Numerical and Experimental Studies on DNA Combing Used in Fabricating Nanochannel Electroporation (NEP) Chips

Abstract

Microelectromechanical processes were used to generate a stamp with array of micro pillars. This stamp was subjected to DNA combing and imprinting to form nanostrands between the micro pillars, followed by sputter coating with gold, vapour deposition and imprinting processes in order to produce the required nanochannels for the gene chip. These preparation processes have been widely used to create implementations for cell manipulation and electroporation. However, the underlying mechanism of DNA stretching has only been demonstrated experimentally and is not fully understood. It, therefore, arrives unstable yield rate when process parameters are changed. This study investigated the DNA combing and imprinting processes using two-phase flow and moving mesh methods to analyse the variation of flow field at the micron level. It shows that while withdrawing from water, a smaller velocity difference in each location and the velocity difference of pillars are the major determinants of DNA stretching and curing. The simulation results showed that a bigger α and θ led to a greater difference in flow velocity on the PDMS stamp surface; greater flow velocity difference could affect the adhesion of DNA (subsequently compromising the formation of the nanochannels). As suggested by our experimental data, longer nanochannels (3 μm) displayed a wider range of stretching speed with yield rate >90%.