I am trying perform PAGE of bio synthesized nanoparticles in order to understand capping protein's molecular weight, but getting smear, how to tackle with this issue?
Hi Sourabh, for nanoparticles, you might want to look at doing agarose electrophoresis.
http://www.captura.uchile.cl/bitstream/handle/2250/6690/Olmedo_Ivonne.pdf?sequence=1
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656902/
I have no personal experience with this, but I would guess that the varying lengths of whatever polymer your nanoparticles are made of is the source of the smearing. Another possibility is that a chemical crosslinking procedure used to attach the protein to the nanoparticles caused crosslinking and/or degradation of the protein, which results in smearing on the gel because of the variable protein molecular weight. Both of these problems might apply.
If you added a purified capping protein, you should already know its molecular weight. If you are concerned that the molecular weight might have changed, is there some way you can remove the protein from the nanoparticle prior to gel electrophoresis?
It would help to have more details about the formulation and how you prepare it for electrophoresis.
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