On Sat, 21 Feb 2004 06:31:00 +0000 (UTC), 
TomHendricks474  wrote:

>Someone else wrote:
>> I suggest there had to be at least 3 positions to have a center 
>> one. The center one was protected by being in the center with at
>> least a base on either side and at least it is sticking 2 bases 
>> outside of the fold so it is accesible. >>
> 
> Perhaps too the center one would hold with h-bonds under certain
> conditions, if it was protected on both sides with other bases, 
> and had base stacking etc.

The interaction between two trinucleotides (3 "bases") is governed
almost entirely by stacking interactions. The hydrogen bonds play
an insignificant role in the overall stability of the double-stranded
molecule. The hydrogen bonds are necessary for complementarity
but that's a different matter altogether.

You need to have three nucleotides in order to have stacking
interactions.

> Perhaps the key number of 3 base pairs has to do with what was 
> necessary to have this h- bond with any other molecule

No, you need three nucleotides in order to get stacking interactions
that make the formation of double-stranded molecules thermodynamically
favorable.

> If this is so then it suggests the first connection between RNA 
> and Amino acids. If they could bond together they would be less 
> likely to be denatured in the high heat of this early period on 
> hot Earth.

The melting point of a double-stranded trinucleotide is probably
less than room temperature.


Larry Moran
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