Molecular Sorting: Gel Electrophoresis

Part of the series: Biochemical Tools

You are a biochemist holding a sample containing a tangle of DNA fragments. For your experiment, you need just one specific piece. This leaves you with two essential challenges:

How do you isolate your target fragment from the rest?

How can you confirm that you have isolated the correct one?

The solution, one of the most valuable tools in modern biology, is a technique known as gel electrophoresis. This is the story of how we harness electricity and a porous gel to bring precise order to molecular complexity.

The Core Principles

Gel electrophoresis separates molecules by exploiting their fundamental physical properties: size and charge.

• DNA, RNA, and proteins carry a net charge under the conditions of gel electrophoresis. For DNA and RNA, the negatively charged phosphate backbone provides a uniform negative charge. Proteins are more complex; we often use the detergent SDS (sodium dodecyl sulfate) to coat them, masking their native charge and giving them a uniform negative charge.

• When placed in an electric field, charged molecules migrate and negatively charged molecules move toward the positive electrode (anode).

• The gel matrix acts as a molecular sieve, allowing smaller molecules to move through the gel quickly and slowing down larger molecules.

How I imagine what a DNA fragment in the gel matrix might look like.

What is the result?

After a set time, the electrical current is turned off, and the once-complex mixture is ordered into discrete bands based on size. By comparing these bands with known bands on a ladder, a biochemist can confidently identify the exact fragment of interest.