Modeling mechanical properties of DNA: allosteric protein binding, loop formation, and longitudinal fluctuations 
Xinliang Xu, Ph.D., Cao group 
Department of Chemistry, MIT
 
Introduction
The deformability of DNA has great impacts on its overall shape as well as on many biological functions, such as protein-DNA binding, chromosomal DNA packaging, DNA damage repair, and regulation of gene expression. Here we present our recently developed coarse grained mechanical model of DNA that studies the local deformations of DNA from its canonical structure. In collaboration with recent experimental studies, the correlation between local deformations is unveiled and identified as the underlying mechanism for the observed allosteric protein binding. This newly discovered correlation improves our understanding of the flexibility of DNA and suggests modification of the traditional description of DNA as an elastic rod, which is valid only for long DNA chains and has been challenged by recent experimental studies at shorter length scales. With explicit consideration of the length scale over which local deformations are correlated, our improved model predicts a length dependent flexibility. While our model reduces to the traditional worm-like chain model in the long chain limit, it predicts that DNA becomes much more flexible at shorter sizes that are of biological importance, in good agreement with recent loop formation measurements of short DNA fragments around 100 base pairs.
 
About the speaker
Dr. Xinliang Xu is currently a MIT-SUTD postdoc fellow in the group of Prof. Jianshu Cao at MIT chemistry. He received his B.S. in physics from Tsinghua University in 2002. After that he went to the University of Chicago and worked with Prof. Stuart A. Rice. After getting his Ph.D. in 2007, he joined Prof. Aaron R. Dinner’s group as a postdoc associate.
 
Date and Time: July  2nd , 2014,  10:30-12:00
Venue: Room P203, Experiment Building  
 All are welcome