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/.