Nucleosome arrangements can be assessed from the appearance and the analysis of the nucleosome ladder, which is also called the MNase ladder after the nuclease used to cleave the chromatin, micrococcal nuclease (MNase). Partial MNase digestion of nuclei cleaves the chromatin with a very high preference for linker DNA, rather than for the DNA within the (approx 150-bp) nucleosome core particle. After purification of the partially cleaved DNA and gel electrophor-esis, a ladder pattern is produced reflecting the DNA sizes associated with each of the nucleosome oligomers excised, generally extending from monomer to 10-mer DNA lengths. To assess the ladder in a particular region of the DNA, a Southern blot is performed. More ordered nucleosome arrays have ladders with more DNA bands than less ordered nucleosome arrays, and the bands are more distinct over the continuum of background DNA fragments produced. Additionally, in highly ordered nucleosome arrays, the bands of the ladder are multiples of a unit repeat. The nucleosome repeat length can be measured with a precision of about ±5 bp by carefully determining the sizes (bp) of the centers of each nucleosome oligomer band on the autoradiogram, using an adjacent size marker lane to calibrate the gel and then plotting the nucleosome oligomer size vs the nucleosome oligomer number. The slope of the best straight-line fit gives the nucleosome repeat length (15).

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