Computing in mammalian cells with nucleic acid strand exchange

• Type of Material: Article
• Authors: Benjamin Groves, University of Washington; Yuan-Jyue Chen, University of Washington; Chiara Zurla, Georgia Institute of Technology; Sergii Pochekailov, University of Washington; Jonathan L. Kirschman, Georgia Institute of Technology; Philip Santangelo, Emory University; Georg Seelig, University of Washington
• Language: English
• Date: 2016-03-01
• Publisher: Nature Publishing Group
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2016 Macmillan Publishers Limited.
• Final Published Version (URL): http://dx.doi.org/10.1038/NNANO.2015.278
• Title of Journal or Parent Work: Nature Nanotechnology
• ISSN: 1748-3387
• Volume: 11
• Issue: 3
• Start Page: 287
• End Page: 294
• Grant/Funding Information: Additional support for was provided by NSF CAREER Award No. 1253691 (PJS), regarding RNA imaging, and NIH GM094198 (PJS), for the use of hRSV cell models during development.; This material is based upon work supported by the Defense Advanced Research Projects Agency (DARPA) under Contract No. W911NF-11-2-0068 to GS and PJS.
• Keywords: Materials Science; TRANSPORT; Science & Technology; HYBRIDIZATION; COMPUTATION; Technology; ANTISENSE OLIGONUCLEOTIDES; EXPRESSION; NANOTECHNOLOGY; Materials Science, Multidisciplinary; DNA ORIGAMI; Nanoscience & Nanotechnology; DISPLACEMENT-REACTIONS; CASCADES; Science & Technology - Other Topics; AMPLIFICATION
• Research Categories: Engineering, Biomedical; Computer Science

Abstract

DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution.