For the past several weeks, I have been working on "digesting" my sample, and running sample os varying degrees of digestion with gel electrophoresis. The first step of the process is to do a "trial digest," in which different concentrations of micrococcal nuclease are added to the nucleosomes. Micrococcal nuclease effectively "eats" the DNA, slowing down when it approaches the histone core. A higher concentration of micrococcal nuclease will "eat" more DNA, so the optimal amount that will digest only the linker DNA is sought.
Next, proteinase K is added to the nucleosomes, which digests the histone proteins. There is now free DNA in the sample, and its length is determined by the amount digested by the micrococcal nuclease. Gel electrophoresis can be done on the variously digested samples to qualitatively see how long the DNA is for each micrococcal nuclease concentration (proteinase K concentration stays the same). The goal of this "trial digest" procedure is to determine what concentration of micrococcal nuclease digests just the linker DNA, so that all we are left with in the sample is the histone core and DNA wrapped around it. It is known that there is approximately 146 bp of DNA around a histone core (without the linker DNA).
It took several attempts to get a successful gel though. Examples of successful and unsuccessful gels are below.