engleski

Study of Urea Influence on G-Quadruplex Structure by Surface-Enhanced Raman Scattering Spectroscopy

G-Quadruplexes (G4) are ordered structures of nucleic acids that can form within repetitive guanine-rich DNA or RNA strands. They are built of G-quartets which are planar structures consisted of four guanine bases connected by Hoogsteen hydrogen bonds that are stacked on top of each other by π-stacking interactions, forming four- chain spiral structure. Different topologies of G4 are known depending on the length and composition of the nucleic base sequence and the presence of chemical species, such as Na+ and K+ ions [1]. Sodium ions are coordinated by carbonyl oxygen atoms of guanine in the central cavity of G- quadruplex and thus stabilize the resulting structure. Unlike alkali ions, urea is a well- known denaturing agent and has been used for decades in the study of proteins and their structures, given that it affects the equilibrium between unfolded and folded structure. G4 have globular shape and are less charged compared to other nucleic acids, that makes them similar to globular proteins [2]. The research objective was to investigate the effect of urea on the structure of G4. For this purpose, surface-enhanced Raman scattering (SERS) spectroscopy was applied, which is based on amplification of scattered radiation during adsorption or chemical binding of analytes to a nanostructured metal surface [3]. SERS spectroscopy was used to investigate the structure of human telomeric sequence d[TTAGGG]4 (Tel24) in the absence and presence of stabilizing Na+ ions (100 mM NaCl) as well as after addition of urea. Characteristic marker bands of unfolded Tel24 structure were observed in the SERS spectra without Na+ ions [4]. After heating Tel24 with Na+ ions the SERS spectra confirmed the expected presence of ordered G-quadruplex. The intensity ratios of the bands originating from breathing vibrations of adenine and guanine rings proved the presence of the folded telomeric sequence on the surface of silver nanoparticles. Addition of urea induces destruction of the ordered G4 structure, which was clearly visible from the SERS spectra looking like the spectra of unfolded Tel24.

G-Quadruplex ; Urea ; SERS

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