<< But to prevent dimers on the proto mRNA side, 
you would be limited to only one coding -
alternating purines/pyrimidines such that there is
never two pyrimidines together.
Thus the only dimer free proto mRNA possibility 
would be a single strand with this coding:

pur/pyr/pur/pyr/pur/pyr/pur/pyr/pur/pyr/pur/pyr/
etc.

TH (day later)
As a friend pointed out, you can code for many
amino acids with an alternating code, but some of
the main ones are excluded. (see list below)
So I began to think about that and came up with
this.

IF there was some dimer protection only on
the proto tRNA side (and this may be due to
base stacking or strand folding)

THEN you have opened up the possibility of
having not only alternating pyr/pur/pyr
but any codon with two purs in a row
(if the two complementary paired pyrs that
are adjacent in the tRNA
anti-codon, would be safe from dimers)

Now we can add a number of amino acid
possibilities.
First here are the 9 that could be coded
with an alternating pyr/pur/ coding:
Ala, Arg, Cys, His, Ile, Met, Thr, Tyr, Val (and start)
 
Now add to that those with 2 purines adjacent:
Asn, Asp, Gln, Gly, Ser, Trp, and stop - giving us 
a total of 15 out of 20 plus stop.

And with the remaining ones , IF there was dimer
protection on the proto tRNA such that there could
be 3 pyrimidines in an anti codon without dimer
damage,
we can add Glu, and Lys leaving only 3 codons
outside dimer protection and the 20 amino acids
of the code: Leu, Phe, Pro

Comment on dimer impact on the genetic code?

(snipped)
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