Design and Optimization of a DNA Electrophoretic Stretching Device Using Brownian Dynamics Simulations

• Main Authors: Tsung-Hsien Lin, 林宗賢
• Other Authors: 謝之真
• Format: Others
• Language: zh-TW
• Published: 2011
• Online Access: http://ndltd.ncl.edu.tw/handle/84954853898528129000

碩士 === 國立臺灣大學 === 化學工程學研究所 === 99 === We use Brownian dynamics-finite element method (BD-FEM) to design microfluidic devices that are capable to efficiently and uniformly stretch DNA for the application of gene mapping. Our design is based on the devices proposed by Kim and Doyle[1] that stretches DNA electrophoretically with the electric field gradient generated in a hyperbolic contraction. To enhance DNA stretching, we propose two strategies that pre-condition DNA before they enter the contraction. For the first approach, we pre-stretch DNA in the direction perpendicular to the funnel axis with a expansion geometry. The partially stretched chains are then turned to align with the axial of the funnel, and experience the second stretching. As a result, DNA chains adapt more extended configurations before going into the funnel, and therefore achieve a higher degree of extension. For the second approach, we pre-condition DNA conformation using an oscillating extensional electric field that has been shown to effectively reducing the population of folded DNA at an ideal condition. However, this approach shows negligible effect in our design, and we find that the original prediction was actually wrong due to the erroneous choice of flow filed. We further examine the efficiency of our design for stretching longer DNA. It is found the performance of the pre-conditioning strategy deteriorates with increasing DNA molecular weight. By analyzing the probability distribution of DNA extension in the device, we propose a new design that utilizes the excluded volume effect of the device boundary to prevent the formation of folded DNA. Our simulation results indeed show that the design with both tricks can provide very uniform, highly stretched DNA even under relatively low field gradient.