General principles

=Definition= We'll talk here about site specific recombination.

Site specific recombination: "reciprocal exchange between DNA sites". transposition is excluded from the strict definition according to (1).

=Outcome=

Basically, outcome can be:
 * integration
 * excision
 * inversion

Recombinase is an enzyme that recognize specific DNA sequences, is able to breack and rejoign DNA while conserving the Phopho-diester bond energy ( no DNA synthesis or Nucleotide cofactor)

=Process=


 * Minimal elements:

1/ a recombinase

2/ a pair of recombination sites

mechanism

 * Recombinase binding
 * Pairing of the 2 recombination sites (synaptic complex)
 * Cleavage, strand exchange, rejoining
 * Synaptic complex break down, release of recombination products.

Additional players
Sometimes recombination require cofactors which serve different purposes, structural, regulatory, or both.

stabilization of the synaptic complex activation of the recombinase directionallity of the reaction.

Molecular mechanism
Recombinases use tyr or Ser mediated catalytic action:

1/ nucleophilic attack of the hydroxyl group on the phosphate of the phospho-diester bond.

2/ Covalent recombinase/DNA reaction intermediate

3/ free hydoxyl group from DNA partner attack the phosphate of the Recombinase/DNA intermediate, leading to release of the recombinase and joining of the 2 DNA stands.