s in comparison to hybrid and antiparallel G4s and to other non-canonical structures. Fluorescent properties of Rhodamine 6G-G4 complexes should be applied for the detection of parallel G4s both in vitro and in vivo.

Thanks: 

This work was supported by the Grant Agency of the Slovak Ministry of Education (VEGA No. 1/0138/20) and Internal Scientific Grant System of P. J. Šafárik University (VVGS-PF-2020-1431).

Sources: 

[1] Viglasky, V.; Hianik, T.: Gen Physiol Biophys, 2013, 32(2), 149.
[2] Lavis, L. D.: Annu. Rev. Biochem, 2017, 86, 825.
[3] Masiero, S.; et al.: Org Biomol Chem, 2010, 8(12), 2683.

Discussion

Thank you for your contribution, nice study. In the conclusion you state that fluorescent properties of Rhodamine 6G-G4 complexes can be utilized for detection of parallel G4s (apart from in vitro) also under in vivo conditions. This implies that the aptamers are sufficiently biocompatible and photostable. Are there any studies on this issue? Thank you.
iwa

Dear Assoc. prof. Waczulíková, thank you for your comment. In terms of biocompatibility and photostability, we have not done such analyses yet. This is our hypothesis and goal of next work. The aim of our next studies are fluorimetric analyses of G4-Rh6G interactions also. There is possiblity to use Rh6G-G4 complexes as aptasensors. The formation of parallel G4s could be accompanied by binding of G-rich ssDNA to the substrate (e.g. protein). When parallel G4 is formed, rhodamine shuld interact with them. Based on our previous studies, Rh6G exhibits selectivity for G4 compared to other DNA motifs. This fact is a guide for us. We will still combine available biophysical methods that may be helpful to us.
Many of aptamers are used in clinical practice nowdays. This topic is „hot“, because there is potential for practical use e.g. in diagnostics. For example, the thrombin-binding aptamer (TBA), which was also reported in our study, was introduced to a clinical trial with positive results. In clinical studies, there are many of its new analogues reported.
There are some articles about aptamers and aptasensors where application of fluorescent probes is used:
Zhao, H.; Ma, C.; Chen, M.: Mol. Cell. Probes, 2019, 43, 29.
Suzuki, Y.; Yokohama, K.: ChemBioChem, 2009, 10, 1793.
Roxo, C.; Kotkowiak, W.; Pasternak, A.: Molecules, 2019, 24, 3781.

Thank you for your answe and I wish you a very good luck to you and your work.
iwa

A remark (in case you are not already informed about the upcoming event):

"Katedra genetiky a biochemie v spolupraci s obcianskym zdruzenim Natura pozyva na 121. prednasku v ramci Kuzelovych seminarov:

prof. Katrin Paeschke
University Clinic Bonn, Department of Hematology and Oncology, Nemecko

Ying and Yang of G-quadruplexes for genome stability

ktora sa uskutocni 1. juna 2021 (utorok) o 16:00 ako webinar: meet.google.com/pjt-tstf-vcr

Viac o prednasajucej a prednaske: http://www.naturaoz.org/seminare_files/Pozvanka_Katrin_Paeschke.pdf
tesime sa na posledne jarne stretnutie v ramci Kuzelovych seminarov.
Za organizatorov,
L. Tomaska
Katedra genetiky PriF UK

Thank you for the information. I know about this event and I'm looking forward to it. In addition, there is a series of webinars called "NUCLEIC ACID SECONDARY STRUCTURES: G4s AND BEYOND". This event takes place every thursday at 2 pm CET. Prof. Katrin Paeschke is one of the organizers there.