The backbone of DNA contains phosphoric acid moieties
which ionize at physiological pH leaving a negatively charged electron
behind. Thus the DNA molecule itself is negatively charged and will
migrate towards a positive charge or an anode.
Agarose is a polysaccharide which forms
a liquid colloid or gel. In an agarose
electrophoresis gel, the matrix is formed from the polysaccharide with
the ìholesî filled with buffer. The DNA molecules
themselves do not move through the gels in a straight line. Rather
they are long, string-like molecules which twist and writhe through the
pores. This movement is referred to as "serpentining"
(after
the way serpents move). Long molecules are more likely to get tangled
and retarded, so on average they migrate more slowly.
Agarose gels can be prepared in different concentrations to produce pores
with different sizes and densities depending upon the molecular
weight of the DNA being separated.
Detection
ethidium bromide---
putting EtBr in gel rather than staining and destaining gives a stronger
signal.
