The intended application of the potential tag is an essential factor and restricts the number of suitable tags to be used. In this regard, it is important to decide either for a small-size or a large-size tag according to the application of interest. Smaller tags usually have less effects on structure, activity or characteristics of the tagged protein. While larger tags can be used to improve features of the target protein. A major concern of using larger tags however is the loss/alteration of the biological activity or increased toxicity of the tagged target protein. It might be necessary to remove large tags by either a specific protease recognition site between the tag and the target protein or sequence encoding for a protein with self-splicing capacities.
Another consideration is the location of the tag within the protein of interest. Most of the tags are preferrably placed at the C- or N-terminus of the target protein to avoid interference with active sites. The positioning of the tag at one of the termini moreover ensures the exposure of the tag to the surface of the protein in order to allow the interaction with its ligand (e.g. for purification). In general, the oligonucleotide encoding for a tag is prevalently inserted at the 5’ end of the gene of interest to ensure a good translational initiation. In some cases it might also be possible to choose a location inside the gene sequence.
In order to increase the sensitivity of a tag, especially small-size tags, it is possible to attach tandem copies increasing signal strength and reinforcing signal-to-noise ratio. It is also possible to use a tandem tag system combining features of different tag groups. This is mainly used in the Tandem-Affinity Purification (TAP) allowing the isolation of protein complexes and the reduction of non-specific background based on two consecutive purification steps.