The column geometry which provides a good distribution of cleaning solution is essential for complete removal of contamination. Especially in the region around the adaptor sealings, dead spaces have to be avoided because of their susceptibility to contamination with microrganisms. Most important is the nature of the sample and the total amount of crude extract injected onto the column. In general, each column should be cleaned thoroughly after each separation step or at least after the experiments have been finished. Cleaning of the column has to be considered also when the gel bed is changing colours or the back pressure is increasing.
Various methods are feasible for cleaning chromatographic media.
Chemical stability of the material and the type of contamination have to be taken into consideration. In addition to organic solvents, bases and acids are being used. They can also withstand treatment with acids in contrast to media based on carbonhydrates. In case of anion exchangers with quaternary ammonium groups, application of 1 M NaOH should not be long-termed because it may cause successive cleavage of the functional groups. 1-2 column volumes can be applied without causing any problems.