23s/16s rRNA ratio

[IanMc]

"yotsawat pomyen" <yotsa from yahoo.com> wrote in message 
news:mailman.806.1188842838.11350.methods from net.bio.net...
> Hi all,
>
> I have to extract total RNA from E.coli for microarray
> experiment. I analyzed my RNA using 2100 Bioanalyzer
> and it provides information about rRNA ratio. I did
> some search and found that mostly 23s/16s rRNA ratio
> for good RNA quality is about 2:1. My results from
> Bioanalyzer are vary from 1.8 to 2.6.
> My questions are:
> 1. What rRNA ratio tell me about my RNA?
In general the 23S rRNA is more labile than the 16S. So the ratio will 
decrease as the 23S degrades. The lower the ratio the more degradation has 
ocurred.

> 2. Why they said that the 23s/16s ratio of 2:1 is
> good? Why 2:1?

There are more nucleotides per molecule to bind the dye used in the assay so 
the 23S peak should be larger given a 1:1 molecular ratio of rRNA subunits. 
I guess the exact figure is dependant on the organism.

> 3. Is my RNA in good shape judging from rRNA ratio
> that I got?

Yes. Other things to look for are 23/16S peaks of about the same height and 
a relatively flat baseline. Agilent now sell software which gives an RNA 
Integrity Number but I am not sure how well validated it is for prokaryotic 
organisms.

Regards,

IanMc

>
> Thank you
>
> Yotsawat Pomyen
>
>
>
>
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