Real-World Problem:  Gel Electrophoresis

Gel electrophoresis is a standard molecular biological technique for separating nucleic acids and proteins by size.  DNA, RNA or protein samples are placed in a special gel and subjected to an electric field. Negatively-charged nucleic acid fragments or proteins move toward the positive electrode while positively-charged ones move toward the negative electrode. Those fragments or molecules that are smallest travel farthest from their original location in the gel, while the largest ones remain closest to the origin. After the samples have been separated, the resulting bands are stained with dyes such as ethidium bromide or methylene blue so that they can be seen. 

Fragments of DNA from 200 to 50,000 base pair (bp) can be separated using standard electrophoresis techniques.  DNA strands have a phosphate-sugar backbone with two negatively-charged phosphate compounds per base pair.  The molecular weight of an average base pair is 635 daltons (a dalton is the mass of a single hydrogen atom, or a proton).  The molecular weight of DNA in a haploid nucleus is 1.9x10 12 daltons.  Typical DNA analysis using gel electrophoresis takes 30 to 60 minutes.  With this information, what is the net force on a DNA fragment as it migrates toward the positive electrode?

A Physlet that simulates gel electrophoresis can be found at: http://webphysics.davidson.edu/applets/biogel/biogel.html
Try varying the different parameters and observe the results.  The electric field can be adjusted from 0.1 to 5.9, but no units are given.  If a typical gel box measures 4" x 7" and uses an applied voltage of 50 to 150 volts, what units are implied in this simulation?  What happens to the rate of migration as the strength of the electric field is increased?  Is the effect linear or non-linear?  Make a qualitative sketch of the rate of migration as a function of the applied electric field.  What could explain the fact that as the applied voltage is increased, larger DNA fragments migrate proportionally faster than smaller fragments?  What would happen if the electrodes were points instead of lines?  What other physical insights can be learned from this application of an electric field for biological analysis?

Web resources that may be of interest:
http://web.utk.edu/~khughes/GEL/sld001.htm
http://gslc.genetics.utah.edu/units/activities/electrophoresis