A High-throughput Route to Synthetic Antibodies for Array-based Cancer Detection

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DESCRIPTION (provided by applicant): The ability to monitor the levels of large numbers of proteins for indicators of disease (biomarkers) holds great promise for the detection and treatment of many diseases, including cancer. Although most analytical techniques for detecting protein levels in human serum currently rely on ELISA-based assays or mass spectroscopic analysis, protein capture arrays have gained considerable interest as a future technology for proteome-wide analysis. The studies described in this application seek to develop a comprehensive array of high affinity synthetic antibodies (synbodies) that can be used to detect and profile cancer and cancer-related proteins in human blood and saliva. In contrast to immunoglobins, for which high costs and slow production rates limit the availability of suitable quality affinity reagents, the rapid synthesis of artificial antibodies from low cost chemical reagents offers a possible solution to the protein ligand problem. The goal of this application is to develop synthetic antibodies to five known cancer biomarkers using a technology that we call systematic recombination of ligands and linkers (SRLL). This technology combines the multiplex capability of surface plasmon resonance (SPR) with the nanometer-scale precision of DNA self-assembly to identify optimal peptide pairs and peptide pair separation distances needed to produce multivalent binding agents from monovalent ligands previously identified by screening or selection methods. We have termed the ligands that emerge from this process "synbodies". The Specific Aims of this proposal are to: 1. Determine the minimum number of selection steps needed to produce modest affinity peptide ligands to five well-established cancer biomarkers. 2. Generate an array of high affinity synthetic antibodies to the five cancer biomarkers targeted in Specific Aim 1.The relevance of the proposed research resides in the potential for early cancer detection based on routine proteome-wide analysis using synthetic antibody arrays to detect cancer biomarkers presymptomatically.