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Specific cross-reactivity with unrelated proteins

Typically, antibody epitopes are about 5-8 amino acids in length. The smallest epitope, which we have mapped so far, comprised only three amino acids and part of the adjacent peptide bond. This poses a possible problem for both peptide and monoclonal antibodies: For statistical reasons, identical (or closely related) sequence stretches of a relevant size may occur in various unrelated proteins. Indeed, identities of - let's say five - consecutive amino acids are essentially inevitable.

This may be sufficient to elicit a specific (!) cross-reactivity with an protein otherwise unrelated in sequence and function. "Specific" - because this antibody was raised (and purified) against this sequence and hence the reactivity is legitimate and desired with the "correct" antigen but disastrous with the "wrong" protein. Therefore, it is mandatory to put a special focus on this fact when designing a peptide antigen.

ambiguous sequence
Ambiguous peptide sequences should be taboo: Possible x-reactivity of anti-albumin antibodies with LMBR1-DCP2 and vice versa