User:Brourd/Homopolymer AMP

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Revision as of 18:27, 12 August 2014 by Brourd (talk | contribs) (Page creation)
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Based on previous experiments, when there are more than nine or so consecutive, unpaired adenine residues, the first six-seven residues running from 3' to 5' are exposed to chemical modification, and all residues before these last 6 adenine residues are protected from chemical modification.


<img src="http://i.imgur.com/c0w8aM4.png" alt="12AMP" />

 

However, all of these experiments (so far) have been focused solely on unpaired adenine residues, which does not provide much detail on the structure of poly-adenine sequences. The experiment that I propose would try to tease out information on the nature of this protection signal. What happens when these chemically modified adenosine are  are incorporated into a base pair?


<img src="http://i.imgur.com/84nuKkH.png" alt="ProvsExp" />
The experiment essentially focuses upon the four unpaired residues in the 4x4AAAA/AAAA 2-way junction. What will their SHAPE signal be? There are several possible outcomes.
<img src="http://i.imgur.com/nRokzEz.png" alt="What happens" />
  • So, the first outcome: the reactivity signals indicate that the first two residues of the 4x4 are protected from chemical modification, and the last two residues are exposed. The reactivity signals of the uracil strands do not differ.
  • Second outcome: The Reactivity signals indicate that the first two residues of the 4x4 are protected from chemical modification, and the last two resudues are exposed. The reactivity signals for the uracil strands are amplified in some way. For example, the uracil residues that would base pair with the protected adenine residues are "cold spots" indicating that there was little to no chemical modification, and the uracil residues that base pair with the supposed to be exposed adenine strand, are "hot spots," indicating above average chemical modification and mobility of the backbone. (or both)
  • Third outcome: the reactivity signals for the four residues in the 4x4 junction indicate that they are all exposed to chemical modification. This would prove the presence of a structure, and would probably pave the way for a greater number of tests, to determine which adenine residues must remain unpaired for the structure to form.
Other outcomes exist, depending on a variety of factors, and what the data from the other sequences indicate.
You can check the 10 sequences submitted in this pilot project
<img src="http://i.imgur.com/br2QQ9J.png" alt="HalfnHalf" />