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let's make a piece of RNA
I'm not concerned about the bases in the middle
and I'm not concerned about the bases on the ends
so I'm kind of leaving them out
but notice, for this RNA sequence
A hybridizes with U G hybridizes with C
U hybridizes with A and C hybridizes with G
so this piece of RNA will form a loop structure as its lowest energy form
which is to say the appropriate base pairs will hybridizes with their match
and make a hybridized section but there is a loop on the end
it is not any great mystery but I think it needs to be emphasized
that RNA is a structural compound things are made out of RNA in a very big way
this stem loop is the primary structure of RNA much the way the alpha helix
is the primary structure of protein
things that are made out of RNA, of course, include tRNA
which looks something like this in two dimensions
and perhaps better image of it is something like this
which is a computer model.... it's a three-dimensional model
and then ribosomes are about 60% RNA and 40% protein they have a very complicated structure
but they're made largely of RNA and the RNA is largely in the form of stem loops
RNA, whether it's messenger RNA
or whatever kind of RNA.... RNA is a product of transcription
which means that if there is a stem loop in the RNA
that must've been there must've been a stem loop in the associated DNA
so let's just change this little piece of RNA into a piece of double-stranded DNA
change the U's to T's and put on the second strand
so,,, if the RNA is forming a stem loop the DNA must have that potential too
so that this piece of DNA is going to want to form a stem loop structure
that looks like this
and ... truthfully, I don't know exactly what that means
but I do know this
when the bio informatics people write computer programs to look for stem loop potential
they find stem loops absolutely everywhere .... all parts of the genome
in all organisms
The "junk" DNA has stem pools...
Is there something that we do not understand? I got this idea from Forsdyke