DNA mechanics

Protein-DNA binding modifies the local structure of DNA. The question whether this modification is local or if its information can be picked up far away along the DNA chain is relevant to the problem of DNA damage location efficiency.

DNA flexibility is key to our understanding of how a really long DNA molecule packages itself into a tiny volume such as chromosome. It is of interest to see how the correlation between DNA local modifications influences DNA global flexibility.

The deformability of DNA has great impacts on its structure and on its many biological functions. Between the well studied atomistic description and continuous description, DNA mechanical behaviors at the intermediate length scales are of great biological significance but have not been systematically studied. Our work is to develop a coarse grained model at these intermediate length scales, to identify the DNA configurations underlying the properties observed and hopefully to provide new insight that drives future experiments. Motivated to better understand DNA biological functions such as DNA packaging, DNA transcription, and gene regulation, currently interested problems include: the end-to-end distance distribution of DNA chain, size dependent DNA opening up rate, and DNA supercoiling.