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 . They are also used for labeling of small organic molecules and biomacromolecules and for funcioning of nanoparticles and fluorescent probes with high quantum yield .
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 . 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.