Ionic liquid (IL), asymmetric chemical consist of bulky cations and tiny-mobile anions, has been known as promising DNA extraction, separation and preservation agent due to its strong interaction with DNA. However, the interaction underlying DNA-IL complex forming mechanism remains to be elucidated. Herein, we employed three types of ILs (EMIM-Cl, BMIM-Cl, and OMIM-Cl) to investigate the changes of DNA morphology upon the alkyl chain length of ILs by using solid-state nanopore technology combining with atomic force microscopy (AFM). The results of AFM show the different forms of DNA, including aggregate, stretching, and bundling shapes in terms of EMIM-Cl, BMIM-Cl, and OMIM-Cl, respectively, assuming that the shape of DNA-IL complexes is responding to the alkyl chain length of ILs. In DNA translocation experiment. From the alteration of blockade current signals during the DNA pass through the nanopore, we estimate that the shapes of DNA are changed due to the treatment with BMIM-Cl, and OMIM-Cl, which not only increased the blockade current signals about 2-4 times in the case of OMIM, but also decrease the event showing translocation of DNA folding, implying that the alkyl chain affect to DNA stretching and bundling. The results indicate the length of hydrophobic alkyl group of IL plays an important role in determination of DNA morphology, providing their further application in nanopore technique for slowing DNA translocation speed toward discovering protein-DNA interaction or DNA sequencing.

Ionic liquids (ILs) are organic salts with low melting point by asymmetric ionic strength between cation and anion. They have been known as promising DNA extraction, separation and preservation agent due to their hydrophilic, hydrophobic interaction with DNA. However, few studies have been performed about how DNA-ILs complexes form and their mechanism. Herein, we present three types of ionic liquids (EMIM-Cl, BMIM-Cl, and OMIM-Cl) change the DNA structure depend on alkyl chain length of ionic liquids. Structural changes of DNA by ionic liquids are observed by Atomic force microscopy, gel electrophoresis, zeta potential and solid-state nanopore technology. The results of AFM show the different structures of DNA, including aggregate, stretching, and bundling shapes in terms of EMIM-Cl, BMIM-Cl, and OMIM-Cl respectively. In DNA translocation experiment, DNA/EMIM-Cl show rare translocation signal due to aggregated structure by neutralized surface charge. DNA/BMIM-Cl and DNA/OMIM-Cl show slowing down the translocation speed due to changes of DNA net charge and structure. Especially, OMIM-Cl make slowing down the DNA translocation speed about 102~104 times compared to translocation speed of bare DNA by unzipping the bundling shape of complex. In conclusion, the morphology of DNA could be modified by the incorporation with different alkyl chain length of ILs, providing their further application in nanopore technique for slowing DNA sequencing or understanding protein-DNA interaction.