Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns

A. A. Kornyshev, D. J. Lee, A. Wynveen, S. Leikin

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their structure to optimize their intermolecular interactions. In addition to the double helix symmetry revealed by Watson and Crick, classical X-ray diffraction patterns of DNA contain information about the flexibility, interactions and sequence-related variations encoded within the helical structure. To extract this information, we have developed a new diffraction theory that accounts for these effects. We show how double helix non-ideality and fluctuations broaden the diffraction peaks. Meridional intensity profiles of the peaks at the first three helical layer lines reveal information about structural adaptation and intermolecular interactions. The meridional width of the fifth layer line peaks is inversely proportional to the helical coherence length that characterizes sequence-related and thermal variations in the double helix structure. Analysis of measured fiber diffraction patterns based on this theory yields important parameters that control DNA structure, packing and function.

Original languageEnglish (US)
Pages (from-to)7289-7299
Number of pages11
JournalNucleic acids research
Volume39
Issue number16
DOIs
StatePublished - Sep 2011

Bibliographical note

Funding Information:
Leverhulme Trust grant F/07568, EPSRC grants EP/ H010106/1 and EP/H004319/1, HFSP grant RGP0049/ 2010-C102 (to A.A.K.); Max-Planck Society (to D.J.L.); Intramural Research Program of NICHD (to S.L.); Alexander von Humboldt Foundation (to A.W.). Funding for open access charge: Intramural Research Program of NICHD, National Institutes of Health.

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