Chapter 8: DNA Electrophoresis

DNA electrophoresis is a fundamental laboratory technique that separates DNA fragments according to their molecular size and electrical charge by applying an electric field through a supporting medium. This chapter examines the theoretical foundations and practical applications of electrophoresis, with particular emphasis on its critical role in forensic DNA analysis and identification. The separation process relies on support matrices such as agarose gels or polyacrylamide gels, each with distinct advantages for different analytical purposes. Polyacrylamide gel formation involves controlled polymerization and cross-linking reactions that establish the porosity and separation capacity of the medium, directly influencing the resolution of fragment separation. Traditional slab gel electrophoresis using both agarose and polyacrylamide matrices remains a foundational methodology in molecular biology laboratories. However, modern forensic applications increasingly depend on capillary electrophoresis, a technique that provides significantly improved resolution, reduced analysis time, and enhanced automation capabilities compared to conventional slab gel methods. The chapter also addresses contemporary miniaturized technologies including microfluidic devices, which integrate multiple analytical functions on a single chip platform and represent the future direction of forensic DNA processing. These integrated and modular microfluidic systems enable sample preparation, amplification, and separation to occur in a unified device, reducing reagent consumption and human handling errors. Additionally, the chapter discusses quantitative methods for determining the molecular weight of DNA fragments, including techniques based on relative migration patterns within the gel matrix and the local southern method, which provides more precise size estimation. Understanding these separation and quantification methods is essential for interpreting DNA profiles in forensic investigations, paternity testing, and other applications requiring accurate fragment identification.