Elucidating the DNA−Histone Interaction in Nucleosome from the DNA−Dendrimer Complex
Yen-Chih Huang1*, Chun-Jen Su2, Chun-Yu Chen2, Hsin-Lung Chen1, U-Ser Jeng2, Nikolay V. Berezhnoy3, Lars Nordenskiöld3, Viktor A. Ivanov4
1Department of Chemical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
2X-ray Scattering Group, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
3School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
4Physics Department, Moscow State University, Moscow, Russian Federation
* presenting author:YEN-CHIH HUANG, email:huang.yc@gapp.nthu.edu.tw
The electrostatic complex of DNA with poly-(amidoamine) G6 dendrimer (called “dendriplex”) is used as a model system to resolve if pure electrostatic interaction can lead to the key structural features of nucleosome. Both dendrimer and histone octamer (HO) are found to attract DNA to wrap helically around them with comparable pitch lengths; however, the superhelical trajectory in the dendriplex is loose and fluctuating, whereas that in nucleosome is tight and rigid. The DNA-wrapped dendrimer particles are closely spaced along the dendriplex fiber, while the nucleosome core particles (NCPs) in the nucleosome array are separated by relatively long linker DNA. The clear contrast in structural features attests that DNA−HO interaction is beyond electrostatics, as additional specific interactions exist to fix DNA superhelical trajectory and to select the favored DNA sequence for constituting the NCP.

Keywords: nucleosome core particle, PAMAM dendrimer, dendriplex, Small Angle X-ray Scattering