How are DNA fragments separated in gel electrophoresis?

DNA fragments are separated in gel electrophoresis based on size and charge. In this technique, an electric current is applied to a gel matrix that contains the DNA samples. DNA molecules are negatively charged due to the phosphate backbone of the DNA structure. When the electric current is turned on, the DNA fragments migrate toward the positive electrode.

Smaller DNA fragments move through the gel matrix more easily and travel faster than larger fragments. This size-based separation occurs because larger fragments encounter more resistance within the gel's pores, which slows their movement. Thus, after a set period of time, the fragments will be arranged in a pattern where smaller ones are further away from the well than larger ones. The result is a size-based separation that can be visualized, typically through staining, allowing for the analysis of the different DNA fragment sizes.

Other methods mentioned—like temperature differences or color differences—do not apply to the principles of separation in gel electrophoresis. Molecular weight generally correlates with size but is not directly used as a method for separation in the context of electrophoresis; thus, it is not the most accurate way to describe the separation process in this technique.