Bacterial IS elements (Insertion Sequence) and equivalent eukaryotic elements have a diagnostic structure: a central protein coding region containing genes for transposition enzymes; flanking Inverted Repeats that serve as recognition sequences for the transposase; and distal flanking short direct repeats. The Inverted Repeats are part of the transposon and are the same for all copies in a genome. Distal flanking repeats are derived from the host DNA and are different at each site of insertion.
For an inverted repeat the two copies of the repeated sequence are on opposite strands of the DNA. They are thus read 5’ – 3’ in inverted orientation. Conversely, for a direct repeat the two copies of the repeated sequence are on same strand of the DNA and are read 5’ – 3’ in the same direction.
|Excision||In the first step of transposition, the IS element is excised from the DNA at the outside edges of the inverted repeats, and the target DNA undergoes a staggered cleavage.|
|Ligation||In the second step, the excised IS element is ligated to the exposed 5’ ends of the target DNA.|
|Filling In||Filling in of the gaps left by the staggered cleavage and ligation results in complete insertion into the target with a duplication of the sequence between the staggered cuts.|