Hi Bhagya i think you mean that using agarose insteade of polyacrylamide and i say that is possible but a standard melting temperature agarose is recommend for routine separation while When proteins are to be recovered for further analysis, a low melting temperature agarose is recommend. Agarose Concentration based on Protein Size (kDa) where 20 - 200 kDa need 5% agarose 150 - 300 kDa 3%, 300 – 600 kDa 2%, 1,000 - 5,000 kDa 1.0% agarose respectively. The buffer systems used for agarose electrophoresis are similar to those used for polyacrylamide electrophoresis but we have found that a Tris-borate provide greater resolution. The procedures for dissolving and casting agarose gels for protein separation are the same as the procedures used for nucleic acid separation. Sample preparation and amount of protein that can be loaded on agarose gels is essentially the same as for polyacrylamide gels

Hi Bhagya i think you mean that using agarose insteade of polyacrylamide and i say that is possible but a standard melting temperature agarose is recommend for routine separation while When proteins are to be recovered for further analysis, a low melting temperature agarose is recommend. Agarose Concentration based on Protein Size (kDa) where 20 - 200 kDa need 5% agarose 150 - 300 kDa 3%, 300 – 600 kDa 2%, 1,000 - 5,000 kDa 1.0% agarose respectively. The buffer systems used for agarose electrophoresis are similar to those used for polyacrylamide electrophoresis but we have found that a Tris-borate provide greater resolution. The procedures for dissolving and casting agarose gels for protein separation are the same as the procedures used for nucleic acid separation. Sample preparation and amount of protein that can be loaded on agarose gels is essentially the same as for polyacrylamide gels

@ Ehab,

Thanks for you valuable idea. should it be run using the same buffer which is used to prepare the agarose gel? normally we use TBE buffer to prepare agarose gels. So, I should use the same buffer for running the gel, shouldn't it? for the polyacrylamide gels we use a buffer contain tris, glycine and sds.

Hi. it is possible. see these articles

http://link.springer.com/protocol/10.1007%2F978-1-61779-821-4_10

@ Mohsen,

Thanks a lot.