Figure 7.

Characterization of large volume DNMT3A/3L complexes with CpG containing DNA substrates by SFM imaging. (A) SFM images of representative large volume DNMT3A/3L complexes bound to the D6 and D9 substrates in 3D (top) and top view (bottom). Image areas are ∼130 × 130 nm². The scale bar at the right indicates the heights in the 3D images in units of nm. Complex volumes are 206 nm³ (D6) and 217 nm³ (D9), both consistent with two heterotetramers. The heights of these complexes are 0.69 nm and 1.18 nm and their lengths on the DNA are 18.9 and 9.4 nm for D6 and D9, respectively. (B) Heights (left) and lengths (right) of large volume DNMT3A/3L complexes bound at CpG sites separated by 6 bp (D6 substrate) and 9 bp (D9 substrate). The Gaussian fit centers indicate average heights of complexes on CpG pairs of ∼0.6 nm for D6 and ∼1.1 nm for D9. Average lengths of complexes on D6 and D9 are ∼20 and 10 nm, respectively. The distributions of heights and lengths of single heterotetramers (based on volumes) bound to the different DNA substrates are shown in Supplemental Figure S7.