Peptide microarrays:

     After the sequencing of the genome, there has been a strong emphasis on the need to assign a function to every protein that a gene encodes. Function of a protein is tantamount to it’s interaction with other biomolecules and peptide microarrays are emerging tools for study of peptide-ligand interactions in parallel on amino acid level

My research involves the development of an integrated system for routine and flexible parallel synthesis of oligopeptides on microfluidic chips. In such a system, solid phase peptide synthesis, photogenerated reagent chemistry, laser illumination and fluorescence imaging techniques are optimized and combined to generate high-density peptide microchips. To demonstrate synthesis efficiencies, on-chip metal binding assays are performed, making the chip a potential tool for detecting heavy metal presence in water, up to micromolar concentrations. The other applications include using peptide libraries on a microfluidic microarray platform for mapping of epitopes of proteins which are relevant to certain diseases.

     These applications are demonstrated by using the peptide microarray to identify synthetic peptide based vaccines that would induce appropriate neutralizing antibodies and cellular responses against various antigens. The initial step is to analyze crystal structure of the given protein and determine exposed regions of the protein that maybe used to generate specific antibodies. Computational methods that analyze the primary sequence of a protein are used to identify most likely epitope sequences on the basis of hydrophilicity, solvent exposure, protrusion and atomic mobility. On-chip peptide libraries are synthesized based on this design and used for positional scanning against antibodies and consequently for epitope enhancement by mutational and deletional analysis.