title: Multiplexed Sequence Encoding: A Framework for DNA Communication.
abstract: Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA.
authors.affiliation: Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States of America.|MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, United States of America.
authors.forename: Bijan
authors.initials: B
authors.lastname: Zakeri
authors.affiliation: MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, United States of America.|MIT Lincoln Laboratory, 244 Wood Street, Lexington, MA 02420, United States of America.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Carr
authors.affiliation: Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States of America.|MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, United States of America.
authors.forename: Timothy K
authors.initials: TK
authors.lastname: Lu
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D008969:Molecular Sequence Data
chemical_list: D004247:DNA