Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): a molecular simulation study

The packing structures of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) thiolates on implicit gold surfaces were studied in explicit aqueous solutions of 1M NaCl using molecular dynamics simulations. The simulations were based on individual DNA chains placed in hexagonal simulation boxes of different sizes, representing various packing densities. The total potential energy per DNA chain was compared. The optimal packing structures were determined based on the minimal potential energy within the limits of the conditions that were evaluated in this study. The optimal packing density of ssDNA was found to be 0.19 DNA chains/nm(2), which is consistent with that determined experimentally. Furthermore, the optimal packing density of dsDNA was shown to be approximately 58% of the packing density for ssDNA, indicating that the packing of ssDNA should be approximately 58% of its optimal packing in order to achieve the best hybridization.