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PDBsum entry 1m6f
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References listed in PDB file
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Key reference
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Title
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Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove.
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Authors
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B.Nguyen,
M.P.Lee,
D.Hamelberg,
A.Joubert,
C.Bailly,
R.Brun,
S.Neidle,
W.D.Wilson.
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Ref.
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J Am Chem Soc, 2002,
124,
13680-13681.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Headers
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