The final step is elution, which usually requires centrifugation, although vacuum systems are also widely used. As with any lab procedure, many factors must be considered, such as downstream application, budget, space, and ease of use. Premade kits have the advantage of having predictable time and expense, and are usually very simple to use. When choosing a HT plasmid prep system, the intended use of the plasmid must be considered. At the other end of the purity spectrum are PCR and DNA sequencing, both of which can generally tolerate lower levels of plasmid purity.
Purity is an expression of the relative amounts of impurities and contaminants.
Impurities include bacterial DNA, RNA, carbohydrates, and endotoxins, whereas contaminants are substances added during preparation such as residual solvents and ligands. The advantage of a kit is that the provider has already taken care of quality control issues. Nevertheless, there are so many variables involved that finding the best system requires empirical testing. For example, different combinations of bacterial host strain and plasmid can result in different levels and types of impurities that can affect different extraction systems. An additional consideration is waste disposal, though the trend has been to use smaller volumes, solid phase systems, and fewer toxic organic solvents.