S1 File - Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers

Table A, Percentage of hydrogen bonds and vdW interactions between amino acids and oligonucleotides in non-homologous sets of protein-dsDNA complexes; Table B, Number of acceptor and donor sites for each base pair A-T and C-G in dsDNA; Fig A, Schematic representation of the acceptor and donor sites available for hydrogen-bond interactions in base pairs thymine-adenine and cytosine-guanine; Fig B, Schematic diagram of the bidentate interactions between the amino acids arginine and lysine, and guanine. (Adapted from Luscombe et al.11); Fig C, Total hydrogen-bond interactions (expressed in percentages) between each amino acid and phosphate groups, nitrogenous bases and deoxyribose found in protein-dsDNA complexes; Fig D, Total vdW interactions (expressed in percentages) between each amino acid and phosphate groups, nitrogenous bases and deoxyribose found in protein-dsDNA complexes; Fig E, Radial distribution function of DNA, the dendrimer, water and counterions (Na+/Cl-) in each complex. a) PAMAM-Arg and b) PAMAM-Lys. The distribution was calculated with respect to the center of mass of the dendrimer; Fig F, a) Solvent accessible surface area (SASA) of dsDNA alone in solution (black line), in complex with PAMAM-Arg (blue line) and PAMAM-Lys (green line).b) dsDNA shortening (%) as a function of time in the presence of PAMAM-Arg and PAMAM-Lys; Fig G, Histogram of the density of charges exposed to the solvent, expressed as the ratio between the normalized number of charges and surface area (nm2). Data were obtained from a single subset of non-homologous dsDNA-protein complexes.
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