What do you think are some factors in determining the distance in which molecules move through the gel ?

A number of factors can affect the migration of nucleic acids. This includes;

1. The dimension of gel pores (gel concentration)- The viscosity and the pore size in the support media or gels used for electrophoresis influence the rate of migration. Increased viscosity or gel concentration, slows the migration and increased pole size speeds up the migration.
2. Net charge of the molecule- The net charge of the molecule affects its mobility. The greater the net charge, the greater the mobility or the more quick the molecule migrates. The net charge of a particular compound depends upon the buffer and the resultant PH set by that buffer.
3. Size and shape of the molecule- The larger the size, the slower the molecule will move in electrophoresis.
4. Voltage-Increasing the strength of the electrical field by raising the voltage and increasing the temperature used for the electrophoresis will increase the mobility and rate of migration.
5. The ionic strength of the buffer- the ionic strength of the buffer affects the thickness of the ionic cloud, the rate of migration, and the sharpness of the separated solutes. Increase in buffer strength ionic strength increases the buffer ions in the cloud and slows the movement of molecules.