Digestion of chromatin by micrococcal nuclease (MNase) provides a relatively simple method for obtaining information about the locations of nucleosomes along DNA strands. When nuclei in permeabilized cells are exposed to MNase in the presence of a divalent cation, the enzyme makes double-stranded cuts between nucleosomes. Treatment of chromatin substrates with very high concentrations of MNase yields mononucleosome-length DNA prodominantly, while lower concentrations of the enzyme generate one double-stranded cut at intervals of 10 to 50 nucleosomes, depending on the concentration of the enzyme and the substrate. MNase can also make single-stranded DNA cuts at the sites of histone octamers, and, thus, attempts to map the positions of nucleosomes are usually performed with native double-stranded DNA.
Digestion with MNase of Purified Genomic DNA
MNase-digested free DNA, digested to the same relative extent as DNA from a chromatin digest, should be analyzed simultaneously in cleavage mapping studies.
Purification and Characterization of DNA after Digestion of Chromatin
This method has been optimized to maximize the recovery of small amounts of DNA from chromatin digests and, also, so that the resulting DNA is suitable for direct analysis and should not require further concentration.
For a detailed introduction to assays of nucleosome assembly and the inhibition of histone acetyltransferase activity, please go here: "http://www.natureprotocols.com/2007/07/30/assays_of_nucleosome_assembly.php":http://www.natureprotocols.com/2007/07/30/assays_of_nucleosome_assembly.php