Conformational Changes Followed by Complete Unzipping of DNA Double Helix by Charge-Tuned Gold Nanoparticles

The complete unzipping of DNA double helix by small size gold nanoparticles having weakly positive surface charge has been monitored using ensemble and single molecule fluorescence resonance energy transfer (smFRET) techniques. We believe, as the gold nanoparticles have positive charge on the surface, the DNA and nanoparticles were pulled together to form two single strands. The positively charged ligands on the nanoparticles attached to the DNA, and the hydrophobic ligands of the nanoparticles became tangled with each other, pulling the nanoparticles into clusters. At the same time, the nanoparticles pulled the DNA apart. The conformational changes followed by unzipping have been investigated for long DNA (calf thymus DNA) as well as for short DNA (similar to 40 base pair) using ensemble methods like circular dichroism (CD) spectroscopy, fluorescence intercalation assay, viscometric method, and single molecule FRET imaging. This observation not only reveals a new aspect in the field of nano-bio interface but also provides additional information about DNA dynamics.