EpiScope Nucleosome Preparation Kit

Genomic DNA regions occupied with nucleosomes are quantified or identified with downstream applications, such as qPCR, DNA sequencing, and microarray

Genomic DNA regions occupied with nucleosomes are quantified or identified with downstream applications, such as qPCR, DNA sequencing, and microarray.

Protocol overview

Protocol overview.

Analysis of nucleosomal DNA size distribution

Analysis of nucleosomal DNA size distribution. Nucleosomal DNA preparation from HeLa cells (1 x 106 cells) was performed with various amounts of micrococcal nuclease (0.02 , 0.05, and 0.2 ul). Nucleosomal DNA was purified with the NucleoSpin Extract II, yielding 50 ul of DNA solution, of which 5 ul was analyzed by agarose gel electrophoresis. For samples treated with lower amounts of micrococcal nuclease (0.02 ul, 0.05 ul), the electrophoretic results showed bands for mononucleosomal, dinucleosomal, and trinucleosomal DNA fragments. For samples treated with 0.2 ul of micrococcal nuclease, mostly mononucleosomes were evident. In addition, the higher the amount of micrococcal nuclease used, the shorter the size of the mononucleosome-derived DNA fragment observed. This result may reflect the trimming activity at both ends of the DNA (Clark et al. 2010).