On Wed, 21 Jan 2004 04:39:19 +0000 (UTC), 
TomHendricks474  wrote:
>What fascinates me is why a purine - A or G.
>  
>  One suggestion is that the unpaired discriminator position N73 can
> still base stack on the first base pair (1-72) stem helix and extend
> the stacking in this stem. The larger purines would have greater
> stacking energy than smaller pyrimidines and hense be selected. The
> same thing is has been "seen" in position 37 where, when the
> anti-codon (34-36) is binding to the codon, N37 filps outward and base
> stacks to increase the total base stacking energy. The unpaired
> position 37 is mostly a purine also.
>  In fact, one might explain the importance of the codon position in
> the genetic code by the base-stacking contribution. The 2nd codon
> postion has 2 base-stacking interactions and is most critical, the 1st
> position has 1 1/2 interactions (counting the unpaired N37 as 1/2 an
> interaction) and the 3rd position has just 1 interaction and is least
> critical.
>  William L Hunt
> 
> TH
> I think Mr. Hunt has something important here. And if the 3rd base 
> has the least interaction, it may well explain 3rd position wobble for 
> the first time.

Tom, 

I'd like to make two points.

  1. For several years, many of us have been trying to teach you about 
     stacking interactions. They are much more important than hydrogen
     bonds. The reason why A/T-rich DNA melts at a lower temperature
     than G/C-rich DNA is becasue of differences in stacking interactions
     and NOT because of differences in the number of hydrogen bonds.

  2. This is not the "first time" that stacking interactions have been
     invoked as an exlanation for wobble. It may be the first time
     that you've heard about it but that's not the same thing. I'm
     pretty sure that Bill was not claiming to be original. He 
     probably learned about it as an undergraduate, just as I did.




Larry Moran
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