How does size affect the movement of DNA fragments in gel electrophoresis?

In gel electrophoresis, the movement of DNA fragments through the gel matrix is primarily influenced by their size. Smaller fragments encounter less resistance from the gel's porous structure, allowing them to navigate through the gel more easily and, consequently, move faster compared to larger fragments. The gel is made up of a network of fine pores, and as DNA fragments migrate toward the positive electrode, they must traverse these pores. Larger fragments, due to their size, get stuck more frequently within the gel matrix, resulting in slower movement. This is why, when running a sample of DNA in gel electrophoresis, you will observe that smaller fragments are found further down the gel compared to the larger ones after the electric field is applied.

Understanding this principle is essential for effectively analyzing DNA fragments in various applications such as genetic fingerprinting, PCR product analysis, and cloning, where size differentiation is crucial for interpretation.