The structural dynamics of two nucleosomes, one was H3 containing and other was CENP-A containing nucleosome, were characterized with molecular dynamics simulations and the findings were experimentally confirmed. The simulations showed that histone proteins of both, which is the core structure of nucleosome, are structurally stable and maintain the structure determined by x-ray crystallography, while the wrapped DNAs are highly flexible at the entry or exit region and largely deviate from the crystal structures. In particular, about 20-25 bp DNAs of entry or exit of the CENP-A containing nucleosomes showed several times of open and close conformational changes within 100ns simulations, which was not observed on the H3 containing nucleosomes. The detailed analysis clarifies that this dynamics difference is due to the difference in two basic amino acids at the a-N helix, two Arg residues of H3 are mutated to Lys residue at the corresponding sites. The difference in ability of forming hydrogen-bond to the DNA controls the flexibility of the nucleosomal DNA at entry or exit region. This increase in flexibility was confirmed with a nuclease susceptibility assay of a nucleosome that contains H3 mutant with the two Arg residues replaced with Lys.