The movement of transposable elements from place to place in genomes results from the actions of a special element-encoded recombinase on special DNA sequences at the tips of the element. In virtually all such elements, these special recombination sequences at the ends of the transposon include transposase binding sites arranged as inverted repeats. It is these sites that define where the breakage and joining events must occur. Because identical (or nearly identical) terminal sequences are arranged as inverted repeats, the disposition of the transposase at both ends relative to the transposon ends is identical, so that the breakage and joining will occur in the same relative positions at both ends.
The terminal inverted repeats are usually composed of special sequences at the extreme tips of the transposon that signal exactly where that breakage and joining should occur, plus more internal binding sites for the transposase (1, 2) (Fig. 1). In some elements, there are multiple binding sites for the transposase, including the one that is part of the terminal inverted repeat and others internal (3). These interior sites probably play a role in loading the transposase appropriately onto the termini and may be dispensable after the initial stages of transposition have occurred, for example, after synapsis of the transposon ends. For some elements, a binding site for a host factor important for recombination may also be part of the terminal repeat.
Figure 1. The ends of IS10. Special sequences at the ends of the element specify the position of transposase binding and also provide signals to prompt DNA breakage and joining. Transposase binding is specified by sequences from position 6 to position 23, and the positions from 6 to 13 are most critical. Although particular sequences at positions 1, 2, and 3 are not required for transposase binding, they are necessary to prompt the chemical steps of DNA breakage and joining. The identity of positions 4 and 5 is not critical. The outside and inside ends of IS10 have the same transposase binding motifs, but the outside end has in additional a binding site for integration host factor (positions 3042), a bacterial protein, that is a cofactor in reactions involving the outside ends.
Although multiple transposase binding sites may be present, breakage and joining is restricted to the terminal inverted repeats because of the presence of a transposase binding site adjacent to the special sequences at the extreme tips of the element that provoke cleavage (1, 2). Alteration of these "cleavage signal" nucleotides generally blocks cleavage, but transposase binding still occurs. Often there is a spacer region of a few nucleotides between the transposon binding site and the cleavage nucleotides at the tip.
