The conditions to play around with are:
- glycerol concentrations 0 to 10%
- polyacrylamide concentration or bis to acrylamide ratios
- matrix type. MDE gels are a modified acrylamide derivative that in some
cases give much better resolutions of SSCP
- gel running temperature, 4 degrees C to room temperature
- power of electrophoresis. constant power from 4W to 10W. this obviously
will affect the gel temperature if you do not have an efficient cooling
system or if you do not have Stratagene's special SSCP power supply unit.
Different conditions may be needed for different sized DNA fragments.
There is a huge development time involved in setting up SSCP conditions
because situations are always different. If there is someone else SSCPing the
same size of DNA as yours, their conditions may not be suitable because
sequence differences are so important.