I have isolated RNA from a few fish samples, and need to synthesize the first strand of cDNA and check if cDNA has been synthesized or not agarose gel electrophoresis has to be performed.
How will I know the size of the cDNA synthesized and what percent of agarose has to used accordingly?
Depends on how you generated your cDNA.
If you used random primers you will get a mix of sizes while if you used oligo-dT or a gene specific primer you expect a size from the primer site to the start of the transcript (assuming your enzyme was able to synthetise the full length). You also need to remember that.
1. cDNA levels are usually low and may be hard to detect.
2. EtBr doesn't bind ssDNA very well so you will need to use another dye such as Sybr gold.
Often you get small amounts of cDNA that amplify very well but are invisible on agarose gels. I would go directly to the amplification stage of your work with pcr which will probably work even on samples not visible in gels
It is not possible to check cDNA reactions on any kind of gel because the reaction product includes both the RNA sample that was the template as well as the cDNA. These can not be distinguished by visualization, especially since the RNA will often be in great excess to the cDNA. To assess the success of your cDNA reaction, you need to compare "plus RT" and "minus RT" reactions in a subsequent (spliced)gene-specific PCR. Ideally the "minus RT" sample will be identical to the "plus RT" reaction in every respect except that the reverse transcriptase is replaced by water. In practice, you can usually just use an appropriate amount of the template RNA--adjusting to the appropriate dilution. It is preferable that the primers for this reaction span a splice junction because there is likely some genomic DNA contamination of your RNA prep potentially allowing amplification of a genomic DNA product.
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