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Face-to-face and edge-to-edge pi-pi interactions in a synthetic DNA hairpin with stilbenediether linker

Egli, M., Tereshko, V., Mushudov, G.N., Sanishvili, R., Liu, X. and Lewis, F.D. (2003) Face-to-face and edge-to-edge pi-pi interactions in a synthetic DNA hairpin with stilbenediether linker. Journal of the American Chemical Society, 125 (36). pp. 10842-10849. ISSN 0002-7863

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Abstract

Synthetic conjugates possessing bis(2-hydroxyethyl)stilbene-4,4‘-diether linkers (Sd2) form the most stable DNA hairpins reported to date. Factors that affect stability are length and flexibility of the linkers and π-stacking of the stilbene moiety on the adjacent base pair. The crystal structure of the hairpin d(GT4G)−Sd2−d(CA4C) was determined at 1.5 Å resolution. The conformations of the two molecules in the asymmetric unit differ both in the linker and the stem portions. One of them shows a planar stilbene that is stacked on the adjacent G:C base pair. The other displays considerable rotation between the phenyl rings and an unprecedented edge-to-face orientation of stilbene and base pair. The observation of considerable variations in the conformation of the Sd moiety in the crystal structure allows us to exclude restriction of motion as the reason for the absence of Sd photoisomerization in the hairpins. Conformational differences in the stem portion of the two hairpin molecules go along with different Mg2+ binding modes. Most remarkable among them is the sequence-specific coordination of a metal ion in the narrow A-tract minor groove. The crystal structure provides unequivocal evidence that a fully hydrated Mg2+ ion can penetrate the narrow A-tract minor groove, causing the groove to further contract. Overall, the structural data provide a better understanding of the origins of hairpin stability and their photochemical behavior in solution.

Item Type: Article
Institution: The University of York
Academic Units: The University of York > Chemistry (York)
Depositing User: York RAE Import
Date Deposited: 03 Apr 2009 14:58
Last Modified: 03 Apr 2009 14:58
Published Version: http://dx.doi.org/10.1021/ja0355527
Status: Published
Publisher: ACS American Chemical Society
Identification Number: 10.1021/ja0355527
URI: http://eprints.whiterose.ac.uk/id/eprint/6889

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