Difference Between Gel Electrophoresis and SDS PAGE

The main difference between gel electrophoresis and SDS PAGE is that gel electrophoresis is a technique used to separate DNA, RNA, and proteins whereas SDS PAGE is a type of gel electrophoresis used mainly to separate proteins. Generally, SDS PAGE gives a better resolution than the regular gel electrophoresis.  

Gel Electrophoresis and SDS PAGE are techniques in biotechnology that help in the separation of macromolecules based on the charge and size. Typically, gel electrophoresis uses agarose gel stabs for the separation while SDS PAGE uses polyacrylamide gel stabs.  

Key Areas Covered 

1. What is Gel Electrophoresis
     – Definition, Procedure, Importance
2. What is SDS PAGE
     – Definition, Procedure, Importance
3. What are the Similarities Between Gel Electrophoresis and SDS PAGE
     – Outline of Common Features
4. What is the Difference Between Gel Electrophoresis and SDS PAGE
     – Comparison of Key Differences

Key Terms: Agarose, DNA, Gel Electrophoresis, Polyacrylamide, Proteins, SDS PAGE 

Difference Between Gel Electrophoresis and SDS PAGE - Comparison Summary

What is Gel Electrophoresis 

Gel electrophoresis is a technique that separates fragments of macromolecules such as DNA, RNA, and proteins based on their size and charge. During gel electrophoresis, macromolecules move under the influence of an electric field on a gel matrix, which contains pores through which the macromolecules move. Gel electrophoresis is the general technique that analyzes DNA from PCR, RFLP, cloning, DNA sequencing or blotting techniques. Nanoparticles can also be separated by gel electrophoresis. The gel stab is prepared from a polysaccharide called agarose derived from seaweed. Agarose gels consist of long-chain agarose molecules interlinked as a spider web. The video 1 describes the preparation of an agarose gel. 

Both DNA and RNA contain phosphate groups at each of their monomer nucleotide. Hence, they possess equal negative charge throughout the molecule. Moreover, they migrate towards the positive electrode under the electric field. The speed of migration depends on the size of the nucleic acid. Shorter molecules migrate faster through the pores while the larger ones take some time.  

Difference Between Gel Electrophoresis and SDS PAGE

Figure 1: DNA Bands on an Agarose Gel

What is SDS PAGE 

SDS PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) is an analytical technique used to separate charged molecules based on the size. In this process, SDS is used to isolate proteins by denaturing them. As SDS is a detergent; the tertiary structure of proteins is disrupted by it, bringing the folded protein down into a linear molecule. Also, it coats that linear protein molecule with a uniform negative charge. SDS PAGE consists of two gels with different concentrations. The top layer is called the stacking gel to which the samples are loaded while the bottom layer is called the resolving gel. The polyacrylamide concentration of stacking gel is 3.5-4% (large pore size) and it concentrates proteins in one band. The polyacrylamide concentration in the resolving gel is 4-20% (small pore size) and it separates proteins based on their size. The video 2 shows the preparation of an SDS PAGE. 

SDS PAGE provides a quick separation of proteins, aiding the subsequent analysis such as Western blotting.  

Main Difference - Gel Electrophoresis and SDS PAGE

Figure 2: Protein Bands on SDS PAGE

Since the resolving power of SDS PAGE is higher than a regular agarose gel, SDS PAGE helps to separate small DNA fragments with 5-500 bp in size.  

Similarities Between Gel Electrophoresis and SDS PAGE 

  • Gel electrophoresis and SDS PAGE are techniques that separate macromolecules based on their charge and size. 
  • Both techniques use a gel stab with small pores through which macromolecules move. 
  • The driving force is the potential difference between the two electrodes. 

Difference Between Gel Electrophoresis and SDS PAGE 


Gel Electrophoresis: Technique used to separate fragments of macromolecules such as DNA, RNA, and proteins based on their size and charge

SDS PAGE: An analytical technique used to separate charged molecules based on the size 


Gel Electrophoresis: Equal throughout the whole gel; made up of agarose 

SDS PAGE: Two gels with different concentrations; made up of polyacrylamide 

Run Configuration 

Gel Electrophoresis: Horizontal run 

SDS PAGE: Vertical run 

Casting Methodology 

Gel Electrophoresis: Sets as it cools 

SDS PAGE: Sets by a chemical reaction 

Pore Size 

Gel Electrophoresis: Pore size is not uniform; higher the agarose concentration, smaller the pore size 

SDS PAGE: Pore size is uniform; the ratio of acrylamide to bis-acrylamide determines the pore size 


Gel Electrophoresis: 0.5-2%  

SDS PAGE: 6-15% 


Gel Electrophoresis: 50-20,000 bp nucleic acids 

SDS PAGE: 5-250,000 Da proteins 


Gel Electrophoresis: Generally run under native conditions 

SDS PAGE: Denaturing conditions 


Gel Electrophoresis: Simple 

SDS PAGE: A complex process 


Gel Electrophoresis: With ethidium bromide 

SDS PAGE: Coomassie staining or silver staining  


Gel electrophoresis is an analytical technique that separates macromolecules such as DNA, RNA, and proteins based on their size. SDS PAGE is a type of gel electrophoresis mainly used to separate proteins under denaturing conditions. SDS PAGE has a higher resolving power when compared to regular gel electrophoresis. The main difference between gel electrophoresis and SDS PAGE is the type of macromolecules separated and their procedure. 


1. “Gel Electrophoresis.” Khan Academy, 
2. “SDS Polyacrylamide Gel Electrophoresis (SDS-PAGE).” Diamantina Institute, 26 Apr. 2017, 

Image Courtesy:

1. “Gel electrophoresis 2″ Von Mnolf – Photo taken in Innsbruck, Austria () via  
2. “Coomassie3″ By Yikrazuul – Own work () via

About the Author: Lakna

Lakna, a graduate in Molecular Biology & Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things

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