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

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds the DNA major groove
Simulations of DNA coiling around a synthetic supramolecular cylinder that binds the DNA major groove
In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(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.
bio-supramolecular chemistry, DNA recognition, helical structures, molecular dynamics, noncovalent interactions
0947-6539
3493-3506
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Hannon, Michael J.
e591d615-ab89-432b-9b6d-9ebd07ab8554
Rodger, Alison
af928914-8be9-4009-99ed-20109b3b3d97
Rodger, P. Mark
87999bdc-cc9b-4365-bfa1-bfbd72594243
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Hannon, Michael J.
e591d615-ab89-432b-9b6d-9ebd07ab8554
Rodger, Alison
af928914-8be9-4009-99ed-20109b3b3d97
Rodger, P. Mark
87999bdc-cc9b-4365-bfa1-bfbd72594243

Khalid, Syma, Hannon, Michael J., Rodger, Alison and Rodger, P. Mark (2006) Simulations of DNA coiling around a synthetic supramolecular cylinder that binds the DNA major groove. Chemistry - A European Journal, 12 (13), 3493-3506. (doi:10.1002/chem.200501168).

Record type: Article

Abstract

In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(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.

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More information

Published date: 24 April 2006
Keywords: bio-supramolecular chemistry, DNA recognition, helical structures, molecular dynamics, noncovalent interactions

Identifiers

Local EPrints ID: 48166
URI: http://eprints.soton.ac.uk/id/eprint/48166
ISSN: 0947-6539
PURE UUID: 1ca7c5fa-c77f-4a43-897c-269b0bb92e46
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 31 Aug 2007
Last modified: 17 Dec 2019 01:44

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