Schematic representation of cut-and-paste transposition. (A) Transposition of Tc1/mariner elements (like Sleeping Beauty and Frog Prince) leads to double-stranded breaks and formation of a 2 or 3 bp 3′-overhang at the excision site (a 3 bp overhang is shown). DNA repair by host-encoded enzymes creates a characteristic footprint at the excision site. Integration occurs at TA dinucleotides which are duplicated upon transposition. The single-stranded gaps are repaired by host-encoded enzymes. (B) PiggyBac-mediated excision is followed by hairpin-formation at the transposon ends. After integration into TTAA target sites that are consequently duplicated, the single-stranded breaks are repaired by ligation. The 5′ TTAA overhangs created at the excision site anneal, thus repairing the double-stranded break without leaving any footprint. (C) hAT transposition creates hairpins at the ends of the flanking donor DNA. Integration is targeted to NTNNNNAN target sites, and as with Tc1/mariner and piggyBac families, hAT-mediated integration creates target-site duplication. Excision site repair leaves a random footprint.