Molecular dynamics (MD) methods have been used to study the conformation of DNA and its interaction with neighboring DNAs having the same base pair (bp) composition on a flat gold surface. Most of the simulations refer to a DNA that is surrounded by six other DNAs, with the initial distance between the DNAs chosen to be 27 Å to simulate high packing conditions. A six-carbon alkylthiolate linker connects each DNA to the gold surface, and there is an A10 spacer between the alkylthiolate and an 18 bp double-stranded (ds) region for each DNA. In addition, there is a 5 base dangling end on each DNA to match recent experiments in which the dangling ends appeared to show important interactions. We performed 20 ns MD simulations in water with high salt concentration, and it is found that the ds-DNA maintains Watson-Crick B-DNA conformations. The tilt angle (relative to the surface) of the central DNA in the cluster is 27° ± 5°, whereas the tilt angle of the surrounding DNAs is 11° ± 5°. The average angle between this middle ds-DNA and the surrounding ds-DNA is 25° ± 10° and the distance between DNAs is 37 ± 5 Å. These structural parameters arise because counterion-mediated osmotic effects cause the DNAs to move apart (the alkylthiolates always lie flat on the surface) and splay outward. The resulting DNA density is consistent with experiment for flat surfaces. However, in spite of this tendency for the DNAs to move apart, the dangling end of the middle DNA has close contact with its counterpart on one of the neighboring DNAs as a result of base stacking and non-Watson-Crick hydrogen bonding. This shows that DNA-DNA interactions not related to hybridization can stabilize closely packed aggregates of DNA-functionalized gold nanoparticles. We also find that the salt concentration around the middle DNA is increased by a factor of 2.3 relative to the bulk concentration. This increase corresponds to an increase in melting temperature of ∼14 K, which is consistent with our previous estimates of cooperative melting behavior.
ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Electronic, Optical and Magnetic Materials
- Surfaces, Coatings and Films