DNA intercolation

[holden]

Fellow Researchers,

   One of the members of my research group has taken data on the 
intercolation of a flat compound into the DNA chain.  If a formula
could be made that would either proove or disproove her theory it
would be greatly appreciated for her thesis.

   Here is the problem:

   The real life question I'm trying to solve is that of an emitting
agent that can fit inbetween two sets of base pairs in the DNA chain.
Only those agents that are between AT-AT pairs with out any GC-GC pairs
on either side of those can emit (postulate).  So in other words, if 

   example:
     This can emit          This can emit      This cannot emit
     from 2 places          from 1 place       at all

         A-T                    A-T               A-T 
         A-T                    A-T               A-T
         A-T                    A-T               G-C 
         A-T                    G-C               A-T
         G-C                    A-T               A-T 

   This is an easy case and it also looks like the number of sets of 
three could be counted to give the emittence, but with a long chain of
groups this might ot be the case as the real number are >800. Therefore  
if given either the total number of AT and the total number of GC base 
pairs, or the percent composition of AT and GC base (assuming all possible
combinations of one such ratio(AT:GC)) is it possible to calculate the 
average emission?

   Any input would be appreciated.  Thanks in advance.

                       -Holden Harris

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|  Holden Harris               |  The McMillin Group        |
|  hharris at sage.cc.purdue.edu  |  Purdue University         |
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