Directed Evolution of Functional Materials
Over billions of years, biological systems have evolved into complex organisms by utilizing three powerful elements of mutagenesis, selection, and amplification. By synthetically harnessing these elements in the laboratory, our group develops novel technologies for Rapid In Vitro Directed Evolution (RiDE) to create organic materials capable of performing complex functions such as molecular recognition, conformation switching and self-assembly. Our techniques enable synthesis of materials that normally do not exist in nature, but can perform extremely useful functions for many biotechnological applications including molecular diagnostics and targeted therapies. Some of the recent publications are presented below:
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Rapid mRNA-Display Selection of an IL-6 Inhibitor Using Continuous-Flow Magnetic Separation
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In the postgenomic era, there is a pressing need to accelerate the pace of ligand discovery to elucidate the functions of a rapidly growing number of newly characterized molecules and their modified states. We report herein a rapid, low-cost highly efficient method for generating high-affinity antibody mimetics using small-scale continuous-flow magnetic separation (CFMS). A high-affinity IL-6 ligand generated using this process is capable of inhibiting signaling through gp130, thus indicating the molecules potential value and demonstrating the effectiveness of CFMS for rapidly identifying clinically relevant molecules.
C. A. Olson, J. D. Adams, T. T. Takahashi, H. Qi, S. M. Howell, T-T Wu, R. W. Roberts, R. Sun and H. T. Soh. Rapid mRNA-Display Selection of an IL-6 Inhibitor Using Continuous-Flow Magnetic Separation. Angewandte Chemie International Edition , Vol. 50, 1-5 (2011)
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Selection of Phage-Displayed Peptides on Live Adherent Cells in Microfluidic Channels
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We report the successful directed evolution of phage libraries that targets live, adherent cell surfaces using microfluidics technology. As a model, we have targeted neuropilin-1 (NRP-1), a membrane-bound receptor expressed at the surface of human prostate carcinoma cells. Using this microfluidic phage selection (MiPS) system, we are able to discover unique peptide sequences to an important cancer biomarker neuropilin-1 (NRP-1) with superior affinity and specificity than the best sequences discovered through a conventional biopanning method.
J. Wang, Y. Liu, T. Teesalu, K. N. Sugahara, V. R. Kotamraju, J. D. Adams, B. S. Ferguson, Q. Gong, S. S. Oh, A. T. Csordas, M. Cho, E. Ruoslahti, Y. Xiao and H. T. Soh. Selection of Phage-Displayed Peptides on Live Adherent Cells in Microfluidic Channels. Proceedings of the National Academy of Sciences, USA, Vol. 108, No. 17 (2011)
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Quantitative Selection of DNA Aptamers through Microfluidic Selection and High-Throughput Sequencing
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We describe the integration of microfluidic selection with high throughput DNA sequencing technology for rapid and efficient discovery of nucleic acid aptamers. The Quantitative Selection of Aptamers through Sequencing method tracks the copy number and enrichment-fold of more than 10 million individual sequences through multiple selection rounds, enabling the identification of high-affinity aptamers without the need for the pool to fully converge to a small number of sequences. As a demonstration, we have identified aptamers that specifically bind to PDGF-BB protein with Kd < 3 nM within 3 rounds.
M. Cho, Y. Xiao, J. Nie, R. Stewart, A. Csordas, S. S. Oh, J. Thomson and H. T. Soh. Quantitative Selection of DNA Aptamers through Microfluidic Selection and High-Throughput Sequencing. Proceedings of the National Academy of Sciences USA, Vol. 107, No. 35, 15373-15378 (2010)
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In vitro Selection of Structure-Switching, Self-Reporting Aptamers
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Unlike most conventional affinity reagents (e.g. antibodies), aptamers can also be engineered to perform complex molecular functions beyond binding. However, the selection process required to directly isolate aptamers with the desired function poses a significant technical challenge. We demonstrate a purely in vitro selection-based approach for obtaining self-reporting aptamers (SRAs) that function in both buffer and complex mixtures such as blood serum.
S. S. Oh, K. Plakos, X. Lou, Y. Xiao and H. T. Soh. In vitro Selection of Structure-Switching, Self-Reporting Aptamers. Proceedings of the National Academy of Sciences USA, Vol. 107, No. 32, 14053-14058 (2010)
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Micromagnetic Selection of Aptamers in Microfluidic Channels
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We describe an aptamer discovery system that is rapid, highly efficient, automatable, and applicable to a wide range of targets, based on the integration of a magnetic bead-based SELEX process with microfluidics technology. As a test of our M-SELEX method, we have demonstrated the isolation of DNA aptamers against BoNT/A-rLc protein with low-nanomolar Kd after a single round of selection.
X. H. Lou, J. Qian, Y. Xiao, L. Viel, A. E. Gerdon, E. T. Lagally, P. Atzberger, T. M. Tarasow, A. J. Heeger and H. T. Soh. Micromagnetic Selection of Aptamers in Microfluidic Channels. Proceedings of the National Academy of Sciences, USA, Vol. 106, No. 9, 2989-2994 (2009)
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