Lab & analytical techniques · Reference
What is gel electrophoresis?
Gel electrophoresis separates DNA, RNA, or proteins by driving them through a porous gel with an electric field, so molecules sort by size and charge as smaller ones travel further.
The physics of the separation
Nucleic acids carry a uniform negative charge from their phosphate backbone, so in an electric field they migrate towards the positive electrode. As they move through the cross-linked mesh of a gel, they are sieved by size: short molecules thread through the pores easily and travel far, while long molecules are held back. After a set time the field is switched off and the separated molecules form bands. Staining — for example with a fluorescent dye — makes the bands visible, and their positions are compared with a size marker to estimate length.
Agarose versus polyacrylamide
The gel material is chosen to match the molecules. Agarose gels have large pores and are used to separate medium-to-large DNA and RNA fragments.
Polyacrylamide gels have a finer, more uniform mesh and resolve smaller fragments and proteins at high resolution. In SDS-PAGE, proteins are coated with a detergent that gives them a uniform charge, so they separate essentially by size alone.
Uses in research
Gel electrophoresis is a routine step in molecular biology. Researchers use it to check the size and purity of DNA fragments after PCR or restriction digestion, to assess RNA integrity, and to separate proteins prior to detection. It is the separation step that precedes a Western blot, and it underlies many fragment-sizing and fingerprinting methods used in genetics and forensics research.
Key facts
At a glance
- Separates: DNA, RNA, or proteins by size and charge
- Driving force: an applied electric field
- Medium: a porous gel that sieves molecules
- DNA/RNA gels: usually agarose
- Protein/small-fragment gels: polyacrylamide (e.g. SDS-PAGE)
- Readout: stained bands compared with a size marker
Common questions
FAQ
How does gel electrophoresis separate molecules?+
An electric field pulls charged molecules through a porous gel. Smaller molecules pass through the pores more easily and travel further than larger ones, so the sample resolves into bands sorted by size.
What is the difference between agarose and polyacrylamide gels?+
Agarose gels have larger pores and are used for medium-to-large DNA and RNA fragments, while polyacrylamide gels have a finer mesh that resolves smaller fragments and proteins at higher resolution.
The step most authors miss
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