The chemical difference between RNA and DNA is the missing 2\'-hydroxyl group in

Question

The chemical difference between RNA and DNA is the missing 2'-hydroxyl group in the nucleotides that build DNA. The major effect of that change that I know of is the higher stability of DNA compared to RNA. But I'm wondering whether this difference has significant implications for the ability of DNA to form compex, three-dimensional structures.

RNA is known to be able to from complex tertiary structures and function as ribozymes. It clearly has the ability to form a wide range of structures and can catalyze a variety of chemical reactions.

As far as I know, there are no naturally occuring catalytic DNAs known. But a number of synthetic DNA enzymes have been created in the lab, so it is generally possible for DNA to form catalytic structures (see Breaker and Joyce 1994 for the first created DNA enzyme).

I'm wondering whether the missing 2'-OH means that DNA has less potential to form complex structures compared to RNA? I imagine it changes the ability to create hydrogen bonds, but I don't know if it would significantly decrease the potential structures that DNA could adopt.

Explanation / Answer

The answer lies entirely in the thermodynamic stability that is provided with having a 2'-OH. As mentioned by Aleksandra, RNA will adopt only the C3'-endo conformation whereas DNA adopts both the C2'-endo and C3'-endo. Effectively, this makes the DNA strand more flexible not RNA. In doing so, a single stranded DNA oligomer will be able to adopt more states.

DNA/RNA helix formation is dominantly enthalpically driven. When a helix forms, RNA will only adopt an A-form Helix where as DNA will adopt both a A-form and B-form. While there are more possible conformations for DNA, the reduction in the entropic contributions make it significantly more unfavorable. Interestingly, this is why RNA analogs like PNA and morpholinos have good binding properties as they will form more entropically stable base-pairing with their target sequence.

For these reasons, it is much more common so see structured Ribozymes and non-coding RNAs in nature even though it is physically possible to produce DNAzymes. Again, one of the many reasons why the RNA world hypothesis makes sense.

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