Hi Muhammad Fozan

1. You can use DEPC-treated water to prepare your gel, assuming your RNA is getting degraded in the gel.

2. You can use a different buffer system like MESA + formaldehyde agarose gel, which as per my experience gives best results for RNA.

3. Also take note of your visualization reagent's sensitivity. For Gel Red it is ~50ng DNA/RNA.

Hope it helps!

Subham Basak Thank you very much.

RNA electrophoresis can be performed on both agarose and acrylamide gels. Agarose gels are commonly used for RNA electrophoresis as they are easier to prepare and are more forgiving in terms of sample loading and buffer conditions. MOPS-Formaldehyde gel is a type of agarose gel that is commonly used for the visualization of RNA.

The buffer formulation for RNA electrophoresis can vary depending on the type of gel used. For agarose gels, commonly used buffers include MOPS, MOPs-HEPES, TAE, and TBE. The choice of buffer can affect the resolution and quality of the RNA bands obtained. For example, MOPS is known to produce sharper and more defined bands, while TBE buffer is commonly used for RNA sequencing applications.

In addition to the buffer, other factors that can affect the quality of RNA electrophoresis include the RNA extraction method, the integrity of the RNA sample, the amount of RNA loaded onto the gel, and the running conditions (voltage, time, temperature, etc.).

If you are not getting the desired results with your RNA extraction kit, it may be helpful to troubleshoot the extraction protocol and ensure that you are obtaining high-quality RNA before proceeding with electrophoresis.

These video playlists might be helpful to you:

https://www.youtube.com/playlist?list=PLzBiAPKi8vOPbE7Db9mKwloe34E8rXXEU

https://www.youtube.com/playlist?list=PLzBiAPKi8vONSqjcweFWHMRy13y3484bE

https://www.youtube.com/playlist?list=PLzBiAPKi8vOMheKwb0mu1dcZRaeGUFSlw