In my origin scenario I suggested that a single RNA strand folded upon itself with two ends loose.
This was one of the first and earliest key developments in the origin.
Now I think a more reasonable scenario for this early period, is short complimentary strands base
paired together with 4 ends sticking out. This lets each end have a loose 3' end that is stacked but
not base paired.
Its on these two ends that I think other prebiotic material h-bonded to. And remember though h-bonds
are slight there is no reason to think that these 'loose ends' are limited to h-bonding to just one
aa, or one other rna. They could be quite long and have many h-bond partners. Enough so that for
every 3 (allowing a protected middle spot) there could be h-bonding to either an aa or other rna.
(Later this would lead to the tRNA system with aa at one end and mRNA at the other)
This set the stage for the adaptor molecule to connect up the two worlds of aa's and rna's. The h-
bonding is possible between aa and proto-tRNA yet is very weak. But because it is possible it
probably happened, and would be hard to stop from happening.
This building on the loose 3' ends of a paired proto RNA was thermally stable and helped all survive
in a type of chemical symbiosis.
Notes: Whether this means anything or not, I find it strange that in the anticodon loop, there is a
2nd loop cleaved. It has this coding uuu - ACCA (as in the acceptor stem) -cuacg - aaa. Base 76 is
not stacked. That leaves a 3 base stacked but unpaired row of 73 (discriminator base) 74, 75. I
wonder if these 3 didn't once act as the codon does or vice versa. I think the anticodon loop was
first a loose end that later evolved to a closed loop. The process of making a tRNA seems to suggest
that possibility. Thus it looks like that on earliest times, we had an RNA molecule with two 3'
loose ends.
Note in both ends there is the 3rd base in least stacked or naked end territory. That would seem to
suggest wobble in that position. Also note how important shape is for the 3rd wobble position. it
seems that for every codon either pyrimidine can code and is interchangeable in 3rd and almost in
every case, either purine can code in 3rd.
Comment?