Diagnostic Methods in Biotechnology: Electrophoresis
What is the role of electrophoresis in modern molecular biology? Discover the fundamental principles, safety risks, and strategic advantages of this matrix-based separation technique.
Fundamentals and Principles of Gel Electrophoresis
Electrophoresis is one of the diagnostic techniques widely used in molecular biology and biotechnology.
The basic principle of electrophoresis is based on the separation of molecules with a specific charge in an electric field, as they move toward the electrode with the opposite charge.
Its purpose is to separate biomolecules such as DNA, RNA, and proteins based on their molecular weight.
When these charged biomolecules are placed in a specific separating medium under a specific electric field, they migrate.
This separating medium is a special matrix, such as agarose gel or polyacrylamide.
Choosing the Right Separating Medium: Agarose vs. Polyacrylamide
So, what type of separating medium should we use?
Agarose gel or polyacrylamide gel?
The choice between these two depends entirely on the size of the biomolecules you want to analyze.
Smaller molecules, such as proteins, require better resolution, so polyacrylamide gel electrophoresis (PAGE) is used. However, for larger molecules, such as DNA, agarose gel is used.
This matrix contains pores of different sizes, allowing molecules to migrate based on their size.
For example, electrophoresis is most commonly used in the following applications:
• It is used to verify the accuracy of products amplified using the PCR technique.
• It is used in restriction fragment analysis.
Although the separation of biomolecules by electrophoresis is sufficient for diagnosis on its own, in some cases it serves as a preliminary step.
For example, when information about the nature of biomolecules is needed, additional techniques such as Western blotting or Southern blotting are applied after the electrophoresis process.
However, this is the subject of another article.
In cases such as paternity testing or any other forensic cases, a clinical diagnosis can be made using a technique called DNA fingerprinting, in which electrophoresis is again important.
Advantages of Electrophoresis
It is a low-cost technique; it can be performed using a simple electrophoresis apparatus and a power supply.
It is advantageous because it can be used for all types of biomolecules, including DNA, RNA, and proteins.
Biomolecules separated in the gel can be recovered by cutting the gel; this makes it an effective method for purifying biomolecules.
Although agarose gel or polyacrylamide gel electrophoresis is much simpler and older than sequencing techniques for determining DNA sequences, it is a widely used technique for rapid decision-making processes, such as checking sample quality.
Disadvantages of Electrophoresis
Although it is a simple method, it can be somewhat labor-intensive, especially until you learn how to cast polyacrylamide gels.
The number of samples you can separate in the gel is limited by the loading area (wells); in other words, it is not a high-throughput technique.
The separated biomolecules are visualized indirectly through staining rather than directly, so the method is semi-quantitative in nature.
Although there are dyes available today that are considered less harmful, ethidium bromide—which is known to be carcinogenic—is still commonly used in routine laboratories for DNA visualization.
Although it can be easily performed by trained individuals, if factors such as buffer pH, voltage adjustments, and gel concentration are not properly set by inexperienced users, the resolution—that is, the separation power—will be weak, and the expected benefits will not be achieved.
At Rapdi Biotech, we also frequently use electrophoresis in the development of aptamer-based biosensors, particularly to verify the sizes of the products obtained after PCR.
If you are working on aptamer selection or biosensor validation, optimizing your electrophoresis parameters is critical; therefore, at Rapdi Biotech, electrophoresis conditions are important to us.
For any questions or consultation needs regarding your research on this type of aptasensor technology, please feel free to contact us at any time.
References:
Lee, P. Y., Costumbrado, J., Hsu, C. Y., & Kim, Y. H. (2012). Agarose gel electrophoresis for the separation of DNA fragments. Journal of Visualized Experiments, (62), 3923.
Sonagra, A. D., Zubair, M., & Dholariya, S. J. (2025). Electrophoresis. StatPearls. StatPearls Publishing.
Disclaimer:
The information provided in this article is for educational and informational purposes only, based on current scientific literature. It does not constitute medical advice, diagnosis, or treatment. For any medical concerns or diagnostic needs, always consult with a qualified healthcare professional.