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How to get RNA sample denature to get a nice band on gel electrophoresis

How to get RNA sample denature to get a nice band on gel electrophoresis - RNA Techniques Forum

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Old 04-02-2010, 01:28 AM
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Default How to get RNA sample denature to get a nice band on gel electrophoresis



Hi everyone,
I am working with single strand plant virus RNA. I have had run many gels, but I am not able to get a nice band of my sample. I have tried agarose gel and page. Urea doesnt denature my RNA sample at all, so im trying to run it on agarose gel. It looks like my RNA sample doesnt like to lose its secondary structure.

Does anyone knows a good denaturing reagent that can help me denature my sample to get a nice clear band?

Thank u
Sara
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Old 04-02-2010, 06:26 PM
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Default Re: How to get RNA sample denature to get a nice band on gel electrophoresis

Too little info, but the likely problem is the RNA isolation/preparation.
RNA shouldn't be that difficult to denature. You may be drying it out too long, who knows. How do you extract it?
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Old 04-02-2010, 06:52 PM
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Default Re: How to get RNA sample denature to get a nice band on gel electrophoresis

Im doing phenol/ chloroform extraction.
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Old 04-02-2010, 06:58 PM
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Default Re: How to get RNA sample denature to get a nice band on gel electrophoresis

well let me explain little bit more. I extracted, purified, and crystallized Satellite Tobacco Mosaic Virus (STMV) first from the plant. Then do the phenol/ chloroform extraction on the crystal virus.
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Old 05-05-2010, 07:52 AM
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Default Re: How to get RNA sample denature to get a nice band on gel electrophoresis

hi sara simply my the RNA was degraded during extraction process for the deanturation of the RNA i simple but it in the pcr for 5 min at 72 degree celsius that works fine with me for PVY PVX bovine fever virus try it and tell me if it works otherwise i will try to find way more easier than that
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Old 05-12-2010, 08:18 AM
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Default Re: How to get RNA sample denature to get a nice band on gel electrophoresis

thank you so much
well I added ETDA to my RNA sample before denaturing it and then denatured it in 80 degree with excess Famide and actually I got nice bands
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