I am interested in the structural differences caused by benzopurines and benzopyrimidines at the oligonucleotide level between RNA and xRNA, both in single-stranded and double-stranded form.

I am aware of RNA's tendency to be found in the A-form, of which the details are found here. However, other than the obvious nucleobase expansion, I can't seem to find any details about xRNA's secondary structure.


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The only paper I found that examined the question is "Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases". They state

The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist.

They also have a picture comparing the structures of conventional DNA and xDNA:

enter image description here

So while the basic structure seems similar, the difference in diameter and twist look rather large to me.

This is for xDNA, I would assume that xRNA behaves comparably if double-stranded. It would have to somehow fit the larger nucleobases into the helix like xDNA. And the structure of single-stranded RNA is variable, helical parts would probably look similar to xDNA, hard to say how the modified nucleobases would affect tertiary structure.


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