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

ARI ZEIDA; MATÍAS R. MACHADO; PABLO D. DANS; SERGIO PANTANO

PHYSICAL REVIEW E

AMER PHYSICAL SOC

Lugar: New York; Año: 2012 vol. 86 p. 21903 - 21910

1539-3755

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 ∼80% of the DNA curvature present in experimentally solved structures.