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 A coherence length, which is similar to approximately 150 A coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800-1200 A, consistent with its theoretically predicted role in interactions between DNA at close separations.
Bibliographical noteFunding Information:
This work was supported by a fellowship from the Alexander von Humboldt foundation (A.W.). It was funded by the Engineering and Physical Sciences Research Council (GR/S31068/01, A.A.K and D.J.L.), the Royal Society (A.A.K. and A.W.), the Liverhulme Trust (F/07058/AE, A.A.K.), and the Intramural Research Program of the National Institute of Child Health and Human Development, National Institutes of Health (S.L.). Funding for Open Access publication charge: Intramural Research Program, NICHD, NIH.