*Estimation of the size of DNA molecules following digestion with restriction enzymes, e.g., in restriction mapping of cloned DNA.
*Estimation of the DNA concentration by comparing the intensity of the nucleic acid band with the corresponding band of the size marker.
*Analysis of products of a polymerase chain reaction (PCR), e.g., in molecular genetic diagnosis or genetic fingerprinting
*Separation of DNA fragments for extraction and purification.
*Separation of restricted genomic DNA prior to Southern transfer, or of RNA prior to Northern transfer.
*Separation of proteins, for example, screening of protein abnormalities in clinical chemistry.
Agarose gels are easily cast and handled compared to other matrices and nucleic acids are not chemically altered during electrophoresis. Samples are also easily recovered. After the experiment is finished, the resulting gel can be stored in a plastic bag in a refrigerator.
Electrophoresis is performed in buffer solutions to reduce pH changes due to the electric field, which is important because the charge of DNA and RNA depends on pH, but running for too long can exhaust the buffering capacity of the solution. Further, different preparations of genetic material may not migrate consistently with each other, for morphological or other reasons.