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UC San Diego engineer provides insights to decades-old DNA squabble
Date:7/31/2009

aborators suggest that the structure of chromatin is actually a combination of both of these models.

Some researchers suggest that its structure is like a solenoid, where the chain of nucleosomes follows a helical path along the chromatin axis such that adjacent nucleosomes along the chain lie side by side on the chromatin fiber also and thus the linker DNA connecting the two needs to maintain a highly bent conformation. Other researchers suggest that chromatin has a zigzag structure where the nucleosome chain follows a zigzag path along the chromatin fiber such that adjacent nucleosomes on the chain actually lie on opposite sides of the fiber such that the linker DNA is straight. (The nucleosome is the basic unit of chromatin that consists of two turns of DNA wrapped around a protein spool).

Arya and his team have developed a very sophisticated model of chromatin that is computationally accessible yet detailed enough to provide insights into its structure and dynamics. By simulating this model under physiological conditions using fast computer algorithms, Arya has provided the first evidence that chromatin does not exist uniquely in solenoid or zigzag forms but rather exhibits a "heteromorphic" structure where both types of structures are in balance with each other. Arya's collaborators have developed an innovative experimental approach called Electron microscopy assisted nucleosome capture technique to corroborate Arya's findings.

"What we did was extract the most important features of DNA and the associated proteins in the model, using techniques called coarse-graining," Arya explained. "You cannot simulate something as large as a chromatin fiber containing tens of nucleosomes at molecular detail for periods of time longer than a few nanoseconds. That will not tell you much. You need to reduce the complexity of the system without sacrificing important details, which is exactly what we have done. We're trying to reduce the total number o
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Contact: Andrea Siedsma
asiedsma@soe.ucsd.edu
858-822-0899
University of California - San Diego
Source:Eurekalert  

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