* The "in vivo transposition frequency" data here refers to the relative number of colonies obtained containing transposon insertions following electroporation of electrocompetent E. coli cells with a synaptic complex (Transposome™ Complex) formed between a transposon and the respective transposase.

** HyperMu™ MuA Transposase can insert transposons with Mu Ends having free 3'-termini into another DNA, but is unable to excise the transposon from another DNA.

Transposition efficiency is one important criterium for judging a transposon system. High transposition efficiency is especially desirable for insertion of primer-binding sites into large BAC or fosmid clones in vitro in order to determine its complete sequence. High transposition efficiency is also important for insertion of a transposon into DNA in a living cell in vivo. EZ-Tn5 Systems have very high transposition efficiencies for in vitro insertion, as well as for in vivo insertion of an EZ-Tn5 Transposome™ Complex, the synaptic complex formed between an EZ-Tn5 Transposase and an EZ-Tn5 Transposon. Although Epicentre's HyperMu™ MuA Transposase is at least 50 times more active for in vitro transposition than the MuA transposase from other suppliers and almost as active as the EZ-Tn5 System in vitro, the HyperMu Transposome™ Complex generates 10-100 times fewer insertions than the EZ-Tn5 System in vivo using E. coli. Tn7-based transposon systems are quite efficient for in vitro insertion, but have undetectable activity as a synaptic complex, probably because the active Tn7 transposase consists of 3 proteins, which may be difficult to electroporate into the cell as a complex. The Ty1 system has very low transposition efficiency.

For most applications, it is also important that transposition is random. Based on our experience with different systems, we believe that the EZ-Tn5 System is the most random. However, all four transposon systems seem to be sufficiently random for most applications, including for determining the complete sequence of BAC or fosmid clones. Although Tn7 insertion is highly specific in the presence of the TsnE Protein, target specificity is not observed using a transposase consisting of only the TsnABC proteins. A study comparing all systems using transposons with the same selectable marker and other identical transposon features into identical target sequences has not been published. Comparisons using different selectable markers or other transposon features, or different targets are flawed because variations in transposon features and in the DNA target chosen can affect which insertions are viable and selected for analysis.

In general, it is desirable that the length of the transposase recognition sequences in the "transposon ends" are short when primer binding sites in the transposon are used for sequencing. Shorter transposon ends maximize sequence data obtained from the target DNA and minimize undesired sequence data from the end of the primer to the end of the transposon.