Looking at a tRNA I saw that there were two keys spots where
there are always single strands and always two pyrimidines.
(I'd seen the one at the acceptor stem before. But just
yesterday I discovered the one before the anticodon
IF UV dimers were a major part of selection in the genetic
code (and nothing could base pair from a UV caused dimer)
THEN every tRNA has two pyrimidine sets or 'dimer'
positions.
1. The first is in the acceptor stem which is always CCA in
the 74,75,76 positions. The two C's are pyrimidines
2 The other precedes the anitcodon in positions
34,35,and 36:
Position #32 always has a pyrimidine (either C or U)
Position #33 always has a U
Thus it seems that the tRNA molecule is folded such that it
takes advantage of the pyrimidine dimers to
a. keep the acceptor stem from base pairing
b. keep bases 32 and 33 from base pairing which would close
the anticodon loop.
BUT also notice this - how it effects wobble in 3rd position
of the anticodon #34
Because position 32 and 33 are both pyrimidines There is
chance for a dimer in those positions, but if the last base
in the anticodon #34, or the wobble position, is a
pyrimidine, there is some danger of a dimer between not only
32 and 33, but 33 and 34 too.
Perhaps that in some way explains why there is wobble
(dimers would hurt position 3 in the anticodon if it was a
pyrimidine)
and why the curve of the anticodon loop is between position
33 and 34 - to prevent the dimer problem if 34 was a
pyrimidine too.