The major task in plasmid isolation methods is to separate Plasmid DNA from genomic DNA. Here we have compared some of the important differences that can be valuable to understand plasmid isolation. These differences are utilized by some of the commonly used plasmid isolation methods such as Alkaline lysis and boiling lysis methods.
| Properties | Genomic DNA | Plasmid DNA | Remarks |
| Nucleic acid type | Double-standard DNA | Double-standard DNA | |
| Building blocks | Deoxyribonucleotides | Deoxyribonucleotides | |
| Size | Relatively very large | Small | Some plasmids are high molecular weight and require special methods for isolation |
| Geometry | Circular/Linear and tangled | Covalently-closed circular and supercoiled | Linear plasmids also exist |
| Solubility | Less soluble | Highly soluble | Due to their small size, plasmids dissolve rapidly |
| Reanealing after denaturation | Often form precipitate due to random association between both strands | Annealed in the right orientation due to its small size and supercoiled closed circular structure, remains soluble | A basis for the alkaline lysis method |
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