I performed a nucleic acid extraction using 2 protocols for RNA extraction (Dengue Virus) and one parameter I need to evaluate is the integrity of my RNA samples. In this case, I can't use a RNA ladder. Also, I recently performed a RT-qPCR for the same RNA samples and I have the cDNA.
Comparison with a DNA ladder may not be exactly accurate but it should be useful for comparison between electrophoresis runs because it should run at the same size range for a given buffer system
Hello Gabriel,
You cannot use DNA ladder for RNA samples. Though RNA and DNA ladders may serve the same purpose, they are specific to their respective nucleic acids.
There are differences between them.
1. RNA ladders will contain RNA fragments of varying sizes.
2. You will have to run RNA samples in a denaturing electrophoresis gel in order to determine fragment sizes.
3. RNA migrates faster than DNA through electrophoresis gel.
You need to consider these differences before you plan your experiment.
However, if you are interested in checking the integrity of your RNA samples, you need not use the ladder. Run RNA samples in a denaturing electrophoresis gel (a denaturing agarose gel containing formaldehyde).
If your RNA samples are intact, you will observe a sharp and clear 28S and 18S rRNA bands. The 28S rRNA band should be approximately twice as intense as the 18S rRNA band. This 2:1 ratio for 28S:18S is a good indication that your RNA sample is intact.
Best.
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