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Description:
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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 . |