What is the most commonly used technique to separate DNA molecules by size?

Gel electrophoresis

The process of cutting DNA using restriction endonucleases results in the formation of DNA fragments. These fragments can be separated using a technique called gel electrophoresis.

Since DNA fragments are negatively charged molecules, they can be separated by applying an electric field, causing them to move towards the anode through a medium or matrix.

Agarose, a natural polymer extracted from seaweeds, is commonly used as the matrix.

The DNA fragments separate based on their size due to the sieving effect provided by the agarose gel. Smaller fragments move farther compared to larger fragments.