The dynamic structure of DNA in vivo is the key to answer how DNA manages to participate all cell activities while under so many structural constraints. We are thus interested in investigating how DNA methylation, one of the most common means of DNA regulation, changes the dynamic structure of DNA in nucleosome, a structural modification of DNA in all eukaryotes. The protein component of nucleosome was successfully made with a improved protocol. DNA methylation was performed with methytransferase SssI. A state-of-the-art method, combining 3D-RISM, ensemble optimization method, and cgDNA was implemented, and it has shown the best fit of B-form DNA SAXS data so far. With all of these components, an SAXS experiment on nucleosome with methylated DNA is possible, and the experiment data can be interpreted. The result on DNA modeling also hints on future directions for developing better energy model of DNA in solution.