RNA sizes

David F. Spencer dspencer at is.dal.ca
Fri May 30 16:02:24 EST 1997

In article <338C0991.1E9D at ukbf.fu-berlin.de>, schmidt-ott at ukbf.fu-berlin.de

> Hello!
> I made a weird observation concerning RNA sizes: I ran total RNA 
> from tissue cultures on a non-denaturating agarose gel to check for
> integrity, using a DNA size marker (100 bp-Marker). On repetition of the
> experiment, the 18S and 28S bands appeared in different positions
> relative to the DNA marker. I suspect that this might be due to
> different concentrations of agarose in the gel. Has anyone made a
> similar observation ?
> Secondly, I am desperately looking for a source where I can find the
> exact bp sizes of the 18S and 28S RNA bands in different species, for
> example in rats, mice, cattle etc.

The mobility of 18S and 28S RNAs on non-denaturing gels will have no particular
relationship to their actual sizes. These RNAs have considerable secondary
structure and this is responsible for the mobility differences between gels
of different pore sizes. In addition, evaluating RNA quality on non-denaturing
gels will give unreliable estimates of RNA degradation because secondary
structure can hold together pieces that are no longer continuous. You should use
denaturing agarose (formaldehyde) or acrylamide (urea) if that is the goal; the
latter is the more practical for RNA's that are about 2 k or shorter and much
easier to work with. For larger RNAs you're pretty much stuck with either
formaldehyde, gloxal or methylmercury (yuk) agarose gels.

The sizes of mammalian LSUs (28S) vary considerably from a high of more than 5k
for human, to about 4.7 for rodent and can range down to about 3.8 k. But their
mobility on non-denaturing gels will not necessarily reflect their true size;
even on denaturing gels the mobilities of rRNAs are not entirely predictable.



David F. Spencer, PhD
Dept. of Biochemistry
Dalhousie University
Halifax, Nova Scotia, Canada

dspencer at is.dal.ca
dspencer at rsu.biochem.dal.ca

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