Alkaline Running Buffer is primarily used in molecular biology and biochemistry for the separation and analysis of nucleic acids, particularly DNA, through techniques like agarose gel electrophoresis. Its alkaline nature helps denature DNA, ensuring single-stranded DNA fragments are separated based on size. This buffer is essential for applications such as Southern blotting, where DNA fragments are transferred to a membrane for further analysis. Additionally, it is utilized in plasmid isolation procedures to separate supercoiled DNA from linear or nicked forms. Its role in maintaining optimal pH and ionic conditions ensures accurate and efficient DNA migration during electrophoresis.