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I'm a computer science guy, recently crossing over to do some research in computational biology on RNA secondary structure prediction. While looking through the materials I got a crazy idea, what if you could design a synthetic ribosome that acts as a Turing Machine on strings of RNA? (you could do similar things with DNA enzymes)

The immediate applications could be stuff like correcting mutations in RNA to cure genetic diseases, which is a relatively simple computation:

  1. Check if a string is bad.
  2. If so, fix bad letter.

Another could be "shredding" DNA/RNA of viruses:

  1. Check if a string is a virus.
  2. If so, shred it.

I'm not sure the status of the literature on this is, or synthetic biology's ability to create something like that. Do you think it is a good idea to pursue this idea or not?

I realize this is a soft question. Perhaps a better one would be, is this possible?

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There are some papers on simple computations using nucleic acids, if nobody answers I'll look them up later. As for your examples, nature already does some of them (see RNA interference). And for correcting genetic diseases, the hard part is actually correcting the sequence in all cells in your body, not the detection itself. –  Mad Scientist Jun 20 at 18:56
Where would the 'table' of the machine be? In other words how would the 'bad string' be recognised? –  Alan Boyd Jun 20 at 18:57
@AlanBoyd An immediate thought would be to keep a copy of the bad string, say a mutated RNA strand, in the machine. Combine it with an enzyme bound to it with 2 functions, check if the letter it's currently bound to matches the current input letter, and slide right. That could do the check step. For the replace step you could do the same backwards and then splice the correct protein in. For a general Turing Machine, you could keep a string of the current state in RNA, keep the rules in another string, and slide along it to find the rule and execute it. –  Mike Flynn Jun 20 at 19:31
I'm no expert at this but I don't think you need a Turing machine to achieve this, at least for DNA, since in conventional sense (not including carcinogenic factors such as UV) the most probable stage in which a DNA mutation can happen is during DNA replication so DNA polymerase (en.wikipedia.org/wiki/DNA_polymerase) engages in proofread to ensure accurate DNA replication, and then the DNA can get back into being heterochromatic (eventually). This will be more difficult for RNA as they are single stranded although they do fold onto themselves. –  Bez Jun 20 at 19:40
Also there many many strands of RNA that are produced through alternative splicing, VDJ recombination and RAG imprecise rearrangements for antibody production, which can give rise to infinite possible RNA productions. So how would you know what is "good" and what is "bad" in terms of RNA and its production. Half the time we don't even know what they do and what their roles are and the only reason we call something as a "bad" or "faulty" RNA is because it is having a negative effect not because we understand the precise role of the sequence, which means a theoretical table would be useless. –  Bez Jun 20 at 19:59

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