Figure 1.

Schematic of the Cre-loxP recombination mechanism.A, the loxP site is a 34 bp consensus sequence and consists of a central 8 bp nonsymmetrical spacer flanked by two 13 bp palindromic recognition sites. Cre recombinase subunits bind each palindromic sequence and cleavage, exchange, and ligation DNA strand at the central spacer. The spacer provides the orientation of the loxP site. The nucleophilic tyrosine 324 in Cre recombinase attacks the phosphate forming a three phosphotyrosine bond and releasing a free 5′ OH. Cleavage position is indicated by arrow. B, a dimer of Cre subunits bind at the palindromic sequence of each loxP site. A tetrameric Cre structure arranges two loxP sites in an antiparallel fashion to stabilize a synaptic complex. Two opposite Cre subunits cleave and exchange one pair of strands. The released 5′ OH attacks the neighboring strand to form a Holliday junction intermediate. The second pair of Cre subunits is activated by an isomerization of the Holliday junction intermediate. The second pair of strands are cleaved and exchanged to complete the recombination and result in the recombinant products. C, different outcomes of a Cre-loxP recombination depending on the position and orientation of the two loxP sites. If the two loxP sites are in the same orientation, the recombination results in the excision or integration of the DNA segment (e.g., target gene) flanked by the two loxP sequences. If the orientation of loxP elements is in opposite, the result of the reaction is the inversion. Recombination between the two loxP sites located on different DNA strands results in the exchange or translocation.