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I am a computer-scientist working in nucleic acids from the perspective of Formal Language Theory. I am dealing with several papers that analyze the Stem-Loop structure of DNA.

I would like some solid reference that confirms (or negates):

1) The existence of these structures

2) The existence of a (species, subespecies, ...) whose DNA or RNA has been confirmed to have strings which are a pure stem-loop structure.

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    $\begingroup$ The existence of stem loops is well established, so I'm not sure what kind of paper you're looking for in that regard. There are even crystal structures. As for your second question, it seems exceedingly unlikely. $\endgroup$
    – canadianer
    Commented May 18, 2017 at 17:00
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    $\begingroup$ I'm not sure this analogy will be helpful (and I'm sure someone could poke holes in it), but you are somewhat asking for 1) Confirmation that a car with wheels exists, and then 2) Asking if there is a car that is only wheels. $\endgroup$
    – Bryan Krause ♦
    Commented May 18, 2017 at 20:02
  • $\begingroup$ @BryanKrause I'll cite you :D $\endgroup$
    – D1X
    Commented May 19, 2017 at 7:59

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The existence and importance of stem loop structures is well documented.

I'm not sure what the second question means exactly. If you mean 'an organism that has at least one stem loop, try HIV. The MS2 system is also a stem loop binding protein that's used as a tool a lot in biology, I suggest googling it.

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  • $\begingroup$ The second question means if there is any organism whose DNA or RNA has been documented to have at least one strand which is only a stem-loop, not a stem-loop contained within a larger strand. I suppose the answer is no. $\endgroup$
    – D1X
    Commented May 19, 2017 at 8:16
  • $\begingroup$ But anyway, I would like to cite a paper stating something like " (...) it has been observed that stem-loops always appear embeded in larger strands (...)" $\endgroup$
    – D1X
    Commented May 19, 2017 at 9:38
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    $\begingroup$ @D1X Ah I think I might realize now your misconception...stem-loops are typically quite short relative to genomes, from a few base pairs to a few tens of base pairs, versus even viral genomes that are at least several thousand bases and the smallest bacterial genomes in the 100s of thousands. You won't find a citation saying what you state because it's sort of obvious from the underlying math: you could find some papers on the largest stem-loop structures and smallest genomes to make your point, though. $\endgroup$
    – Bryan Krause ♦
    Commented May 22, 2017 at 20:26

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