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 ) which
suggests that significant number of amino acids in specifically interacting proteins are coded by partially complementary
codons. It means that the 1st and 3rd residues of codons coding many co-locating amino acids are complementary but the
2nd 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 2nd 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.