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Role of stacking interactions in the binding sequence preferences of DNA bis intercalators: insight from thermodynamic integration free energy simulations

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Academic year: 2020

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Figure

Figure 1. Chemical structures and amino acid composition of DNA bis-intercalators 2QN (top) and CysMeTANDEM (bottom).
Figure 2. Schematic representation of the DNA base pairs and dummy atoms used in the MD-TI simulations
Figure 3. Schematic and stick representation of the initial complexes studied for 2QN (left) and CysMeTANDEM (right) showing base composition and numbering
Figure 4. Thermodynamic cycles used for the computation of the free energy differences.
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