Fwd: RNA ligation

Chris McDermott-Roe via methods%40net.bio.net (by cjmcdermottroe from googlemail.com)
Sat Nov 21 19:42:34 EST 2009


You're right Nick, it's chemically-decapped mRNA.  You knock the 5'
phosphate off with tobacco acid pyrophosphatase - it's standard to most 5'
'RACE protocols.  On the question of whether its technically correct to
refer to a decapped mRNA moiety as 'mRNA', I don't see any harm since an
uncapped mRNA can still function as a messenger RNA in that it can generate
protein products (albeit reduced in the case of cap-dependent translation
but not in the case of cap-independent translation).


---------- Forwarded message --------
From: Nick Theodorakis <nick.theodorakis from gmail.com>
Date: 2009/11/21
Subject: Re: RNA ligation
To: methods from magpie.bio.indiana.edu


On Nov 20, 9:58 pm, Aawara Chowdhury <aaw... from pontiff-playground.org>
wrote:
> In <4e7e0a8e-85b3-4eda-9190-7740ce3fc... from p35g2000yqh.googlegroups.com>,
>  Nick Theodorakis <nick.theodora... from gmail.com> wrote:
>
>
>
> >> 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.
>
> Then it cannot be mRNA.  It could be pre-mRNA or hnRNA, but mRNA needs
> to be capped.
>

Well, whatever. I'll just assume that the OP knows something about the
RNA he has. But consider it could be:

1) prokaryotic or viral origin
2) mRNA that was chemically decapped or partially degraded
3) he could be looking for degradation intermediates.

If you want to get nitpicky I suppose you can call 2) or 3) "mRNA-
derived RNA fragments" or something, if that will make you happy.

Nick

--
Nick Theodorakis
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