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. 2012 Nov 22;41(2):746–753. doi: 10.1093/nar/gks1126

Figure 3.

Figure 3.

DNase I DNA protection assay in the presence of varying Dan concentrations. (A) DNA was incubated with varying Dan to base pair ratios was treated with DNase I to determine the protection ability of Dan. At ≥1:2 Dan:base pair ratio, DNA showed signs of DNase I protection, whereas lower ratios resulted in complete DNA digestion by DNase I. (B) AFM images of DNA–Dan complexes at a 1:5 ratio of Dan to base pairs suggests incomplete DNA coverage by Dan, causing DNA compaction, whereas the naked DNA portion will be prone to DNase I digestion. The height scale (0–2 nm) is used to facilitate visualization of the naked DNA (∼0.4–0.6 nm) compared with the white spots that are height-saturated compacted Dan-bound DNA portions (∼20–30 nm). (C) At a of 1:2 ratio of Dan to base pairs, DNA is saturated by Dan, resulting in rigid nucleoprotein filament formation that protects DNA from DNase I digestion. A bigger height scale (0–10 nm) is used due to Dan nucleoprotein filament higher height.