Dna electrophoresis in photopolymerized polyacrylamide gels on a microfluidic device

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Title: Dna electrophoresis in photopolymerized polyacrylamide gels on a microfluidic device
Author: Lo, Chih-Cheng
Abstract: DNA gel electrophoresis is a critical analytical step in a wide spectrum of genomic analysis assays . Great efforts have been directed to the development of miniaturized microfluidic systems ( ?lab -on -a -chip ? systems ) to perform low -cost , high -throughput DNA gel electrophoresis . However , further progress toward dramatic improvements of separation performance over ultra -short distances requires a much more detailed understanding of the physics of DNA migration in the sieving gel matrix than is currently available in literature . The ultimate goal would be the ability to quantitatively determine the achievable level of separation performance by direct measurements of fundamental parameters (mobility , diffusion , and dispersion coefficients ) associated with the gel matrix instead of the traditional trial -and -error process . We successfully established this predicting capability by measuring these fundamental parameters on a conventional slab gel DNA sequencer . However , it is difficult to carry out fast and extensive measurements of these parameters on a conventional gel electrophoresis system using single -point detection (2 ,000 hours on the slab gel DNA sequencer we used ) . To address this issue , we designed and built a new automated whole -gel scanning detection system for a systematic investigation of these governing parameters on a microfluidic gel electrophoresis device with integrated on -chip electrodes , heaters , and temperature sensors . With this system , we can observe the progress of DNA separation along the whole microchannel with high temporal and spatial accuracy in nearly real time . This is in contrast to both conventional slab gel imaging where the entire gel can be monitored , but only at one time frame after completion of the separation , and capillary electrophoresis systems that allows detection as a function of time , but only at a single detection location . With this system , a complete set of mobility , diffusion , and dispersion data can be collected within one hour instead of days or even months of work on a conventional sequencer under the same experimental conditions . The ability to acquire both spatial and temporal data simultaneously provides a more detailed picture of the separation process that can potentially be used to refine theoretical models and improve separation performance over ultra -short distances for the nextgeneration of electrophoresis technology .
URI: http : / /hdl .handle .net /1969 .1 /ETD -TAMU -2685
Date: 2009-05-15

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Dna electrophoresis in photopolymerized polyacrylamide gels on a microfluidic device. Available electronically from http : / /hdl .handle .net /1969 .1 /ETD -TAMU -2685 .

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