<P> It is still not entirely clear how the strand exchange occurs after the DNA has been cleaved . However, it has been shown that the strands are exchanged while covalently linked to the protein, with a resulting net rotation of 180 ° . The most quoted (but not the only) model accounting for these facts is the "subunit rotation model" (Fig. 2). Independent of the model, DNA duplexes are situated outside of the protein complex, and large movement of the protein is needed to achieve the strand exchange . In this case the recombination sites are slightly asymmetric, which allows the enzyme to tell apart the left and right ends of the site . When generating products, left ends are always joined to the right ends of their partner sites, and vice versa . This causes different recombination hybrid sites to be reconstituted in the recombination products . Joining of left ends to left or right to right is avoided due to the asymmetric "overlap" sequence between the staggered points of top and bottom strand exchange, which is in stark contrast to the mechanism employed by tyrosine recombinases . </P> <P> The reaction catalysed, for instance, by Cre - recombinase may lead to excision of the DNA segment flanked by the two sites (Fig . 3A), but may also lead to integration or inversion of the orientation of the flanked DNA segment (Fig . 3B). What the outcome of the reaction will be is dictated mainly by the relative location and the orientation of sites that are to be recombined, but also by the innate specificity of the site - specific system in question . Excisions and inversions occur if the recombination takes place between two sites that are found on the same molecule (intramolecular recombination), and if the sites are in the same (direct repeat) or in an opposite orientation (inverted repeat), respectively . Insertions, on the other hand, take place if the recombination occurs on sites that are situated on two different DNA molecules (intermolecular recombination), provided that at least one of these molecules is circular . Most site - specific systems are highly specialised, catalysing only one of these different types of reaction, and have evolved to ignore the sites that are in the' wrong' orientation . </P>

What are the dna sequence requirements for site-specific recombination