<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>In the post-genomic era, validation of candidate gene targets frequently requires proteinbased
strategies. Phage display is a powerful tool to define protein-protein interactions by
generating peptide binders against target antigens. Epitope phage display libraries have the
potential to enrich coding exon sequences from human genomic loci. We evaluated genomic
and cDNA phage display strategies to identify genes in the 5q31 Interleukin gene cluster
and to enrich cell surface receptor tyrosine kinase genes from a breast cancer cDNA
library. A genomic display library containing 2 ×  clones with exon-sized inserts was
selected with antibodies specific for human Interleukin-4 (IL-4) and Interleukin-13. The
library was enriched significantly after two selection rounds and DNA sequencing revealed
unique clones. One clone matched a cognate IL-4 epitope; however, the majority of clone
insert sequences corresponded to <italic>E. coli</italic> genomic DNA. These bacterial sequences act as
‘mimotopes’ (mimetic sequences of the true epitope), correspond to open reading frames,
generate displayed peptides, and compete for binding during phage selection. The specificity
of these mimotopes for IL-4 was confirmed by competition ELISA. Other <italic>E. coli</italic>
mimotopes were generated using additional antibodies. Mimotopes for a receptor tyrosine
kinase gene were also selected using a breast cancer SKBR-3 cDNA phage display library,
screened against an anti-erbB2 monoclonal antibody. Identification of mimotopes in
genomic and cDNA phage libraries is essential for phage display-based protein validation
assays and two-hybrid phage approaches that examine protein-protein interactions. The
predominance of <italic>E. coli</italic> mimotopes suggests that the <italic>E. coli</italic> genome may be useful to
generate peptide diversity biased towards protein coding sequences.</p> <p>Abbreviations used: IL, interleukin; ELISA, enzyme linked immunoabsorbant assay;
PBS, phospho-buffered saline; cfu, colony forming units.</p>
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Comp Funct Genomics. 2002 Jun; 3(3):254-263