Design and Production of Specifically High Affinity Reacting Peptides (SHARP®-s)

A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests that significant number of amino acids in specifically interacting proteins are coded by partially complementary codons. It means that the 1 and 3 residues of codons coding many co-locating amino acids are complementary but the 2 may but not necessarily be complementary: like 5’-AXG-3’/3’-CXT-5’ codon pair, where X is any nucleotide.

A mixture of 45 residue long, reverse, partially complementary oligonucleotide sequences (target pool) was synthesized to selected epitopes of query mRNA sequences. The 2^nd codon residues were randomized. The target oligonucleotide pool was inserted into vectors, expressed and the protein products were screened for affinity to the query in Bacterial Two-Hybrid System. The best clones were used for larger-scale protein syntheses and characterization. It was possible to design and produce specific high affinity reacting (Kd: ~100 nM) oligopeptide reagents to GAL4 query oligopeptides.

Second codon residue randomization is a promising method to design and produce affinity peptides to any protein sequences. The method has the potential to be a rapid, inexpensive, high throughput, non-immunoglobulin based alternative to recent in vivo antibody generating procedures.