04 March 2021 4 5K Report

Hi, I have problems with running gel electrophoresis. I have tried agarose gel electrophoresis and native PAGE.

I have two proteins, which have molecular weights of ~30kDa and ~180kDa

and two aptamers (oligonucleotide), one is 51nt and the other is 18nt

I have to check whether they bind: ~30kDa with 51nt, and ~180kDa with 18nt

So, what I did was put different amounts of protein (10-80 pmol) with 10 pmol of the corresponding aptamer and fill the volume with nuclease-free water. Incubate the samples for >1 hr and do gel electrophoresis.

Under Bio-Rad Chem Doc, I see bands at the top and the bottom of the gel (for both samples).

First, did electrophoresis with 1.5% agarose gel and I saw no binding.

Then, I tried native PAGE with different pH buffers and that did the same thing as the agarose.

These aptamers do bind with corresponding proteins because numerous research articles have used the same sequences.

Please help. What should I do now?

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