An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies

Abstract

Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL-DNA could be used as a basis for future development of specific ILs for nucleic acid technology.

Interaction studies of cholinium-based ionic liquids with calf thymus DNA: Spectrophotometric and computational methods

“…1 (a, b) and [24,27]. Micaelo and co-workers [27] showed enhancement in emission intensity when an IL is added to the solution containing DNA-bound pyrene, which was attributed to the space constraints imposed due to the electrostatic interaction between DNA and IL, resulting in the release of pyrene into the solution and hence enhanced emission intensity. However, in the present study, we found that the intensity of the DNA-bound pyrene remained almost unchanged even after the addition of cholinium based ILs.…”

“…Combining these two, several articles have been published describing the interaction of DNA with imidazolium, morpholinium, etc. based ILs [21][22][23][24][25][26][27][28][29]. For example, Liu and co-workers studied the impact of alkyl chain length present on imidazolium-based ILs [23] towards ct-DNA through extensive photophysical methods.…”

Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I

“…Thus the ct-DNA interact pyrene with higher binding constant in excited state than CTAB. It is well known that there are intercalations of pyrene with DNA bases at the grooves [21,22]. where free pyrene would no more available, suffered a systematic quenching with the increasing concentration of CTAB in the solution, as shown in Fig.…”

Molecular dynamics simulation of membrane in room temperature ionic liquids

“…PVDF molecules used in this simulation consists of 7 monomers [19]. 1,3-dialkylimidazolium bromide IL was selected as the simulation ILs [20]. The structure of water can be found in the library of GROMACS package.…”

“…This method makes the calculation cheap and simple. Recent research focus on composite membrane of PVDF to investigate the possibility of increasing the performance of the material in term of reliability and anti-erosion properties [4,[16][17][18][19][20].…”