Synthesis of low-viscosity hydrophobic magnetic deep eutectic solvent: Selective extraction of DNA

Fast extraction of high-purity nucleic acid from complex biological sample is the key to downstream nucleic acid analysis. In this work, two low-viscosity hydrophobic magnetic deep eutectic solvents (HMDESs) were synthesized for the selective extraction of DNA. The conformation of the HMDES was simulated by density functional theory (DFT) calculation. Characterization of HMDESs’ physical (magnetism, density, viscosity, and hydrophobicity) properties and thermal (melting point and decomposition temperature) properties were conducted. Based on the HMDESs, a vortex-assisted liquid-liquid micro-extraction (VALLME) DNA method was developed. Single stranded DNA that was extracted by HMDESs could be quickly collected by an external magnet. Factors that could impact the DNA extraction process, such as HMDESs volume, temperature, extraction time, and pH were systematically investigated via single-factor experimental analysis. Under the optimized condition, the proposed extraction method has been demonstrated with the extraction of DNA from a series of complex sample matrices, including metal mixture, protein mixture and E. coli cell lysate. The DNA extracted by using HMDES-based VALLME method was well suitable for PCR amplifications. After extraction, the retained DNAs could be readily recovered by simply using Britton-Robison (BR) buffer. In addition, the interaction and corresponding binding sites between HMDESs and DNA were investigated by FT-IR and DFT calculation. This work provides a new green magnetic solvent and a rapid and environmental-friendly extraction method for the enrichment of DNA and other biological macromolecules.