the 'on a silicon substrate' is a bit problematic here, a substrate typically is a lot larger than just a few atoms, the neat thing about DNA is that it is a three dimensional encoding, you are talking about a two dimensional encoding scheme, not three dimensional (an atomic force microscope typically moves in two dimensions and uses an electrical charge to deposit the atoms).

You could stack the atoms three dimensionally but then there would be no easy way to read them out again.