Size of 23s and 16s RNA different - (Apr/24/2006 )
I did DNA extraction from B. subtilis sample, but did not use any RNase to remove RNA in my sample. Two distinct bands appear at size 1.2kb and 1.7kb. I am suspecting they are 16s and 23s rRNA. However, I found out the size of 23 and 16s respectively are 2.9kb and 1.5kb.
Does electrophoresis conditions will affect the size of the RNA? I run normal agarose gel by the way, under non-denaturing conditions. Any other factors will affect the size of the RNA from different bacteria?
I'm not very familiar with this topic, but I remember two possibilites:
It is the RNA you mention, but already fragmented. Or second, the RNA is somewhat folded, i.e. having a secondary structure and so appearing to be smaller as expected on the gel.
But this are only guesses.
sizes of rRNAs will depend on percentage of gel, whether you use TBE or TAE.....try a RNase digest to see if you remove them if it is a problem.....?
You can't accurately size RNA under non-denaturing conditions. You should run a formaldehyde gel if you want to do this, with an RNA ladder rather than a DNA ladder