A novel strategy for microarrays of selective binding agents

There is a continuing need for high-throughput assays of multiple substances at particular levels of biological organisation, the so-called omics methods. Microarrays have been widely used for transcriptomics, and occasionally for proteomics (protein microarrays). In the latter case it is necessary to select an antibody or equivalent binding agent for each target. We here propose to develop a novel strategy that can cut the development of selective binding agents by orders of magnitude, and will apply it to a variety of target determinands.

Combimatrix have produced, and will make available to us, an instrument that uses elecrochemically generated acid to effect localised deprotection and thus synthesise defined oligonucleotide arrays (12,000 per chip) in situ. Using this we wish to carry out the following: 1. Evolve nucleic acid aptamers that selectvely bind peptides, proteins, metabolites and other non-nucleotide determinands 2. Tag such determinands so that the extent of binding can be determined quantitatively via fluorimetry and/or electrochemistry 3. Knowing the sequence at every spot in each generation, to optimise in a computational sense in parallel and multi-objectively the sequences that are synthesised during the evolution of the array. 4. Develop MALDI and FTIR methods to effect semi-quantitative detection of peptides derived from a yeast whole-cell lysate that have bound to specific probes 5. Perform electrochemical optimisation in an automated closed-loop manner 6. Evolve aptamers that change quantitatively the fluorescence of a fluorophore when the specific binding metabolite is present 7. Produce a suitable database for storing all the data, and therewith to perform QSAR on selected aptamers to understand the structural basis for the binding specificities obtained 8. To evolve peptide aptamers in a similar way to the evolution of nucleic acid aptamers, above 9. To exploit cleavable nucleic acid arrays for the purposes of reverse transfection. 10. Thereby to deliver a technology that can perform quantitative proteomics in the same way that transcriptomics is now performed in microarrays.