I have run a agarose gel with my RNA samples. The 16S and 23S rRNA bands are absent, but I also do not see a smear on my gel to indicate degradation of the RNA. There was only a blob on the bottom of the gel, which I do not know what it is. Will I still be able to successfully synthesis cDNA from my RNA.
Probably the "blob" represents very tiny (degraded) fragments of RNA. So I would guess that cDNA preparation is not your next step. You need to identify what is causing the RNA degradation in your purification protocol first and make better RNA preps.
I agree that your sample is probably majorly degraded. You probably don't see a smear because even the 'smear' is degraded into smaller pieces! How are you obtaining RNA? And from what source?
I don't think that you should use this RN preparation for cDNA synthesis. You RNA is degraded. Quantitate and load on the gel. Even 250 ng preparation should show rRNA bands. If you don't see band, RNA prep is degraded.
blob in the bottom of your gel represent that your RNA is degraded so u should not use it for cDNA synthsis
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