Hello,
Recently I've been doing a lot of agarose gel electrophoresis, both for RNA and DNA, under different conditions (MOPS FA gels for RNA, TAE 1X gels for DNA). While they're mostly fine, I always have a weird, faint smear upwards coming from the heavier bands. Originally this started happening with my RNA gels, but it wasn't degradation (you can see that in the first image, the first lane after the ladder is clearly degraded, 1,2% gel). Then I started getting the same effect on my DNA gels (second image, 2% gel).
I've been trying to puzzle out what exactly is going on, but haven't come up with anything that can really explain whats going on, beyond being some flaw in the gel making process itself or maybe in the .
Can you please tell what is the size of your nucleic acids (Kb) and what was the voltage under the electrophoresis going on?
Md. Asif Nadim Khan The expected size of the RNA bands should be around 4kb for the 28S subunit and around 1kb for the 18S. The DNA bands should be 552bp. The electric characteristics for each gel were 100V and 500mA for the RNA gels and 100 and 300mA for the DNA gels.
@Gabriel Garrido From my personal experience and knowledge, I suggest you to lower the current around 120mA for both DNA and RNA. Thus you can follow as below.
For DNA: Use TBE instead of TAE, Voltage 100, Current 120mA. Gel concentration 2% is okay (as the size is small).
For RNA: TAE buffer is okay, the Gel concentration should be of around 1%, current 120mA.
I hope my answer will help you to go ahead in your research. Please let me know you become successful.
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