Systematic Design and Fabrication of DNA Electrophoresis Chip with Nanostructures

Separation of DNA molecules in micro electrophoresis chips with nanostructures has been shown great potential in DNA sequencing, genotyping, identification of DNA polymorphisms in human chromosomes and cancer-related genes genomics. The separation in these devices intrinsically involves multi-scale phenomena. The detailed mechanism of this type of separation is still not fully understood. In this study, we systematically investigate the electrophoretic mobility of large DNA molecules and then construct a macro model to predict spatiotemporal behavior of electrophoretic behavior based on the continuum mechanics.;A novel Biased Reptation model with Electroosmosis (BRE) was developed to predict the electrophoretic mobility of long-chain DNA molecules in microchannels with a sub-micron pillar array. The BRE model incorporates effective electroosmosis into classical biased reptation models. The apparent electrophoretic mobilities of different sizes of long-chain DNA, T4 DNA, and lambda DNA at different electric fields were measured in a fabricated electrophoresis chip for the comparison with various theories. The proposed BRE model shows much better agreement with the experimental results compared to the classical BRM model and the Biased Reptation with Fluctuation (BRF). The average standard error between our proposed BRE model and experimental data is 8.13% without any fitting parameters, while the BRM is 343.01% and BRF is 17.54% with one fitting parameter. The BRE model can be only applied for low porosity sieving matrix (e < 0.5) with pillar spacing larger than twice of the persistence length of a DNA molecule with DNA length larger than 48 kbp. For DNA length smaller than 20 kbp, Ogston model can be applied. For DNA length between 20 kbp and 48 kbp, a hybrid model would need to be developed.;For the micro electrophoresis on a silicon or glass wafer, the electroosmotic mobility of DNA buffers plays an important role in the BRE model. Therefore, theoretical analysis and nonlinear 2D numerical simulations are used to study the concentration difference and Peclet number effect on the measurement error of the electroosmotic mobility in microchannels. We propose a compact analytical model for this error as a function of normalized concentration difference and Peclet number in micro electroosmotic flow with experimental validation. The analytical predictions of the errors are consistent with the numerical simulations.;Finally, the systematic model of DNA electrophoresis in the nanostructures can be used to optimize the design of micro-electrophoresis chip with embedded nanostructures. The optimized pillar spacing was found to be four times the length of persistence length and the separation limitation for large DNA molecules is around 48 kbp with resolution requirement of 0.5 per kbp. With the optimized pillar spacing, the silicon based micro-electrophoresis chip was designed and fabricated based micro-electrophoresis chip were designed and fabricated.