marion at SMTPLINK.IPFW.INDIANA.EDU wrote:
> I am running total RNA through formaldehyde gels and
> staining with EtBr. I see 5 bands of ribosomal RNA. Can
> someone tell me the sizes of these bands? I've tried both
> RNA and DNA molecular weight markers in these gels and
> usually only see a smear. Is there a way to treat the
> marker to get clear separation of the bands?
>> Thank you.
> Amy Marion
I always got two ribosomal bands when running fern gametophyte RNA and
may not be able to answer your question. However, there are four
ribosomal RNA bands you should see, sometimes five, depending on your
isolation procedures. The highest band is the 45S ribosomal RNA
precursor, the second is 28S ribosomal RNA, the third is chloroplast
ribosomal RNA, the fourth is 18S ribosomal RNA and the fifth is the
chloroplast 16s ribosomal RNA. At the low molecular weight positions,
you may see several bands and they should be tRNA and 4/5S ribosomal
RNA. Usually, we could not get the 45S ribosomal RNA precursor, and I
do not know why.
If you run a native gel, heat the RNA at 65C for 5min and chill on ice
prior to running, and use 1Kb ladder(BRL) as marker, you may see 28S and
18S ribosomal RNA at the positions of 1.5-2 kb and 1kb, respectively.
The chloroplast ribosomal RNA species are visible, too.