Protein denaturation can be achieved using a loading buffer containing a denaturing agent e.g SDS which is heated at 95-100☌ for 5 minutes Heat denaturation will unfold the protein and enable the antibody to bind its corresponding epitope located within the 3D conformation of the protein. Additionally, reducing agents such as ß-mercaptoethanol and DTT must be left out of the loading buffer and migration buffer.Ĭertain proteins will require denaturation for the antibody to work effectively. When this is the case it is not necessary to denature the sample and therefore SDS should be left out and the sample. In some cases, the antibody used will recognise the protein in native state, as the selected epitope may exist on the surface of the folded structure. This may be achieved by mechanical shearing. It is important to note that when preservation of protein-protein interactions is required a buffer without ionic and non-ionic detergents should be used. Information about the protein form your antibody recognises can be found on the data sheet supplied by the manufacturer. Lysis buffers containing SDS have a denaturing effect on protein, whilst buffers without detergent or mild non-ionic detergents such as NP-40 and Triton X-100 should be used when the antibody will only recognise protein in its native structure. It should also be noted that the lysis buffer used will affect antibody choice further on in the protocol with regards to the protein form it recognizes, either native or denatured. Lysis buffer containing sodium dodecyl sulfate (SDS) and other ionic detergents is considered to give the highest protein yield and is the most damaging to the sample. The choice of lysis buffer used will depend on the yield of protein required and the subcellular localisation of the protein. The protein of interest must be solubilized in order to migrate through the separating gel. The first step of a western blot protocol is protein extraction from cells or tissue.
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