What factors affect the rate of migration of nucleic acids in agarose gels?

The rate of migration of nucleic acids in agarose gels is affected by several different factors including: 

• Agarose Concentration: Agarose concentration determines the pore size of the gel, which affects DNA migration. Higher agarose concentrations result in smaller pore sizes, which typically result in slower migration but improves the separation of smaller DNA molecules. 
• Molecular Weight: The rate of migration of a duplex DNA fragment is inversely proportional to the log molecular weight. When log molecular weight is plotted against mobility a straight line is obtained. 
• Type of agarose: Available agarose differ considerably in terms of pore size, gel strength, melting point, and sieving capacity. All of these factors affect migration of DNA 
• DNA Size: Smaller-sized DNA molecules migrate through the gel faster than larger sized molecules. 
• DNA conformation: Supercoiled DNA, which is tightly coiled and compactly packed, moves fastest through the gel. Linear and relaxed open circular DNA forms migrate more slowly because of their extended conformation. Supercoiled DNA usually moves faster than relaxed DNA because it is tightly coiled and hence more compact.
• Voltage applied: In general, higher voltage facilitates faster migration. At low voltage of 5V/cm, the migration rate is precisely proportional to the voltage applied. However, when the voltage is increased, the rate of migration rate of high molecular weight DNA.
• Presence of intercalating dyes: Intercalation, caused by intercalating dyes such as ethidium bromide, alter the length, charge, and super-helicity of DNA molecules, which affects their rate of migration.