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