Can cDNA be checked on 1% agarose gel before qPCR to confirm the quality of the RNA that it was converted from or the efficiency of the RT reaction
Hello Mennatullah Khalil
Yes, cDNA can be checked on agarose gel, but you need to use the cDNA as a template in a general PCR reaction using PCR primers for any housekeeping gene such as β-actin primers (specific for cDNA). If you get a proper band on the gel, it means that you have synthesized cDNA successfully. Just running cDNA on gel will not provide you with any information. You may or may not get a smear.
Best.
Hi Mennatullah Khalil as Malcolm Nobre mentioned, running just the cDNA on an agarose gel will not reveal anything. However, to confirm the quality of the RNA, you can run bleach gel electrophoresis.
Good luck!
Hi Mennatullah Khalil
Yes, cDNA can be checked on a 1% agarose gel to get a rough idea of RNA integrity and reverse transcription (RT) efficiency. Running RNA on the gel can show distinct bands for intact RNA, indicating it hasn't degraded. Running cDNA can show a smear, indicating a range of cDNA lengths, suggestive of a successful RT reaction. However, agarose gel electrophoresis isn't sensitive enough for small size differences and doesn't provide quantitative data. For qPCR, it's more reliable to use a standard curve or reference genes to ensure reaction efficiency and reliability.
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