Why is the actual band size on a western blot different from the predicted size of the protein?
Western blotting is based on the separation of proteins by their size on a gel. However, migration of proteins through the gel matrix is also affected by other factors, which may cause the observed band size to be different from the predicted size.
Common causes are:
-Post-translational modification; for example phosphorylation and glycosylation increase the size of the protein
-Post-translation cleavage; many proteins are synthesized as precursor proteins, and then cleaved to give the active form
-Multimers, for example dimerization of a protein. This is usually prevented under reducing conditions, although strong interactions can result in the appearance of higher bands
-Splice variants; alternative splicing may result in different sized proteins being produced from the same gene
-Relative charge; the composition of amino acids (charged vs. non-charged)
What are the Invitrogen AP Chromogenic Substrate (BCIP/NBT) and Invitrogen HRP Chromogenic Substrate (TMB)?
- Invitrogen AP Chromogenic Substrate (BCIP/NBT) and Invitrogen HRP Chromogenic Substrate (TMB) are ready-to-use, single component substrates for sensitive immunodetection of alkaline phosphatase (AP) or horse radish peroxidase (HRP), respectively, on western blots or dot blots. The sensitivity of the AP substrate is in the 100 pg range, while the HRP substrate is in the 1 ng range (see Note below).
- Invitrogen AP Chromogenic Substrate consists of a ready-to-use solution of 5-bromo-4-chloro-3-indolyl-1-phosphate (BCIP) and nitroblue tetrazolium (NBT) which forms a black-purple precipitate upon reaction with alkaline phosphatase. It is available as a standalone product (Cat. Nos. WP20001) and is also a component of the WesternBreeze Chromogenic Detection Kits.
- Invitrogen HRP Chromogenic Substrate consists of a ready-to-use non-toxic solution of 3,3',5,5'-tetramethylbenzidine (TMB) which forms a blue precipitate upon reaction with horse radish peroxidase. It is available as a standalone product (Cat. No. WP20004).
Note: Sensitivity may vary depending upon the antigen and antibody used for detection.