South Korea: Modular Chip for Bacterial DNA Extraction

Development of a bacterial DNA extraction modular chip using a magnetic particle and portable vibration motor

Sun Young Lim, Tae Jae Lee, Seol Yi Shin, Nam Ho Bae, Seok Jae Lee & Yoo Min Park | Nano-bio Application Team, National NanoFab Center (NNFC), 291 Deahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea. | 2020 | Analytical Methods; 12, 1197 doi: 10.1039/c9ay02690h

To overcome the limitations of DNA extraction processes that require high power and complicated lab-scale equipment, the Nano-Bio Applications team developed a portable DNA extraction chip. The chip utilizes a portable vibration motor and magnetic particles to eliminate the need for conventional laboratory instruments, such as a vortex or centrifuge. The DNA extraction modular chip was fabricated using a 3D printer with PI, PET and PVC films and consists of a core chamber, vibration jig that contains a minimized rotor and a magnetic jig that holds a small magnet. The main objective of the study was to demonstrate the efficiency of DNA extraction from E. coli 0157:H7 by gene amplification. A real-time qPCR, using Mic qPCR Cycler and its complementary software, was used to evaluate the DNA extraction performance. The extraction on the modular chip was carried out using NX-48 bacterial DNA extraction reagents (Genolution). The process involved lysis of the bacterial DNA, followed by free DNA reacting with magnetic particles in the vibration jig. After, cell lysis and washing were performed using the vibration and magnetic jigs. Finally, the extracted DNA attached to the magnetic particles was purified by employing an elution buffer in the magnetic jig. The DNA extraction using the modular chip was compared using the conventional extraction method (i.e. spin-column method) under the same buffer conditions. The average identification rate of the C_t value between the modular chip and commercial kit was approximately 93.8%, which confirmed the quantitative analysis results with accuracy and precision. The limit of detection for E. coli 0157:H7 is 1.0 x 10¹ CFU/100 mL. The results of the study demonstrated high efficiency and reproducibility of the DNA extraction chip with similar performance to conventional methods. The elimination of costly lab equipment has allowed cost reduction for DNA extraction and the compact size of the chip allows easy deployability. As a result, it has the potential for use for Point-of-Care testing