Comparative analysis of PARP1 and PARP2 binding to DNA containing a single nick. Large scale AFM images (left) of PARP1 (A) and PARP2 (B) binding to nicked 1200-bp DNA and zoomed images (right) of PARP1(2)–DNA complexes. Nicked 1200-bp DNA was incubated with 3.5 nM PARP1 or PARP2 and imaged by AFM in air. Arrows indicate binding of PARP1(2) to DNA ends, nick or undamaged DNA. Scale bar 200 or 500 nm; Z scale: 7 nm. (C) AFM analysis of PARP1(2)–DNA complex formation, number of DNA molecules analysed: 210 for PARP1 and 189 for PARP2. The results represent mean ± SD of three to six independent samples. (D) Analysis of the position distributions of PARP1 and PARP2 on nicked 1200-bp DNA, number of complexes analysed: 145 for PARP1 and 104 for PARP2. The results represent mean ± SD of three to six independent samples. (E) Fluorescence measurements of PARP1 or PARP2 binding to DNA. The reaction mixtures containing the fluorescein-labelled protein PARP1 or PARP2 were titrated with increasing amounts of nicked 1200-bp DNA. Bars indicate the standard error of three independent experiments.