rRNA sizes on Agarose gel

lior lobel · 07-17-2013, 09:14 AM

Hi All,

I ran a Agarsoe gel with my RNA samples and got the attached pattern.
23S rRNA and 16S rRNA are supposed to be ~3000 bps and ~1500 bps, however in this run I see 1500 and 750 bands.

Can this be a gel problem? Has anyone encountered this?

Thanks,

Lior

cliffbeall · 07-19-2013, 06:21 AM

RNA will not run on a gel exactly according to its size because it is single stranded and the secondary structure can be variable. To get an accurate size you need to use a denaturing gel (formaldehyde, urea, methyl mercury) and compare it to RNA standards.

Since you see 2 pretty sharp bands, your RNA is probably fine.

Edit: There is also a bioanalyzer chip for RNA that would be an option if you have access to an instrument.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Disagreement between bioanalyzer and agarose gel for PCR amplicon library	mbirnb	Sample Prep / Library Generation	4	08-03-2015 10:28 AM
Size selection: agarose gel / acrylamide gel	amazonic9	Sample Prep / Library Generation	2	12-05-2012 03:56 AM
Library invisible on gel, despite Nanodrop results. Gel extraction problem?	thdybwf	Sample Prep / Library Generation	5	09-24-2012 05:41 AM
PubMed: A Highly Parallel Single Molecule Amplification Approach Based on Agarose Dro	Newsbot!	Literature Watch	0	11-23-2011 05:27 AM
4% agarose gels?	ik76	Sample Prep / Library Generation	1	04-01-2010 11:39 AM

07-19-2013, 06:21 AM	#2
cliffbeall Senior Member Location: Ohio Join Date: Jan 2010 Posts: 144	RNA will not run on a gel exactly according to its size because it is single stranded and the secondary structure can be variable. To get an accurate size you need to use a denaturing gel (formaldehyde, urea, methyl mercury) and compare it to RNA standards. Since you see 2 pretty sharp bands, your RNA is probably fine. Edit: There is also a bioanalyzer chip for RNA that would be an option if you have access to an instrument. Last edited by cliffbeall; 07-19-2013 at 06:24 AM.