Basket-type G-quadruplex with two tetrads in the presence of TMAO and urea: A molecular dynamics study

• Published in: Journal of molecular structure 2023-02, Vol.1274, p.134375, Article 134375
• Main Authors: Oprzeska-Zingrebe, Ewa Anna, Smiatek, Jens
• Format: Article
• Language: English
• Subjects: Co-solutes; DNA G-quadruplex; Molecular dynamics simulations; Solvents; TMAO; Urea
• ISSN: 0022-2860; 1872-8014
• DOI: 10.1016/j.molstruc.2022.134375

•One microsecond long all-atom molecular dynamics simulations for basket-type DNA G-quadruplex in presence of TMAO and DNA.•Detailed analysis of interactions between TMAO, urea and DNA.•Study of co-solute influence on structural and conformational stability.•Detailed study how TMAO and urea change the number of intra- and intermolecular hydrogen bonds.•Detailed study how TMAO and urea change the twist and groove parameters of DNA. [Display omitted] DNA G-quadruplexes are non-canonical DNA structures, which have been proved to play an important role in key biological processes, such as gene expression, replication, regulation or telomere maintenance. Due to their presence in promoter regions of many oncogenes, G-quadruplexes are also considered as potential target for cancer therapies. Besides their biological implications, G-quadruplexes are present in genomes of various organisms, including deep sea piezophilic microorganisms, who adopt certain levels of co-solutes to protect their internal structures against high pressures. In this work, we study a stable DNA G-quadruplex with only two tetrads in presence of co-solutes. By means of molecular dynamics (MD) simulations, we elucidate the alterations in structural features and solvation properties in pure water and in the presence of physiological levels of trimethylamine-N-oxide (TMAO), urea and combined TMAO:urea solutions. Our simulations unravel the nature of nucleic acid interactions with both co-solutes and water in terms of their impact on the flexibility of the local structure, formation of inter- and intramolecular hydrogen bonds, non-bonded contacts and the location of co-solute molecules around the G-quadruplex.