Gel electrophoresis is a laboratory technique used to separate DNA fragments so scientists can compare, identify, or analyze them. It matters in genetics, forensics, medical testing, and biotechnology because DNA samples often contain many fragment sizes mixed together. By turning invisible DNA pieces into visible bands, electrophoresis makes molecular evidence easier to interpret.
The pattern of bands can show whether a gene is present, whether a DNA sample matches another, or whether a reaction worked.
Key Facts
- DNA has a negatively charged phosphate backbone, so it moves toward the positive electrode in an electric field.
- Smaller DNA fragments move faster and farther through agarose gel than larger fragments.
- Migration distance is roughly inversely related to fragment size: smaller size means greater distance traveled.
- A DNA ladder contains fragments of known sizes and is used as a ruler for estimating sample fragment lengths.
- Electric field strength can be estimated with E = V/d, where V is voltage and d is electrode distance.
- DNA bands become visible after staining because many DNA molecules of the same size collect at the same position.
Vocabulary
- Agarose gel
- A porous gel made from agarose that acts like a molecular sieve for separating DNA fragments by size.
- Electrophoresis
- A method that uses an electric field to move charged molecules through a medium.
- DNA ladder
- A reference sample containing DNA fragments of known lengths used to estimate the sizes of unknown fragments.
- Band
- A visible line in the gel where many DNA fragments of the same or similar length have collected.
- Well
- A small pocket molded into the gel where DNA samples are loaded before the electric field is applied.
Common Mistakes to Avoid
- Loading DNA near the positive electrode, which is wrong because negatively charged DNA must start near the negative electrode to move through the gel toward the positive side.
- Assuming larger DNA fragments travel farther, which is wrong because larger fragments are slowed more by the gel pores and stay closer to the wells.
- Ignoring the DNA ladder, which is wrong because the ladder is needed to estimate fragment sizes instead of judging size by appearance alone.
- Running the gel at too high a voltage, which is wrong because excess heat can distort bands, melt the gel, or reduce separation quality.
Practice Questions
- 1 A gel is run with the wells near the negative electrode. A DNA sample has fragments of 200 bp, 800 bp, and 1500 bp. List the fragments from farthest traveled to closest to the wells.
- 2 The electrodes in a gel box are 12 cm apart and the power supply is set to 96 V. Calculate the electric field strength using E = V/d.
- 3 Two samples produce the same band pattern as each other, but one sample has much fainter bands. Explain what this suggests about fragment size and DNA amount.