July 31, 2012

Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations





Just Published in Phys.Rev. Lett. E.

Bending of the seemingly stiff DNA double helix is a fundamental 
physical process for any living organism. Specialized proteins 
recognize DNA inducing and stabilizing sharp curvatures of the double helix. 


However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. 

Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for  of the DNA curvature present in experimentally solved structures.