Amgen Biotech Experience (ABE) Lab Practice Test

After the cells are broken open with alkaline lysis, the solution is very basic and DNA strands are denatured. The neutralized lysis buffer brings the pH back toward neutral and stops this denaturation, while the salts help precipitate SDS and proteins. Plasmid DNA, being small and supercoiled, renatures quickly and stays in solution, whereas the larger chromosomal DNA and most contaminants precipitate and are removed with the debris. This selective washing and precipitation clean up the lysate so the plasmid DNA can be collected in the next steps. So the buffer’s job is to neutralize the alkaline lysis solution and help keep plasmid DNA intact while separating contaminants. It isn’t primarily about denaturing chromosomal DNA (that happens during lysis), it doesn’t mainly remove RNA, and it doesn’t change plasmid copy number.