Figure 1.

XerCD-dif recombination analysed with TPM. (A) Sequence of dif site with the DNA binding site for XerC (dif ^XerC) for XerD (dif ^XerD) and the central region (dif ^cent) represented. (B) Model for XerCD-dif recombination (9). Recombinases (XerC or XerD) are represented as grey circles, with Y indicating the active tyrosine. DNA molecules are oriented with uppercase and lowercase A and B letters. The reaction is sketched in five steps: synapse formation; first strand cleavage, exchange and ligation to form the first holiday junction (HJ₁); isomerization of HJ₁ into HJ₂; resolution of HJ₂; and dissociation. If XerC cuts first, the process is blocked at HJ₁ step and goes backward. If XerD is activated to cut first, the recombination can be complete. (C) Scheme of TPM setup to measure the length of a DNA molecule. A glass coverslip (g) is coated with PEG (p) and neutravidin (n). A DNA molecule is attached to that surface by biotin bound to one of its 5′ end. A latex bead coated with antidigoxigenin (ad) is bound to the other extremity of the DNA molecule thanks to the presence of digoxigenin on this 5′ end. As explained in the text, the amplitude of the Brownian motion of the bead (Aeq) depends on the size of the DNA molecule that tethers the observed bead to the glass surface (for details see text and M&M). (D) Scheme explaining how XerCD-dif synapse formation may reduce the apparent size of a DNA molecule that contains two dif sites (black box: dif ^XerD; white box: dif ^XerC). (E) DNA molecules used in this work. The representation of dif sites is the same as in (D) and the sizes (bp) of the different segments of these molecules and the 5′ modifications are indicated (b = biotin, d = digoxigenin).