Peptide sequence selection is likely the most difficult step in the development of anti-peptide antibodies.  Although the design of peptides for use as antigens is not exact, several tips can help maximize the likelihood of success in producing antibodies.  It is important to select sequences which are found on the surface of the native protein, contain both hydrophilic and hydrophobic residues, and preferably have antigenic amino acids (e.g. Cys, Leu, Val, etc.).

One of the main advantages to using synthetic peptides for antibody production is that specific epitopes can be targeted.  A BLASTp search should be performed and a sequence with minimal homology selected to reduce the chance of non-specific antibody binding.  However not only should one consider a sequence that can evoke an immune response, but also features including length, hydrophobicity, series of specific amino acids, etc. can render the peptide useless.

Browse the following online resources to analyze your putative antigenic peptide sequence for homologies, determine physical characteristics of your peptide, and predict the antigenicity with 75% accuracy using an online program based on the method developed by Kolaskar and Tongaonkar (1990).  This method for predicting antigenicity of proteins is based on the occurrence of specific amino acid residues observed in experimentally determined epitopes¹.

References

1.  Kolaskar, A.S., and P.C. Tongaonkar.  (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens.  FEBS Lett., 276(1-2):172-174

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Last modified: 09/15/05 00:00:00