RNA ligation

Nick Theodorakis via methods%40net.bio.net (by nick.theodorakis from gmail.com)
Fri Nov 20 07:47:29 EST 2009


On Nov 20, 6:19 am, Aawara Chowdhury <aaw... from pontiff-playground.org>
wrote:
> In <63e4a4c6-9734-4886-baba-dab9a41e7... from a21g2000yqc.googlegroups.com>,
>  Nick Theodorakis <nick.theodora... from gmail.com> wrote:
>
> >> 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 sounds sensible. If the oligo has no terminal phosphates and the
> > RNA is 5' phosphorylated, then the only reactions that should happen
> > are ligation of the oligo to the 5'end of the RNA .. [deleted]..
>
> Won't work for mRNA - there is no free 5'phosphate.
>

He specified that his RNA population is uncapped and phosphorylated in
his original post. I don't know how it got that way, but I can imagine
at least one scenario.

Nick

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Nick Theodorakis
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