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Agarose and polyacrylamide gels differ significantly in their applications for gel electrophoresis. Agarose gels, with larger pore sizes, are ideal for separating larger DNA fragments ranging from several hundred to tens of thousands of base pairs, making them suitable for genotyping and visualization of macromolecules like mucins [2][6]. Polyacrylamide gels, due to their smaller and more controllable pore sizes, provide high-resolution separation for smaller DNA fragments (5-500 base pairs), RNA, and proteins, making them essential for detailed protein analysis and small DNA fragment separation [1][3][4]. Additionally, polyacrylamide gels can achieve better precision in pore size control, enhancing their resolution capabilities [5].

Reference

[1] Stellwagen, N. (2009). Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution. ELECTROPHORESIS, 30.

[2] Day, I., & Humphries, S. (1994). Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose.. Analytical biochemistry, 222 2, 389-95 .

[3] Aksoy, N., & Unlu, S. (2003). Increased Resolution of Macromolecules with Agarose Gel Electrophoresis Compared with Polyacrylamide Gel Electrophoresis. Macromolecular Bioscience, 3, 482-486.

[4] Craig, W., Poulin, S., Ledue, T., & Kamboh, M. (1993). Apolipoprotein (a): A comparison of isoforms identified by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis or by sodium dodecyl sulfate‐agarose gel electrophoresis. ELECTROPHORESIS, 14.

[5] Roncada, P., Cretich, M., Fortin, R., Agosti, S., Franceschi, L. D., Greppi, G., Turrini, F., Carta, F., Turri, S., Levi, M., & Chiari, M. (2005). Acrylamide‐agarose copolymers: Improved resolution of high molecular mass proteins in two‐dimensional gel electrophoresis. PROTEOMICS, 5.

[6] Plan, E., Seneterre, J., Caudie, C., & Quincy, C. (1986). Comparison between agarose gel electrophoresis (Panagel) of cerebrospinal fluid with silver staining, and polyacrylamide disc gel electrophoresis for demonstration of the oligoclonal pattern in neurological disorders. ELECTROPHORESIS, 7.

Rudraraju Niharika we use agarose gel electrophoresis for qualitative analysis but we use the SDS-polyacrylamide gel electrophoresis for quantitative analysis against marker standard

Agarose and polyacrylamide gels both are used in gel electrophoresis, but they are used for different purposes due to their different properties.

For eg. The composition of agarose gel - It is extracted naturally from seaweed agar, which is a polysaccharide and forms a porous matrix when solidifies.

whereas polyacrylamide gel is a synthetic polyacrylamide, which is formed by polymerizing acrylamide and bisacrylamide.

They also differ in pour size agarose has larger pour size, hence use full for separating DNA and RNA and involved in qualitative analysis, but apparently the pour size of polyacrylamide is smaller in size and generally used for separating protein and do quantitative analysis.

Agarose has larger pore size what makes it suitable for DNA extraction while Polyacrylamide gel has smaller pores making it suitable for small nucleotides and proteins.

Polyacrylamide gel is more precise and has high resolution.

Furthermore, we can add SDS, a denaturant in Polyacrylamide gel and make it suitable to unfold the protein and charge it negative so that it can be separated. While in agarose no charge inducer or denaturant is required.

Rudraraju Niharika

Agarose and polyacrylamide gels are both used in gel electrophoresis, but they have key differences:

These differences make each type of gel more suitable for specific types of molecules and experiments.

for more information refer to below pdf:

https://www.cshlpress.com/pdf/sample/2013/MC4/MC4FM.pdf