Question

Why is alkaline SDS used for plasmid DNA isolation but not for genomic DNA isolation?

Answer 1

Alkaline SDS is used for plasmid DNA isolation as it contains sodium hydroxide and SDS which can used for denaturation. Genomic DNA is longer than plasmid DNA. Once genomic DNA is denatured it becomes tangled and cannot re-anneal properly in potassium acetate solution. But as plasmid DMA is smaller it is capable of re-annealing.

Long genomic DNA is tangled in insoluble glob and become contaminated by tangling with RNA and proteins. So, alkaline SDS used for plasmid DNA isolation but not for genomic DNA isolation.