Micrococcal nuclease digestion

2 μg of nucleosomes was incubated with 2 Kunitz units of micrococcal nuclease (NEB) in buffer containing 10 mM Tris HCl pH 7.5, 3 mM CaCl₂, and 1 mM DTT at room temperature. Reactions were quenched at different time points (2, 5, 7, 10, and 20 min) by the addition of 250 μl of PB buffer (Qiagen QIAquick PCR Purification Kit) supplemented with 10 mM of EGTA. DNA from each sample was purified with the QIAquick PCR purification kit, and the extent of DNA digestion was quantified by 2100 Bioanalyzer (Agilent). All experiments were done in triplicates.