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Onset of channeling during DNA electrophoresis in a sparse ordered post array
Jia Ou1, Samuel J Carpenter, Kevin D Dorfman
1Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455 USA.
Biomicrofluidics
|July 21, 2010
Summary
DNA electrophoresis in post arrays shows that DNA channeling, which hinders separation, occurs due to array size and electric fields. This effect is reduced by larger arrays and depends on collision dynamics.
Area of Science:
- Biophysics
- Molecular Biology
- Separation Science
Background:
- DNA electrophoresis is crucial for molecular biology.
- Ordered arrays of posts offer potential for enhanced DNA separation.
- The
- channeling hypothesis
- predicts unhindered DNA movement under specific conditions.
Purpose of the Study:
- To test the
- channeling hypothesis
- for DNA electrophoresis in ordered post arrays.
- To investigate the factors influencing DNA separation and resolution.
Main Methods:
- Studied electrophoretic separation of plasmid DNA (pUC19) and linear DNA (lambda-DNA).
- Utilized a hexagonal array of 1 µm diameter posts with a 7 µm pitch.
- Analyzed DNA behavior at varying electric field strengths using a diffusive model.
Main Results:
- At low electric fields, DNA separation occurred via
- rope-over-pulley
- collisions.
- Resolution was lost at higher fields due to lambda-DNA channeling.
- Channeling at low fields resulted from finite array size, not intrinsic properties.
Conclusions:
- Channeling in DNA electrophoresis is influenced by electric field strength and array dimensions.
- The onset of channeling is a gradual process, not abrupt.
- DNA mobility in post arrays can be higher than predicted by simple collision models.
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