We are trying to perform Western blots looking for a 1KDa protein and can't seem to find any bands in that range. The smaller bands on our ladder don't seem to transfer well when we image them, would a wet transfer be more effective?
I think that your problem may not be cause by the transfer method but by the membrane. Very small proteins can easily get through the membrane without much binding. What is the pore size of membranes that you use 0.2 or 0.45µm? The 0.2 µm is much better for small proteins.
Also there is an interesting discussion on a relatively similar topic: https://www.researchgate.net/post/How_to_detect_small_molecular_weight_proteins_10_11_17_20_KDa_by_western_blot
I use an iBlot myself and I've never have a problem imaging the smaller bands. The ladder I use is SeeBlue Plus2 and while the two larger bands (188 and 98) always have some coloration left on the gel, they've clearly come through on the development. This goes double for the smaller 3 and 6 kDa bands. I have never missed them.
Might I ask what your transfer time clocks in at? I use 7 minutes. The iBlot uses a lot of energy to drive the proteins through and, especially with a nitrocellulose membrane, a longer transfer time could be causing the bands to bleed into the cathode stack.
what program do you use on the iBlot for voltage?
I talked with the company and they suggested program 5 (10V) for about 2min we normally do program 0 for 7min
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