The latest paper I have read was published by the W. Scott group in 2006 (Meyer et al. AAC) ( yeah i know that is not proper refrencing. i get better eventually...ma~nana, ma~nana). Here is a little background scoop before we get into the paper. So Regular chain-terminators (i.e. NRTIs) bind wildtype RT and get incorporated into the elongating DNA chain. But! what is special about RT is that even though the forward reaction (i.e. DNA elongation) is favored, the back reaction (e.i. excision; the removal of an incorporated nucleotide) can happen as well. Now obviously under normal conditions this reaction is significantly unfavored. But! if the forward reaction happens to be slowed down (in this case let's say because of the incorporation of a certain chain-terminator), then the excision reaction becomes more relevant.
Now a number of NRTI-resistance associated mutations function by promoting this reaction. Very popular example of this is TAMs (Thymidine-analogue associated mutations).
So then the next question is...well...how? How are these mutations favoring excision?
To answer that question, we have to have a quick review of teh excision reaction itself. Now when a nucleotide is being incorporated, it has three phosphates right? and two of those get released (hydrolysis) and the nucleic acid and one phosphate (5') remain in the growing DNA chain. The excision reaction is exactly the opposite of that. It is when two phosphates come in and bind to the remaining phosphate on the nucleic acid and hence a nucleotide is released. So relevant to what we are saying here is, where are those two phosphates coming from? in vitro, this can be a simple pyrophophate (PPi, i.e. a molecule consisiting of two phosphates). But it seems that a much more relevant in vivo PPi donor is ATP (Adenosine triphosphate). So the way I like to think about it is that ATP basically backs up the driveway from where PPi normally leaves.
So! to make the story short, if somehow a mutation caused ATP to bind more favorably as a PPi donor, then that mutation could theoretically promote excision. And we thikn this is what is happening with TAMs.
ok so this is the background info necessary for getting into the paper. why don't i continue with the actual paper at our next session.
p.s. i will try to reference the statements that i make. Because 1) it will be better for you 2) it will help me with remmebering who said what where and why.
