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

TL;DR

This study uses small-angle scattering to investigate the flexibility of DNA, revealing that certain sequences can form sharp kinks, which may explain discrepancies in DNA flexibility measurements.

Contribution

It introduces a modified Kratky-Porod model to detect sharp kinks in DNA, providing new insights into sequence-dependent DNA flexibility in solution.

Findings

DNA can have sharp kinks in solution, supporting historical hypotheses.

Sequence-dependent local flexibility can be detected using the proposed method.

Radiation damage increases DNA flexibility by inducing single-strand breaks.

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.