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PDBsum entry 151c
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Electron transport 2
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PDB id
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151c
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References listed in PDB file
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Key reference
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Title
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Binding of hoechst 33258 to the minor groove of b-Dna.
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Authors
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P.E.Pjura,
K.Grzeskowiak,
R.E.Dickerson.
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Ref.
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J Mol Biol, 1987,
197,
257-271.
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PubMed id
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Abstract
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An X-ray crystallographic structure analysis has been carried out on the complex
between the antibiotic and DNA fluorochrome Hoechst 33258 and a synthetic B-DNA
dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G. The drug molecule, which can be
schematized as: phenol-benzimidazole-benzimidazole-piperazine, sits within the
minor groove in the A-T-T-C region of the DNA double helix, displacing the spine
of hydration that is found in drug-free DNA. The NH groups of the benzimidazoles
make bridging three-center hydrogen bonds between adenine N-3 and thymine O-2
atoms on the edges of base-pairs, in a manner both mimicking the spine of
hydration and calling to mind the binding of the auti-tumor drug netropsin. Two
conformers of Hoechst are seen in roughly equal populations, related by 180
degrees rotation about the central benzimidazole-benzimidazole bond: one form in
which the piperazine ring extends out from the surface of the double helix, and
another in which it is buried deep within the minor groove. Steric clash between
the drug and DNA dictates that the phenol-benzimidazole-benzimidazole portion of
Hoechst 33258 binds only to A.T regions of DNA, whereas the piperazine ring
demands the wider groove characteristic of G.C regions. Hence, the piperazine
ring suggests a possible G.C-reading element for synthetic DNA sequence-reading
drug analogs.
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Secondary reference #1
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Title
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Pseudomonas cytochrome c551 at 2.0 a resolution: enlargement of the cytochrome c family.
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Authors
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R.J.Almassy,
R.E.Dickerson.
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Ref.
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Proc Natl Acad Sci U S A, 1978,
75,
2674-2678.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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The cytochrome fold and the evolution of bacterial energy metabolism.
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Authors
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R.E.Dickerson,
R.Timkovich,
R.J.Almassy.
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Ref.
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J Mol Biol, 1976,
100,
473-491.
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PubMed id
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