On Sun, 3 Aug 2014 19:26:34 -0400 (EDT), Tom Hendricks <tom-he...@att.net
>> First, in your original post, you mention that G-C pair with 3- hydrogien bonds and A-T with 2.
>> Then you follow by observing that G-C denatures at a higher temperature and A-T at a lower.
>> While you don't say directly that this is cause of the difference in denaturing temperature there is
>> this implication. And your implication is incorrect. Dr. Moran and I discussed this with you many
>> years ago if you remember? My source then was the book BIOCHEMISTRY, Abeles, Frey and Jencks 1992,
>> and nothing has changed since then. But here is a more complete explanation from Moran:
>> or from Wiki:
>> Notice in the Wiki article that base stacking contribution to melting can be very different for the
>> same set of bases depending on how they stack, for instance, if a G-C is stacked on top of a G-C or
>> on a C-G.
>> William L Hunt
>But so what? Mr. Hunt this doesn't change anything - it adds a slight proviso is all, and that is this: there is a slight difference between G-C stacked on another G-C then stacked on C-G.
My only point was what is causing the differences in melting temperature in strands, where you
implied it was the 3 versus 2 h-bonds.There are differences between G-C and A-T. One is how they
align with 2 h-bonds or 3 h-bonds, another is the larger planar surface area in the G-C where
larger surface contact beween the stacked pairs increases the stacking energy. Both correlate to the
strand melting temperature although the correlation is much better when adding up the individual
base-stacking energies. This hardly matters in any large strand where the different base-stackings
all average out. But for small strands using a calculation that adds up the actual base stackings
gives a better result than just counting the G-C content.
Moran and I think the base-stacking is the causal factor. It is still not clear to me that you
accept this. Though clearly for your purposes it doesn't matter what is the causal factor, only that
there is a correlation.
William L Hunt