Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study

Abstract

The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world due to their controllable diverse and polymorphic structures. Apart from biological and medical significance, G-quadruplex DNAs are widely used in various fields such as nanotechnology, nanomachine, biosensors, and biocatalyst. So far, the applications of the G-quadruplex DNA are mainly limited in the water medium. Recently, a new generation of solvent named deep eutectic solvent (DES) has become very popular and has been widely used as a reaction medium of biocatalytic reactions and long-term storage medium for nucleic acids, even at high temperature. Hence, it is essential to understand the role of DES on temperature-induced conformational changes of a G-quadruplex DNA. In this research work, we have explored the temperature-mediated conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline medium in the temperature range of 300–500 K, using a total of 10 μs unbiased all-atom molecular dynamics simulation. Here, from RMSD, RMSF, R g and principal component analyses, we notice that the c-kit G-quadruplex DNA is stable up to 450 K in reline medium. However, it unfolds in water medium at 450 K. It is found that the hydrogen bonding interactions between c-kit G-quadruplex DNA and reline play a key role in the stabilization of the G-quadruplex DNA even at high temperature. Furthermore, in this work we have observed a very interesting and distinctive phenomenon of the central cation of the G-quadruplex DNA. Its position was seen to fluctuate between the two tetrad cores, that is, the region between tetrad-1 and tetrad-2 and that between tetrad-2 and tetrad-3 and vice versa at 450 and 500 K in reline medium which is absent in water medium at 450 K. Moreover, the rate of its oscillation is increased when temperature is increased.

Microscopic structural features of water in aqueous–reline mixtures of varying compositions

“…45 Reline is also found to protect C-kit G-Quadruplex DNA from severely high temperature. 46 Hydrogen bond mediated electrostatic interaction plays a pivotal role in stabilizing reline microstructure. ESPR, Neutron scattering, and molecular dynamics studies establish the position of the chloride ion at the closer proximity of urea and hydroxyl group of choline cation.…”

Effect of Hydrated Deep Eutectic Solvents on the Thermal Stability of DNA

“…Although this behavior has been always connected to a destabilization effect, especially for dG-dCrich duplex and single strand, little experimental data support this hypothesis. On the other hand, the melting temperatures (T m ) reported in [15] for ChCl/DNA solutions show that the T m values increase at increasing the dG-dC base pair content and Pal et al [10] have recently described the enhanced stability of the G-quadruplex in ChCl:U. Furthermore, the data in Figure 3c-f reveal that a greater concentration of ChCl:U in water does not produce a marked improvement in the transition temperature of sDNA.…”

“…From this point of view, the search for new solvents that ensure a greater stability and more efficient extraction and handling processes is becoming increasingly relevant. The stability and solubility of duplex DNA in DES have been examined by several previous studies [10][11][12][13][14][15]. They have shown that the use of DESs as solvents, anhydrous or in water, guarantees the stability of DNA duplexes for long periods and at high temperatures [12,16].…”

Deep Eutectic Solvents (DESs) and Their Application in Biosensor Development

“…Overall, this study indicates that reline is suitable for long-term nucleic acid storage. Moreover, Pal et al also reported that the hydrogen bonds between reline and the proto-oncogene c-kit G-quadruplex DNA are responsible for its high temperature stability [ 54 ]. The authors studied the conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline in a temperature range of 300−500 K, exploiting a 10 μs molecular dynamics simulation.…”