The electrostatic interaction between the negatively charged phosphate groups of plasmid DNA and the cationic part of hydrophobic Ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim][PF6]), initiate the spontaneous self-assembly to form the functional nanostructures made up of DNA and ionic liquid (IL). These functional nanostructures were demonstrated as promising synthetic non-viral vectors for the efficient bacterial pGFP gene transformation in cells. In particular, the functional nanostructures that were made up of 1µL of IL ([Bmim][PF6]) and 1 µg plasmid DNA can increase the transformation efficiency by 300% - 400% in microbial system, without showing any toxicity on E.Coli DH5α cells. (31)P Nuclear Magnetic Resonance (NMR), Fourier Transform Infrared (FT-IR) spectroscopy and X-ray Photoelectron (XPS) spectroscopic analysis revealed that the electrostatic interaction between negatively charged phosphate oxygen and cationic Bmim(+) tend to initiate the self-assembly process. Thermogravimetric analysis of the DNA-IL functional nanostructures showed that these nanostructures consist of ~16 weight % of Ionic liquid, which is considered to provide the stability to the plasmid DNA that eventually enhanced the transformation efficiency.