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arXiv · 1809.09335

Kinky DNA in solution: Small angle scattering study of a nucleosome positioning sequence

Torben Schindler·Adrián González·Ramachandran Boopathi·Marta Marty Roda·Lorena Romero-Santacreu·Andrew Wildes·Lionel Porcar·Anne Martel·Nikos Theodorakopoulos·Santiago Cuesta-López·Dimitar Angelov·Tobias Unruh·Michel Peyrard
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Abstract

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed X-ray and neutron small-angle scattering on a short DNA sequence containing a strong nucleosome positioning element, and analyzed the results using a modified Kratky-Porod model to determine possible conformations. Our results support a hypothesis from Crick and Klug in 1975 that some DNA sequences in solution can have sharp kinks, potentially resolving the discrepancy. Our conclusions are supported by measurements on a radiation-damaged sample, where single-strand breaks lead to increased flexibility and by an analysis of data from another sequence, which does not have kinks, but where our method can detect a locally enhanced flexibility due to an $AT$-domain.

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Torben Schindler, Adrián González, Ramachandran Boopathi, Marta Marty Roda, Lorena Romero-Santacreu, Andrew Wildes, Lionel Porcar, Anne Martel, Nikos Theodorakopoulos, Santiago Cuesta-López, Dimitar Angelov, Tobias Unruh, Michel Peyrard. 2018-09-25. Kinky DNA in solution: Small angle scattering study of a nucleosome positioning sequence. https://doi.org/10.1103/physreve.98.042417

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