Orthogonal Information Encoding in Living Cells with High Error-Tolerance, Safety, and Fidelity

Information encoding in DNA is of great interest but its applications in vivo might be questionable since errors could be enriched exponentially by cellular replications and the artificial sequences may interfere with the natural ones. Here, a novel self-error-detecting, three-base block encoding scheme (SED3B) is proposed for reliable and orthogonal information encoding in living cells. SED3B utilizes a novel way to add error detecting bases in small data blocks which can combine with the inherent redundancy of DNA molecules for effective error correction. Errors at a rate of 19% can be corrected as shown by error-prone PCR experiments with E. coli cells. Calculations based on this preliminary result show that SED3B encoded information in E. coli can be reliable for more than 12 000 years of continuous replication. Importantly, SED3B encoded sequences do not share sequence space to all reported natural DNA sequences except for some short tandem repeats, indicating a low biological relevance of encoded sequences for the first time. These features make SED3B attractive for broad orthogonal information encoding purposes in living cells, for example, comments/barcodes encoding in synthetic biology. For proof of concept, 10 different barcodes were encoded in E. coli cells. After continuous replications for 10 days including exposure to ultraviolet for 2-3 min (lethality >60%) per day, all barcodes were fully recovered, proving the stability of the encoded information. An online encoding-decoding system is implemented and available at http://biosystem.bt1.tu-harburg.de/sed3b/ .