(37e) Twist Propagation in Two-Nucleosome Arrays: Monte Carlo Simulations and Theory

The distribution of twist within DNA linker of a two-nucleosome array subjected to torsional forces is studied using Monte Carlo simulations. The two-nucleosome array is treated using a mesoscopic model that accounts for the nucleosome/linker geometry along with bending and twisting mechanics of the DNA linkers. A Monte Carlo approach is used to simulate the conformation of the linkers under quasi-static twisting conditions. Our simulations reveal an intriguing finding: the magnitude and sign of the twist measured on one linker relative to the imposed twist at the other linker on the other side of the nucleosome depends strongly on the relative orientation of the entering and exiting linkers, or the DNA wrapping angle in nucleosomes. We have constructed a ``phase diagram'' characterizing the relative sign of the twist in the two linkers as a function of various geometrical parameters. A rough mathematical proof for the observed linker-orientation dependent twist behavior is also provided. Our simulations also reveal a ``buckling'' phenomena, whereby nucleosomes sometimes undergo sudden flipping in response to twisting, leading to drastic changes in the entry/exit conformation of the DNA linker. Our results thus provide insights into the underlying mechanisms by which torsional stress impact chromatin organization and subsequent biological activities and suggests ways by which such torsional stresses could be relieved to promote genomic integrity.