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Your PCR product will need to get cloned in a plasmid and the plasmid needs to be isolated first from a bacterial culture. During plasmid isolation using the Zymo Zyppy miniprep kit, cells are lysed with an alkaline lysis buffer which denatures cellular components, including our plasmid. This reaction is neutralized with an acidic buffer which renatures the cellular components into a chunky mixture which is then centrifuged, thus leaving a supernatant and a pellet in the tube. Where is the plasmid and why?
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