The physical shape of a DNA is determined by both local and long range structural properties. One of the intriguing questions is whether non-local correlations exist in DNA structures and whether such a correlation affects protein/DNA interaction. We performed molecular dynamics simulations to examine and charaterize long spatial correlations in double helix DNA. Consistent with the experimental observations, the major/minor groove correlation coefficients show a clear oscillation with a periodicity of ~10 bp. Such a correlation shows a strong dependence on the sequence of the DNA and can persist up to a few helical turns. Such a "DNA allostery" was found to be dependent on the DNA sequence as well as the chemical modification (methylation of the base cytosine). The analysis of sequencing data also reveals that the CG methylation depends on the local DNA sequence. On the other hand, a long range power-law correlation was found in different cells and believed to reflect the change of chromatin structure at different cellular states. Using Hi-C data and molecular simulations, we reconstructed the 3-D chromatin structures and mapped the different epigenetic markers, including CG methylation, onto these chromatin structures.

Reactive Oxygen Species (ROS) play a role in radiation-induced bystander effects, the phenomenon where irradiated cells can emit signals to affect neighboring cells. Due to such effects, a gradient dosage design demonstrates the potential to achieve a similar tumor killing efficiency as the uniform-dose profile but with less radiotoxicity on neighboring normal tissues. To examine the effectiveness of gradient irradiation in tumor curbing, we monitored the cell viability, intra- and extra-cellular ROS production patterns within 48h following gradient (8-2 Gy) and uniform (5 Gy) irradiation in breast cancer cells (MCF-7). Similar levels of ROS and lower cell viability were observed in the gradient irradiation group as compared to the uniform irradiation group at 48h after irradiation. Our results suggest superior therapeutic effects of gradient irradiation, which promises great potential to be used in current radiotherapy for the benefits of cancer patients.