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Nucleic Acids Research Advance Access originally published online on August 28, 2008
Nucleic Acids Research 2008 36(17):5540-5551; doi:10.1093/nar/gkn514
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Nucleic Acids Research, 2008, Vol. 36, No. 17 5540-5551
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Helical coherence of DNA in crystals and solution

Aaron Wynveen1,2,*, Dominic J. Lee2,3, Alexei A. Kornyshev2 and Sergey Leikin4

1Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany, 2Department of Chemistry, Faculty of Natural Sciences, Imperial College London, SW7 2AZ London, UK, 3Max-Planck-Institut für Physik Komplexer Systeme, Nöthnizer Straße 38, D-01187 Dresden, Germany and 4Section of Physical Biochemistry, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, DHHS, Bethesda, MD 20892, USA

*To whom correspondence should be addressed. Email: awynveen{at}googlemail.com

Correspondence may also be addressed to Sergey Leikin. Tel: +1 301 594 8314; Fax: +1 301 402 0292; Email: leikins{at}mail.nih.gov

Received March 28, 2008. Revised June 25, 2008. Accepted July 28, 2008.

The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however, is obscured by poorly understood variations in the stacking geometry of the same adjoining base pairs within different sequence contexts. In this article, we approach the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers. We evaluate the corresponding helical coherence length—a cumulative parameter quantifying sequence-dependent deviations from the ideal double helix geometry. We find, e.g. that the solution structure of synthetic oligomers is characterized by 100–200 Å coherence length, which is similar to ~150 Å coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800–1200 Å, consistent with its theoretically predicted role in interactions between DNA at close separations.


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A. A. Kornyshev and A. Wynveen
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[Abstract] [Full Text] [PDF]


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