I have realized that it is possible to create a dna computer by programming silicon wafers with dna molecules (attached to aluminum, or by some other procedure), and then removing the inert backside silicon. This results in a wafer that is coated with dna molecules, and some arrangement of silicon dioxide, anodized aluminum, and protected polysilicon.
These wafers can be naturally put together in very complex ways by engineering the dna sequence at certain physical points. By engineering the intersequence complementarity of DNA molecules intended to pair to another wafer, it is possible to create circuits between any one of the layers.
This should make it possible to create highly functional dna-computers as a cap on standard integrated circuits with a small amount of wafer space devoted to dna attachment locations.
I would love to be able to use a computer program to visualize these DNA-connected layers, and also do DNA-sequence layout.