Electrophoresis is a common lab technique used to identify,
quantify, and purify nucleic acid fragments and assess quality.
RNA molecules are negatively charged, and during gel
electrophoresis they migrate toward the anode in the presence of
an electric current. The length of RNA generally determines its
migration in the gel, since longer RNA molecules move slower
than shorter fragments. However, RNA molecules are subject to
extensive secondary structure via intramolecular base pairing,
and this can affect their gel migration. For most applications,
RNA is run using denaturing conditions to disrupt secondary
structure. For applications such as resolving different
conformations of RNA, native (or nondenaturing) gels are
recommended. Nondenaturing RNA Electrophoresis Gel
electrophoresis of RNA under nondenaturing conditions maintains
the secondary structure of RNA molecules. Agarose is generally
preferred to acrylamide because it has lower toxicity and, at
the concentrations needed to resolve typical RNA molecu