The 5' end of DNA is not considered negative in the same way the sugar-phosphate backbone is. The negative charge in DNA comes from the phosphate groups in the sugar-phosphate backbone, not a specific end. DNA molecules migrate towards the positive electrode during gel electrophoresis because of this overall negative charge.
Understanding DNA's Negative Charge
The phosphate backbone of DNA is negatively charged due to the presence of bonds between phosphorus and oxygen atoms. (Byjus.com) This negative charge is consistent throughout the DNA molecule, not localized to one end.
While the 5' and 3' ends of DNA are chemically distinct due to their terminal groups (a phosphate group at the 5' end and a hydroxyl group at the 3' end), this doesn't determine which end is "negative" in terms of electrical charge. The negative charge arises from the phosphate groups present along the entire sugar-phosphate backbone.
Gel Electrophoresis and DNA Movement
Many references highlight how the negative charge of DNA facilitates its movement in gel electrophoresis: "A molecule with a negative charge will therefore be pulled towards the positive end (opposites attract!). DNA is negatively charged, therefore, when an electric current is applied, it moves towards the positive electrode." (yourgenome.org). This demonstrates the overall negative charge of the DNA molecule, but not a directional negativity at either end.
