114 Nucleic Acids Research, 2008, Vol. 36, No. 1 Figure 3. RecN binding to nicked DNA. Nt.AlwI-treated EcoRV-linear DNA (150 nM in nt) and RecN (10 nM) were incubated for 10 min at 378C. Reaction was ﬁxed with 0.1 glutaraldehyde and deposited on freshly cut mica. (A) AFM images of Nt.AlwI-treated DNA–RecN complexes analysed. (B) Geometrical analyses of Nt.AlwI-treated DNA–RecN complexes. The length from the end of the substrate to DNA-bound RecN was measured and shown as a histogram in 250 bp bin. A schematic map of plasmid DNA with the target localization for Nt.AlwI endonuclease and relevant high dA + dT regions (Plac, pUCori and f1ori) are shown at the same scale of the histogram. number of DNA molecules that are associated with RecN complexes of diﬀerent sizes. More than 20% (n ¼ 156 total molecules) of the deposited molecules were found inside these structures that have a mean of ﬁve DNA molecules each (Figure 4). Similar results were observed when ATP was replaced by ADP-Mg2+ or ATPgS-Mg2+, however rosette-like structures were not observed in the presence of AMP-PNP-Mg2+ (data not shown). This is consistent with previous results that AMP-PNP fails to promote CII and CIII complex formation (25).