Ionic Liquid-Driven Modulation of DNA Brush Morphology on Nanoparticle Surfaces

The morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like electrostatic screening and ion bridging. In contrast, ionic liquids, a new class of organic salts, have previously been found to increase the DNA chain length, indicating a distinct mode of interaction between the ionic liquid and DNA chains. This study utilizes self-assembled DNA-AuNPs as a model system to examine changes in the DNA chain morphology and the nanoscale interaction mechanisms in an ionic liquid environment. The DNA chain lengths are measured in solution using X-ray scattering measurements at varying concentrations of two imidazolium ([ $BMIM$ ] acetate and [ $EMIM$ ] acetate) based ionic liquids. Additionally, Molecular Dynamics (MD) simulations are performed mimicking the experimental system. Our results suggest an interplay of electrostatic and groove-binding interactions governing the DNA chain morphology, which depends on IL concentration and the composition of the DNA chains. It has been found that for DNA chains with majority ssDNA, electrostatic interaction dominate, however with increasing composition of double strands, the DNA chains exhibit compaction due to a non-electrostatic hydrophobic groove-binding mechanism.