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If both binding modes were present in equal proportions, the maximal fluorescence for ABCD# should be about 75%, not far from the value actually observed (Fig. 5A).
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°.
Similar(58)
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.
The probable mechanisms and the proposed binding modes were discussed.
These binding modes were subsequently confirmed by X-ray crystallography.
Representative structures for each ligand were analyzed and binding modes were selected according to the mutagenesis data.
Ligand binding modes were analyzed using LigandScout 3 software (www.inteligand.com).
Overtone modes are present for both modes, but only the latter overtone is larger than the corresponding fundamental mode.
The evidence presented here suggests that either of two binding modes are sufficient for UNG2 focus formation at sites of DNA damage.
The authors of the present study reject that model based on two counts: they were not cognate ligand complexes and their binding modes are different.
Although the low energy binding modes are prevalent no significant clustering was observed again suggesting no specificity in binding.
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