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Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

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Khalid, Syma, Hannon, M. J. (Michael J.), Rodger, Alison and Rodger, P. Mark (2006) Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove. Chemistry: A European Journal, Vol.12 (No.13). pp. 3493-3506. doi:10.1002/chem.200501168

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Official URL: http://dx.doi.org/10.1002/chem.200501168

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Abstract

In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron((II)) supramolecular cylinder, [Fe-2(C25H20N4)(3)](4+), and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC)d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.

Item Type: Journal Article
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Science > Chemistry
Journal or Publication Title: Chemistry: A European Journal
Publisher: Wiley - V C H Verlag GmbH & Co. KGaA
ISSN: 0947-6539
Official Date: 14 April 2006
Dates:
DateEvent
14 April 2006Published
Volume: Vol.12
Number: No.13
Number of Pages: 14
Page Range: pp. 3493-3506
DOI: 10.1002/chem.200501168
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access

Data sourced from Thomson Reuters' Web of Knowledge

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