Chris Phoenix, who proposed the desktop nanofactory concept, has wrote several important articles on crnano.
Charting various dimensions of improving capabilities to determine pathways to diamondoid molecular nanotechnology.
Partial list of dimensions:
Precision: Today, a number of lithography tools have a precision of about a nanometer--several atoms wide. The goal is single-atom precision.
Flexibility of molecular construction, Manufactured building block size, Feedstock (molecular) inputs, Product material, Working environment, Sub-part assembly, Actuator performance, Molecular machine capability and Manufacturing machine size.
Cubic micron DNA construction proposal form Chris Phoenix He proposes building multi-billion-atom (cubic micron) solid molecular constructions, using DNA as a backbone, plus other arbitrary molecules precisely positioned within the volume. DNA cubes would be put together using DNA stapling.
Part 2 of the DNA brick discussion. If all these plans work out, then it appears possible with today's technology to build a full exponential molecular manufacturing system out of molecular components that are almost easy to design and construct. The only thing that's missing is good actuators. Diffusive DNA actuators are pretty slow. But remember, these bricks can include other molecules in engineered locations and orientations.
UPDATE: Further refinements of this still evolving idea after some initial feedback.