DNA sequence determinant for Flp‐induced DNA bending

The Flp site‐specific recombinase from Saccharomyces cerevisiae induces DNA bending upon interaction with the Flp recognition target (FRT) site. The minimal FRT site comprises the inverted a and b binding elements, which flank a central 8 bp core region. The DNA bend in a complex of two Flp monomers bound to the FRT site is located in the middle of the core region. When the central AT basepair was replaced with a CG, the DNA bend was positioned at the outside end of the core region adjacent to the a binding element. The other basepairs surrounding the central AT basepair were not important to the position of Flp‐induced bends. The change also decreased Flp‐mediated cleavage of the top strand of the FRT site and increased Flp‐mediated cleavage of the bottom strand. The overall recombination proficiency of the site was impaired. We conclude that the central AT basepair provides a point of flexure in the FRT site, which Flp uses to position the bend in dimeric Flp–DNA complexes, and that the structure of the core DNA influences the functionality of the site.