Are synthetic peptides suitable for the detection of continuous epitopes only?

Present-day methods for the definition of antibody binding sites on antigenic polypeptides show a strong bias toward identification of sequential epitopes. We have employed anti-sequence monoclonal antibodies raised against short synthetic peptides to screen a random-primed cDNA library constructed in an expression vector. Sequence data analysis performed on three clones thus isolated showed that the clones did not cross-hybridize and that the antigenic peptide sequence was found in none of them. Our findings suggest therefore that sequential epitopes may be preferentially identified because of an inherent bias in commonly used epitope mapping protocols which masks available conformational determinants.