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I know that there are two most important directions of genetic information transfer in living organisms: DNA->DNA and DNA->RNA. The first is replication, and the second is transcription. I wonder if there is a reason for this choice of directions. According to this article, all other directions are possible. Why do we use DNA for example? RNA is capable of self-replication since it happens in viruses. And why do we use RNA, not DNA, as messenger molecules? Is it just an accident or is it possible to explain why this is the right way of doing it?

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One reason is surely that DNA is chemically more stable than RNA. – nico Aug 19 '12 at 18:03
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@nico Thank you, I didn't know that. That seems to explain why RNA is not used to store genetic information. Could you explain why RNA is used instead of DNA for communication? Is RNA easier to build? – ymar Aug 19 '12 at 18:31
On top of my head I cannot think of a reason. I will try to write an answer if I can find something about it. – nico Aug 19 '12 at 18:35
RNA folds better than DNA. – bobthejoe Aug 20 '12 at 6:11
For a reference of the RNA folding stability see biology.stackexchange.com/a/769/389 – bobthejoe Aug 21 '12 at 21:31

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DNA is more chemically stable than RNA, which makes it ideal for long-term storage. RNA viruses like HIV have a short lifespan and must replicate to survive, which is why they can get by with a less chemically stable genome.

RNA is a useful format to transcribe since it has multiple forms and functions (e.g. rRNA, mRNA, tRNA, siRNA, snRNA, miRNA, etc.). RNA can sometimes function like a protein in which it carries out cellular actions without needing to be translated. It has been hypothesized that RNA were the first molecules as precursors to life since they can function for both storage and action. The theory is that RNA was the first molecule but was then able to be translated into proteins (which were more variable/useful) and able to be stored as DNA (which was more stable as a storage medium).

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The first sentence of your second paragraph is essentially proof by intimidation: you’re not giving any reason here. Just because RNA can take on multiple forms doesn’t by itself say anything about the suitability of mRNA as an intermediary between DNA and proteins, especially since all the examples you’ve cited are noncoding. – Konrad Rudolph Aug 20 '12 at 15:48
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True, I didn't mention any reason that it's a particularly good intermediary to be translated. I'm taking a different angle in answering the question by suggesting that maybe it has more to do with the sequence of origins instead of its usefulness as an intermediary. – Conner Aug 20 '12 at 15:54
Yes, in fact I’m convinced that sequence of origin is the real reason. The similarity with non-coding RNA is notable only insofar as much of the machinery for treating RNA (any RNA) is ancient and very well conserved, and thus the cell requires less innovation by relying on mRNA than it would by having some kind of mDNA. – Konrad Rudolph Aug 20 '12 at 16:06
@KonradRudolph, or RNA structure is simply more stable. see biology.stackexchange.com/a/769/389 – bobthejoe Aug 21 '12 at 21:31
@bobthejoe While that’s interesting in general (good answer!), here we are talking specifically about mRNA where structure plays no or only a very minor role. – Konrad Rudolph Aug 22 '12 at 8:30
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If you had a complex life form which used only DNA or RNA, it would have no way to tell transcribed mXNA from genomic gXNA. This would cause problems during cellar replication, as you could also replicate your mXNA along with your gXNA. It would also cause problems repairing breaks in your gXNA, as you would run the risk of including mXNA during the repair process.

Therefore it seems advantageous to have a storage system for information which is not currently being translated into protein (i.e., DNA), as compared to just having RNA.

On the other hand a completely DNA organism would need RNA for functional ribosomes anyway. If RNA is being used for ribosomes, using it for mRNA as well to avoid confusion with genomic DNA seems advantageous.

In order to test this hypothesis, you would need to create a completely RNA/DNA based lifeform and investigate its properties. Short of starting life from scratch as RNA based and monitoring its evolution over a few million years, a conclusive proof as to why things are the way they are as opposed to being down to an evolutionary historical accident is difficult to obtain!

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