describe and explain how gel electrophoresis is used to separate DNA fragments of different lengths

Principles of Genetic Technology: Gel Electrophoresis

What is Gel Electrophoresis? 🧬⚡

Gel electrophoresis is a laboratory technique that separates DNA fragments based on their size. Think of it as a race track for tiny beads (DNA fragments) where the longer beads move slower and the shorter ones zip ahead. The track is made of a jelly‑like substance called agarose gel, and an electric field pulls the negatively charged DNA through it.

How Does Size Affect Migration? 📊

The gel acts like a sieve. Smaller fragments find more pathways and move faster. The relationship can be summarised by:

$$v = \mu E$$

where v is the velocity, μ is the mobility (depends on fragment size), and E is the electric field strength. Because μ decreases with increasing fragment length, longer DNA strands travel more slowly.

Step‑by‑Step Procedure

1. Prepare an agarose gel (usually 0.8–2% depending on fragment size).
2. Load DNA samples into wells using a pipette.
3. Apply an electric field (typically 5–10 V/cm).
4. Run the gel until the dye front has migrated an appropriate distance.
5. Stain the gel with a DNA‑binding dye (e.g., ethidium bromide or SYBR Safe).
6. Visualise under UV light and capture an image.

Typical Gel Composition

Practical Example

Suppose you run a gel with fragments of 100 bp, 500 bp, and 1000 bp. After running, you might observe:

• 100 bp fragment at the farthest distance from the well.
• 500 bp fragment midway.
• 1000 bp fragment closest to the well.

This clear separation demonstrates the principle that shorter fragments migrate faster.

Common Mistakes to Avoid ❌

• Loading too much DNA can cause smearing.
• Using a gel concentration that is too low for large fragments leads to poor separation.
• Running the gel for too long can cause the dye front to reach the top, losing resolution.

Quick Summary