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

Torben Schindler 1 Adrián González 2, 3 Ramachandran Boopathi 4 Marta Roda 3 Lorena Romero-Santacreu 3 Andrew Wildes 2 Lionel Porcar 2 Anne Martel 2 Nikos Theodorakopoulos 5 Santiago Cuesta-Lopez 6 Dimitar Angelov 7 Tobias Unruh 1 Michel Peyrard 6
1 FAU - Friedrich-Alexander Universität Erlangen-Nürnberg
2 ILL - Institut Laue-Langevin
3 Universidad de Burgos
4 INSERM U823 - Institut d'oncologie/développement Albert Bonniot de Grenoble
5 Fachbereich Physik [Konstanz]
6 Phys-ENS - Laboratoire de Physique de l'ENS Lyon
7 LBMC UMR 5239 - Laboratoire de biologie et modélisation de la cellule
Abstract : DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of l p ≈ 500 Å 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 Roda, Lorena Romero-Santacreu, et al.. Kinky DNA in solution: Small-angle-scattering study of a nucleosome positioning sequence. Physical Review E , American Physical Society (APS), 2018, 98 (4), pp.042417. ⟨10.1103/physreve.98.042417⟩. ⟨ensl-01910577⟩

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