R&D: DNA Storage in Thermoresponsive Microcapsules for Repeated Random Multiplexed Data Access

Nature Nanotechnology has published an article written by Bas W. A. Bögels, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands, and Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, Bichlien H. Nguyen, Microsoft, Redmond, WA, USA, and Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA, David Ward, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA, Levena Gascoigne, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands, and Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands, David P. Schrijver, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, Anna-Maria Makri Pistikou, Alex Joesaar, Shuo Yang, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands, and Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, Ilja K. Voets, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands, and Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands, Willem J. M. Mulder, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, and Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands, Andrew Phillips, Microsoft Research, Cambridge, UK, Stephen Mann, Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, and Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, People’s Republic of China,Georg Seelig, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA, and Department of Electrical Engineering, University of Washington, Seattle, WA, USA, Karin Strauss, Yuan-Jyue Chen, Microsoft, Redmond, WA, USA, and Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA, and Tom F. A. de Greef, Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands, Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands, and Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.*

Abstract: “DNA has emerged as an attractive medium for archival data storage due to its durability and high information density. Scalable parallel random access to information is a desirable property of any storage system. For DNA-based storage systems, however, this still needs to be robustly established. Here we report on a thermoconfined polymerase chain reaction, which enables multiplexed, repeated random access to compartmentalized DNA files. The strategy is based on localizing biotin-functionalized oligonucleotides inside thermoresponsive, semipermeable microcapsules. At low temperatures, microcapsules are permeable to enzymes, primers and amplified products, whereas at high temperatures, membrane collapse prevents molecular crosstalk during amplification. Our data show that the platform outperforms non-compartmentalized DNA storage compared with repeated random access and reduces amplification bias tenfold during multiplex polymerase chain reaction. Using fluorescent sorting, we also demonstrate sample pooling and data retrieval by microcapsule barcoding. Therefore, the thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access to archival DNA files.“