Size exclusion chromatography applications for separating macromolecules based on subtle differences in size typically use resins with large and varied pore sizes in long chromatography columns. However, for buffer exchange and desalting applications, it is mainly the maximum effective pore size (exclusion limit or molecular weight cut off (MWCO) of the resin) that determines the size of molecules that can be separated. Molecules that are significantly smaller than the MWCO penetrate into the pores of the resin, while molecules larger than the MWCO are unable to enter the pores and remain together in the void volume of the column. By passing samples through a column resin bed with sufficient length and volume, macromolecules can be fully separated from small molecules that travel a greater distance though the pores of the resin bed. No significant separation of molecules larger than the exclusion limit occurs.
In order for the desired macromolecules to remain in the void volume, resins with very small pores sizes must be utilized. For typical desalting and buffer exchange applications choosing a resin with a molecular weight cut off between 5 and 10KDa is usually best. For other applications, such as separating peptides from full-sized proteins, resins with larger exclusion limits may be necessary. The macromolecular components are recovered in the buffer used to pre-equilibrate the gel-filtration matrix, while the small molecules can be collected in a later fraction volume or be left trapped in the resin. One important feature to note when choosing a resin is that the small molecules targeted for removal must be several times smaller than the MWCO for proper separation.