Effects of imidazolium-based ionic liquids on the elasticity of DNA revealed by magnetic tweezers

Abstract

The functions of DNA are related to its mechanical properties, including elasticity and conformational transitions. Ionic liquids, known as green solvents, are used for DNA separation and as a solvent medium for long-term DNA storage. This paper elucidated DNA interaction mechanisms with two imidazolium-based ionic liquids: 1-butyl-3-methylimi-dazolium chloride ([bmim]Cl) and 1-octyl-3-methylimidazolium chloride ([omim]Cl), via magnetic tweezers, bulk techniques and molecular dynamic simulation (MD). By stretching and twisting individual DNA molecules, we measured the elasticity of DNA in the presence of ILs ([bmim]Cl and [omim]Cl). As results, the persistence length, stretch modulus, torsional stiffness and twist-stretch coupling exhibited a significant decrease compared to the DNA without ILs binding. Isothermal titration calorimetry analysis indicated that the ILs in the presence of DNA were thermodynamically favored driven by enthalpy and entropy. DNA underwent size transition and conformational change induced by ILs, and the charges of DNA were neutralized by the added ILs. The binding of ILs induced unwinding and softening of DNA. Circular dichroism spectra and MD results indicated that DNA maintained B-conformation after interacting with ILs. Compared to [bmim]+, [omim]+ showed stronger binding affinity to DNA and tended to aggregate on the DNA surface. ILs binding reduced Na+ and water binding on DNA, which likely prevented the hydrolytic reactions that denatured DNA and helped stabilize DNA for the long term. This research provides a critical theoretical foundation for the utilization of ionic liquids in life sciences.