Based on the slow progress of the last 30 year in 'hard nanotech' and the quite amazing strides in the last couple of years in our understanding of and our ability to synthesize 3 dimensional structures at the nano scale (including DNA), and to harness biological components to do different work.
The two fields are complementary I think, one is pushing from the top down trying to make our existing structures smaller (with all the trouble inherent in that, for instance, at the nanoscale there is no such thing as 'smooth', imagine making a bearing out of sandpaper or whatever you can come up with as the nearest equivalent) the other is coming from the bottom up as we learn how our biological structures are formed and what mechanisms are available both as tools and as a working example to study.
Sooner or later (but most likely a little later) there will be a meeting of minds, where new structures will be produced by re-using or adapting the tools that biology has already given us.
I think initially that will be a purely materials science oriented endeavor, mostly concentrating on the medical applications, or a direct application of synthetic molecules (such as artificial DNA) but it's possible there will be more 'mechanically interesting' applications as well.
Nanotech is a lot more than just moving parts, plenty of it would be classed as 'structural engineering'.
The biological part is the one that is moving fastest at the moment, I think at the present speed that two fields will meet and spawn a third field within a very short time, if that hasn't already happened.
For now this meeting place of technology and biology has been named 'synthetic biology' and there is very good progress there, I expect true nanomachinery to be a spin-off of this new field.