Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea

The digestion of chromosomes using micrococcal nuclease (MNase) enables the analysis of their fundamental structural units. For example, the digestion of eukaryotic chromatin using MNase results in laddered DNA fragments (~150 bp increment), which reflects the length of the DNA wrapped around regularly spaced nucleosomes. Here, we describe the application of MNase to examine the chromosome structure in Archaea. We used Thermococcus kodakarensis, a hyperthermophilic euryarchaeon that encodes proteins homologous to eukaryotic histones. Methods for chromosome extraction and agarose gel electrophoresis of MNase-digested DNA including small fragments (~30 bp) are also described.