Recently, it is reported that the functional nucleosomes, CENP-A nucleosome, H2A.Bbd nucleosome and hexasome, which include variant histone cores, could have flexible and mobile parts of DNA. However, those DNAs are difficult to observe with X-ray single crystal structure analysis. In this proposal, we aim to reveal the DNA configuration and structure of histone core of three functional nucleosomes. In order to observe DNA and histone core separately in the nucleosome, we employ small-angle neutron scattering utilizing contrast variation technique; matching points for DNA and histone core are 69.7% and 42.2% D2O solutions, respectively. With the structural information, we can discuss the mechanism and function of activated nucleosomes.