Deconvolution of Self-encoded Polymer Beads in Random Microarrays for Antigen Biosensing by Raman Spectroscopy
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Deconvolution of Self-encoded Polymer Beads in Random Microarrays for Antigen Biosensing by Raman Spectroscopy Juan P Bravo-Vasquez1, Ramon A Alvarez-Puebla1, David Blais2, Ying Zhang3, Jose Raez3, John P Pezacki2,4, and Hicham Fenniri1,3 1 National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, T6G 2M9, Canada 2 Steacie Institute for Molecular Sciences, 100 Sussex Drive, Ottawa, K1A 0R6, Canada 3 Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Canada 4 Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, K1N 6N5, Canada ABSTRACT Random bead microarray in which each bead has been functionalized with different biomolecules are of great interest. The process by which one would identify the location of each bead is referred to as decoding. The decoding step has played a challenging role in microarray technologies due to the increase in complexity with the increase in array size. Here we report a novel, fast and reliable method of decoding randomly assembled arrays based on polymer beads with unique spectroscopic signatures. Beads were synthesized by dispersion polymerization of a family of styrene monomers and methacrylic acid to generate a spectroscopically encoded bead library. In addition to identifying the self-encoded beads through their unique spectrum in a tetraplex experiment, Raman spectroscopy was used to monitor antibody-antigen binding events on the barcoded beads. The simplicity, versatility and rapid analysis enabled by this self-encoded bead array platform technology demonstrates its potential in high-throughput biomolecular multiplex screening. INTRODUCTION Microarrays consist of spatially addressable, immobilized biomolecules on 2D surfaces, microchannel, microwells, or microbeads.1 The technology, devised for the analysis of complex biological systems, has emerged as likely frontrunner platforms for large scale, high throughput, and parallel proteomic2 and genomic3 analyses. In the field of microarrays, the used of microbeads as microsensors in optical arrays has been gaining increased interest. Upon assembly, the beads (sensors) are randomly distributed on the array substrate. Unlike orderly arranged microarrays4 a randomly assembled array requires a decoding step, in order to identify the location of each bead type. The process by which one would identify the location of each bead is referred to as decoding and is playing a challenging role in microarray technologies due to an increase in complexity as the array size increases. Currently, two methods exist for deconvoluting bead microarrays. The first requires fluorescent dye encoding of microspheres, where each microsphere is labeled with a unique ratio of dyes to identify the attached probe sequence. Clearly this approach is limited by the number of available dyes. The second is based on bead with addressable oligonucleotide sequences that are decoded through iterative hybridization with known probes.2 However, in more complex arrays, these methods requi
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