I think so..But did you find any solution for this issue? Since I design the peptid structure do you think I should change some part of it? I heard somewhere that it might be because of ribosom machinery. It synthesizes the peptide insufficiently and stop some where.
Actually I think they shouldn't be non specific bands, because they are expressed after IPTG induction and they can be seen even after Ni-NTA chromatography(His-Tag). I need a pure recombinant peptide but I don't know why I see multi bands at every steps!
I have cloned a 500bp gene into pET21b and after expression I found out that 3 bands are expressed and after purification it shows 3 bands as well as western blot result. one band is exactly the same as desired protein and the others with lower molecular weights (about 2-5kDa differences). I should point out that I double digested the PCR amplified insert using NdeI and HindIII and the strange thing was that on gel agarose it seems that the digested bands are aggregated and resulted in very heavy band! I incubated them at 50degree and after that it results in 2 bands (one the same as desired and the other heavier). I am not sure if the enzymes are working insufficiently.. and so result in different bands or just the problem is in expression part.
Can anyone give me a suggestion?