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The strikingly similar CD spectra obtained for the complex of Λ,Λ-B with [d CGCGAATTCGCG ]2 and for freshly prepared mixtures of Λ,Λ-B with ct-DNA (before the slow intercalation process has taken place) indicate that a similar binding mode is present with the natural calf thymus DNA/Λ,Λ-B complex.
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Ligand 11 is an exception, as it was modeled based on ligand 9 and the PDB structure ; 3SVG, and two equally plausible binding modes were present, where the trifluorotoluene moiety is flipped by 180°.
The present minor-groove binding mode is proposed to represent the initial surface interactions of binuclear RuII compounds prior to intercalation into AT-rich DNA.
This means that the RNA binding mode is preserved.
The first binding mode is adopted by the H3 peptides, whereas the other mode is adopted by the H4 peptides.
However, their binding mode is entirely different.
This binding mode is consistent with the observed experimental SAR (vide infra) and is significantly different from the two closely related binding modes previously postulated in the literature.
By contrast, binding mode 4 was clearly disfavored in chain A, indicating that this binding mode is incompatible with the partially constrained (active) conformation.
The predicted binding mode was confirmed by X-ray crystallography.
The binding mode was proposed from a docking study.
Similar binding mode was observed in MdOS and EGFR kinase.
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