NMR of a few billion (different) RNA molecules?
 

Hey,

I am working on a VHDL-to-DNA compiler, and one of the inputs has to be RNA molecules that can be used without interfering with the operation of other RNA molecules in the logic circuit or within the solution in general. This would require a simulation of the size of 2^(4^(N)) where N = the number of nucleotides of the RNA molecules. This is computationally infeasible (319 years on a gigahertz machine, a few minutes on a petahertz machine, but these are not generally accessible, and then there's memory IO, anyway, it's just not optimal).

Instead: what if I threw all of these molecules together, let them react, and then find the ones that did not react, that did not combine with the others? I figure this is where NMR comes in. Would this be possible with current NMR technology? What should I look up?

A guy by the name of lupine_85 in #biology on freenode said I'd need some well plates, and if the plate can't have that many wells, then just make an automatic loader with an arm. But I don't see any reason to use wells since it's all mixed and there's nothing specific going on -- I just need to get out a list of the molecules resulting from all of the interactions.

Thoughts? Any software I should look into? Anybody know of some good NMR machines, or how to build one?

- Bryan