<<  As you know, the maturation process of any tRNA is quite involved
with a sequence of many specific base modifications. A problem exists
if a tRNA exits this sequence before it is fully mature; it could
cause mis-translation. Bacteria and eukaryotes seem to solve this
slightly differently. In bacteria a late step in the sequence is to
remove additional nucleotides that were attached to the stem. In your
example, if the tRNA exits maturation early it still has a CCAUC stem
and would never be used. The proper CCA stem tag is a key recognition
point that a tRNA is valid and to be accepted. Eukaryotes typically do
it differently, they don't add the CCA to the stem until late in the
maturation process. Again, if the tRNA exits maturation early it would
have no CCA on the stem and never be accepted for use either at an
aminoacylation site or the ribosome.

 I also have problems with your idea that the stem should have dimers
to resist pairing. The point is that in the RNA-world, for the
ribosome, an rna-aminoacylation site, or any ribozyme to to recognize
a proper tRNA it would probably do so by pairing (h-bonds) with the
stem. Good pairing with the stem would be critical.


TH
Yes but there is also the danger of too much pairing.

I don't think the stem would be there if it could base pair easily.
It would base pair in folding like the rest of the tRNA strand - at least there
would be a real danger of that happening much of the time.
What else would keep it a non paired stem until it was needed?

And as always we are talking about different periods. My idea is that this is
very early on - way before the sophisticated ribosome has materialized.


WLH
 I recall a picture of how today a tRNA-thr (threonine) can regulate
it's own production in a particular bacteria. The rna strand that has
the pre-tRNA sequence for maturation has a leading and following
stem-loop that a tRNA can bridge between. Only the tRNA-thr itself can
form 7 h-bonds at the ends to form this bridge. The anti-codon  binds
to form one side of the bridge (3 WC pairings) and the stem (UCCA)
binds with 4 WC h-bonds on the other side. The bridge only forms if
there is much uncharged tRNA-thr around and its formation presumably
prevents maturation of more (which would be unneeded). This is just an
example of how pairing with the stem is actually required now and I
imagine it was from the beginning also.
  William L Hunt

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