Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study

Adsorption of circular DNA onto bare highly oriented pyrolytic graphite (HOPG) surfaces by the addition of Mg²⁺, Ni²⁺, and Cu²⁺ has been investigated by atomic force microscopy (AFM). AFM results revealed that the topography and height of DNA on HOPG surface by the addition of different metal ions are quite different. After the addition of Mg²⁺ for incubation, DNA molecules tend to form many loops on HOPG surfaces, which are derived from the crossover of intramolecular and intermolecular chains. After the addition of Ni²⁺, DNA molecules can form network on HOPG surfaces, and the density of DNA network was significantly increased with increasing DNA concentration. Consequently, dense DNA network can be obtained by using relatively low concentration of DNA and Ni²⁺. As for the addition of Cu²⁺, angular DNA loops composed of flat chains were observed. The observed flat DNA chains with an average height of 0.52 nm can be ascribed to Cu²⁺ insert into the site between bases and phosphate group of DNA inducing denaturation of DNA molecules. This study is very helpful for understanding the interactions of metal ions and DNA molecules, and for constructing various DNA structures on the carbonaceous surfaces.