What affects the migration rate of nucleic acid in gel?

The migration rete of nucleic acid in gel is determined by a number of factors, such as:

• Agarose concentration: Higher agarose concentration results in smaller pore sizes, which usually lead to a slower migration.
• Type of agarose: Various types of agarose are currently available on market. They differ in gel strength, pore size, sieving capacity as well as melting point, which could make an impact on the migration of DNA molecules.
• Size of DNA: Small molecules travel faster than the larger ones in gel.
• DNA conformation: Supercoiled DNA usually moves faster than relaxed DNA because it is tightly coiled and hence more compact.
• Voltage applied: Higher voltage is favorable for faster separation; however, the resolution may be compromised, and gel may melt when the voltage is too high.
• Presence of intercalating dyes such as ethidium bromide: The charge, length, as well as the superhelicity of DNA molecules could be altered by the intercalation, thus affecting their movement.