Why do DNA fragments move different distances in an agarose gel during electrophoresis?

• A. They have different base sequences
• B. They have different lengths / sizes / masses
• C. They are bound to different proteins
• D. They are all equally charged

Answer: (B)

DNA fragments move different distances in an agarose gel mainly because their size determines how easily they travel through the gel’s porous matrix. When an electric field is applied, DNA carries negative charges along its backbone and migrates toward the positive electrode. The gel acts like a sieve: larger fragments have more length and mass to contend with, so they experience more resistance and move more slowly, covering a shorter distance in a given time. Smaller fragments fit through the pores more easily and thus travel farther. The base sequence of a fragment doesn’t significantly change its movement under standard conditions, and DNA is not typically bound to proteins in a normal gel run, which would alter mobility. So the distance migrated reflects the fragment’s length/size/mass.