Hello everyone,

I’m currently working on extracting the whole genome of bacteria using the phenol-chloroform method. My goal is to sequence the entire genome, including both chromosomal DNA and plasmids. However, when I run the extracted DNA on a gel, I consistently see multiple bands, which seem to indicate the presence of both chromosomal and plasmid DNA.

I want to ensure that both types of DNA are included in my sequencing but am unsure how to handle the multiple bands issue during electrophoresis.

Does anyone have any suggestions on how to optimize the extraction process or the gel electrophoresis to maintain the integrity of both chromosomal DNA and plasmids without them being separated or causing issues?

Thank you in advance for your help!