Abstrakt
G-quadruplexes are good models of DNA structures involved in the metabolism of living cells and are frequently adopted by guanine-rich nucleic acids. They play crucial roles in genome functions and stability, the pathogenesis of several neurodegenerative diseases, and cancer biology. The guanine nucleotide (G) and its derivatives are well known for their property to self-associate into various complexes through H-bonding and stacking interactions. G-quadruplexes are formed at higher concentrations as nanoscale cylindrical structures consisting of G-quartet disks stacked one above the other[1]. These supramolecular assemblies are also potential candidates for nanotechnology and chemical biology applications.
Raman optical activity (ROA), which measures differential Raman scattering of right and left circularly polarized light, is promising for studying nucleic acid structures and their dynamics because of its sensitivity to subtle changes in geometry[2]. Recently, characteristic Raman and ROA spectral changes upon G-association were observed. A combination of molecular dynamics (MD) and quantum-chemical computational techniques have been used to model and interpret the observed Raman and ROA spectral features of G-quadruplexes under various experimental conditions. The fragment-based cartesian coordinate-based tensor transfer (CCT)[3] method is also employed in the spectra calculations to embrace the enormous size of the G-quadruplexes.
References: 1. Wu, G., & Kwan, I. C. , Helical structure of disodium 5'-guanosine monophosphate self-assembly in neutral solution, J. Am. Chem. Soc., (2009), 131(9), 3180-3182. 2. Schrenková, Věra, et al. , Molecular Dynamics and Raman Optical Activity Spectra Reveal Nucleotide Conformation Ratios in Solution, Phys. Chem. Chem. Phys., (2023), 25, 8198-8208 3. Bouř, P., Sopková, J., Bednárová, L., Maloň, P., & Keiderling, T. A. Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra. J. Comput. Chem., (1997), 18(5), 646-659.