Multiplexed Sequence Encoding: A Framework for DNA Communication
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 encodi...
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| Format: | Article |
| Language: | en_US |
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Public Library of Science
2016
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| Online Access: | http://hdl.handle.net/1721.1/103080 https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0002-4639-7248 |
| _version_ | 1811091393761771520 |
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| author | Zakeri, Bijan Carr, Peter A. Lu, Timothy K. |
| author2 | MIT Synthetic Biology Center |
| author_facet | MIT Synthetic Biology Center Zakeri, Bijan Carr, Peter A. Lu, Timothy K. |
| author_sort | Zakeri, Bijan |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T15:01:43Z |
| format | Article |
| id | mit-1721.1/103080 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:01:43Z |
| publishDate | 2016 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/1030802022-10-02T00:06:13Z Multiplexed Sequence Encoding: A Framework for DNA Communication Zakeri, Bijan Carr, Peter A. Lu, Timothy K. MIT Synthetic Biology Center Lincoln Laboratory Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Research Laboratory of Electronics Zakeri, Bijan Carr, Peter A. Lu, Timothy K. 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. National Institutes of Health (U.S.) (NIH Grant 1R01EB017755) National Institutes of Health (U.S.) (NIH Grant 1DP2OD008435) National Institutes of Health (U.S.) (NIH Grant 1P50GM098792) United States. Defense Advanced Research Projects Agency (Air Force Contract #FA8721-05-C-0002) 2016-06-09T14:59:56Z 2016-06-09T14:59:56Z 2016-04 2013-12 Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/103080 Zakeri Bijan, Peter A. Carr, and Timothy K. Lu. "Multiplexed Sequence Encoding: A Framework for DNA Communication." PLoS ONE 11:4 (2016): e0152774. https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0002-4639-7248 en_US http://dx.doi.org/10.1371/journal.pone.0152774 PLOS ONE Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science Public Library of Science |
| spellingShingle | Zakeri, Bijan Carr, Peter A. Lu, Timothy K. Multiplexed Sequence Encoding: A Framework for DNA Communication |
| title | Multiplexed Sequence Encoding: A Framework for DNA Communication |
| title_full | Multiplexed Sequence Encoding: A Framework for DNA Communication |
| title_fullStr | Multiplexed Sequence Encoding: A Framework for DNA Communication |
| title_full_unstemmed | Multiplexed Sequence Encoding: A Framework for DNA Communication |
| title_short | Multiplexed Sequence Encoding: A Framework for DNA Communication |
| title_sort | multiplexed sequence encoding a framework for dna communication |
| url | http://hdl.handle.net/1721.1/103080 https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0002-4639-7248 |
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