RNA ligation

[Aawara Chowdhury]

In <mailman.322.1258653708.1133.methods from net.bio.net>,
 Chris McDermott-Roe <cjmcdermottroe from googlemail.com> wrote:

> Hi,
>
> Yes, they'll both be single stranded.  One will be the mRNA that I want to
> tag (at the 5' end), the other will be a ss oligo.  My concern is that the
> oligo may ligate to the 3' end of the mRNA but I guess this will depend on
> how I have the oligo modified?  Is it sensible to assume that if it (the
> oligo) is 3' hydroxylated but NOT 5' phosphorylated, then it will bond with
> the exposed 5' phosphate on the mRNA and NOT the 3' OH??

That will NOT work.  mRNAs do not have a free 5' phosphate.  As you may
recall, mRNAs are capped with a 7-methylguanosine cap which is covalently 
linked to the first transcribed nucleotide by a 5'-5' triphosphate bond.

There are mammalian/eukaryotic and viral decapping enzymes, but I don't 
know of any that work on all mRNAs in vitro, or in vivo.

AC
-- 
Email: echo 36434455860060025978157675027927670979097959886449930P | dc