DNA templates can be used to self-assemble metal or semiconductor nanoparticles into programmable molecular architectures. The interactions among DNA-nanoparticle system strongly depends on the size and ligand chemistry of nanoparticles. We performed molecular dynamics simulations to investigate the effect of colloidal gold nanoparticle (GNP) as a function of ligands charge and polarity to its ability to bind with DNA molecules. The surface of GNP was decorated by thiolated alkyl ligands with different terminal functionality such as hydrophobic, polar and charged groups. We observed that uncharged GNPs and GNPs with cationic ligand charge density of less than 10% can only bind to the minor groove of DNA. Whereas GNPs with ligands charge density of higher than 10% can bind to major or minor groove.  Binding to major groove result in significant distortion and wrapping of DNA around the GNP corona. The distortions of the DNA helical structure strongly depends on the ligand charge density. Also at higher nanoparticle concentration and low charge densities, the ligand hydrophobicity can disrupt the hydrogen bonding between base pairs of DNA strands and leads to partial denaturation of DNA helix. We observed that by tuning the cationic charge density and polarity of GNP we can control the binding modes and structural mechanics of DNA.

Assembly of gold nanoparticles on DNA: Effect of ligands charge and polarity

243rd National Meeting (2012)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.