The Tn5 transposon system is a model system for the study of transposition and for the application of transposon mutagenesis. Tn5 is a bacterial composite transposon in which genes (the original system containing antibiotic resistance genes) are flanked by two nearly identical insertion sequences, named IS50R and IS50L corresponding to the right and left sides of the transposon respectively. The IS50R sequence codes for two proteins, Tnp and Inh. These two proteins are identical in sequence, save for the fact that Inh is lacking the 55 N-terminal amino acids. Tnp codes for a transposase for the entire system, and Inh encodes an inhibitor of transposase. The DNA-binding domain of Tnp resides in the 55 N-terminal amino acids, and so these residues are essential for function. The IS50R and IS50L sequences are both flanked by 19-base pair elements on the inside and outside ends of the transposon, labelled IE and OE respectively. Mutation of these regions results in an inability of transposase genes to bind to the sequences. The binding interactions between transposase and these sequences is very complicated, and is affected by DNA methylation and other epigenetic marks. In addition, other proteins seem to be able to bind with and affect the transposition of the IS50 elements, such as DnaA.
The most likely pathway of Tn 5 transposition is the common pathway for all transposon systems. It begins with Tnp binding the OE and IE sequences of each IS50 sequence. The two ends are brought together, and through oligomerization of DNA, the sequence is cut out of the chromosome. After introducing 9-base pair 5 ends in target DNA, the transposon and its incorporated genes are inserted into the target DNA, duplicating the regions on either end of the transposon. Genes of interest can be genetically engineered into the transposon system between the IS50 sequences. By placing the transposon under the control of a host promoter, the genes will be expressed. Incorporated genes usually include, in addition to the gene of interest, a selectable marker to identify transformants, a eukaryotic promoter/terminator (if expressing in a eukaryote), and 3 UTR sequences to separate genes in a polycistronic stretch of sequence.