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

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of lp ≈ 500Å 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.Spanish Ministry of Economy, Industry and Competitiveness (BES-2013-065453, EEBB-I-2015-09973, FIS2012-38827). S.C.L. and UC-154 are grateful for the support of Junta de Castilla y Leon (Spain) Nanofibersafe BU079U16. D.A. acknowledges funding from the Agence Nationale de la Recherche through ANR-12-BSV5-0017-01 “Chrome” and ANR-17-CE11-0019-03 “Chrom3D” grants. N.T. acknowledges support by the project Advanced Materials and Devices (MIS 5002409, Competitiveness, Entrepreneurship and Innovation, NSRF 2014-2020) cofinanced by Greece and the European Regional Development Fund