Seeing My DNA on a Gel—My Gel Electrophoresis Breakthrough

 After PCR, I needed to visualize the fragments, so I tackled gel electrophoresis. The idea of separating DNA by size in an agarose gel intrigued me, but casting my own gel was nerve-wracking. I practiced pouring melted agarose into a tray, inserted a comb for wells, and let it solidify. Then I loaded my PCR sample mixed with loading dye and ran the apparatus at 100 V.

I watched the bands migrate toward the positive electrode—smaller fragments moving faster. By placing a DNA ladder in the first well, I could estimate fragment sizes. Sketching the setup and drawing the band pattern helped cement why ethidium bromide (or GelRed) intercalates with DNA and fluoresces under UV light.

Sample SPM Question
“Explain how gel electrophoresis separates DNA fragments and how you determine fragment size.”
• DNA is negatively charged and moves through agarose toward the anode; smaller fragments travel farther.
• A DNA ladder with known fragment sizes is run alongside samples for comparison.