Molecular dynamics simulations for the study of interaction between non-canonical DNA structures and biochemically relevant co-solutes

Abstract

Non-canonical nucleic acid structures, such as DNA G-quadruplexes and i-Motifs, have been proved to play an important role in key biological processes, including gene expression, replication, regulation or telomere maintenance. The presence of G-quadruplexes in promoter regions of certain oncogenes turn them into a potential target for cancer therapies. Besides their biological implications, non-canonical DNA structures are present in genomes of various organisms, who adopt certain levels of co-solutes to protect their internal structures against the harsh environment. This study presents the research on the selected non-canonical DNA structures of particular biological relevance: G-quadruplex with only two tetrads, small DNA hairpin and ssDNA strand as well as canonical double helix. The atomistic molecular dynamics (MD) simulations have been applied to elucidate the structural, configuration and solvation properties of the analyzed structures in the presence of assorted co-solutes, composing the native cellular environment in nature: urea, ectoine and trimethylamine-N-oxide (TMAO). With the application of molecular theory of solutions, one determines and exemplifies the thermodynamic properties of investigated structures in various environments close to the physiological conditions present in living cells. This study uncovers the versatile nature of DNA interaction with diverse co-solutes and water, as well as the cross-interactions between the inorganic components of the biomolecular solution. The cellular mechanisms of DNA structural stabilization and destabilization are hereby described in terms of preferential binding and preferential exclusion, with particular emphasis on the properties of solvent structure within individual solvation shells. In this regards, this work presents a comprehensive study on the intracellular interactions involving nucleic acids, thus shedding light into their microscopic properties and opening the path for further biomedical research.