A fusion protein, or chimeric protein, is created through the joining of two more genes originally coded for separate proteins. The translation of the fused genes is a single protein chain. An example of this is MECT1-MAML2.
The strategy for successfully making an antibody that specifically targets the fusion protein, and not the separate proteins, is essentially the same as for making specific antibodies to exon bridges, point mutations, or post translational modifications such phosphorylations.
In contrast to other projects, designing peptides for antibodies that target a protein fusion site there is not an abundance of possibilities. The peptide has to span the site of course, but even small shifts in sequence can make a significant difference. We want to reduce the number of trivial epitopes – i.e. epitopes that do not contain the join – while having sufficient length to the peptide for the antibody production. The peptide needs to be soluble, and we want a single facility for the conjugation to a carrier molecule.
Having a good immunogenic antibody generating peptide is essential, but it might not be sufficient. There is a possibility that the antibody will cross react with one or both of the singular proteins. This is why the resulting antibody should be tested against the corresponding sequences of the non-fused singular proteins. Removal of the cross reacting antibodies may then be attempted by absorbing them.
Designing a good peptide for immunisation is of course crucial, but the actual quality of the peptide is also important. There is much to be said about producing high quality antibody generating peptides, but the long and the short of it is that there is no room for corner cutting and that means that you need the better raw materials, you need the better synthesis strategy, and you need excellent quality control to match it.
Innovagen was founded in 1992, at a time when anti-peptide antibodies were not as common as they are today. Since then we have provided the research community with numerous antibodies that specifically recognise fusion proteins. Our commitment to providing excellent quality and customer service are things that you and your research project will benefit from as well.
Examples of references of customers using our custom fusion antibody service include;
A. Behboudi, F. Enlund, M. Winnes, Y. Andrén, A. Nordkvist, I. Leivo, E. Flaberg, L. Szekely, A. Mäkitie, R. Grenman, J. Mark & G. Stenman. 2006.
Molecular Classification of Mucoepidermoid Carcinomas—Prognostic Significance of the MECT1–MAML2 Fusion Oncogene
Genes, Chromosomes & Cancer 45:470–481 (2006)
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