J Am Chem Soc. 2002 Nov 20;124(46):13680-1.

Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove.

Nguyen B, Lee MP, Hamelberg D, Joubert A, Bailly C, Brun R, Neidle S, Wilson WD.

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Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA.

Abstract

A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA.

PMID:: 12431090; [PubMed - indexed for MEDLINE]

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Cited by 7 PubMed Central articles

Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove. [J Am Chem Soc. 2009]
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Structures reported by this article

Strong Binding In The Dna Minor Groove By An Aromatic Diamidine With A Shape That Does Not Match The Curvature Of The Groove

PDB: 1M6F

Source:

Method: X-Ray Diffraction

Resolution: 1.78 Å

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