Encoding text into nucleic acid sequences

Abstract

Methods and apparatus are disclosed herein for encoding human readable text conveying a non-genetic message into nucleic acid sequences with a substantially reduced probability of biological impact and decoding such text from nucleic acid sequences. In one embodiment, each symbol of a symbol set of human readable symbols uniquely maps to a respective codon identifier. Mapping may ensure that each symbol will not map to a codon identifier that generates an amino acid residue which has a single-letter abbreviation that is the equivalent to the respective symbol. Synthetic nucleic acid sequences comprising such human readable text, and recombinant or synthetic cells comprising such sequences are provided, as well as methods of identifying cells, organisms, or samples containing such sequences.

Description

CROSS-REFERENCES TO RELATED APPLICATIONS[0001]This application claims benefit of U.S. provisional patent application 61 / 256,913, filed Oct. 30, 2009, and to U.S. application Ser. No. 12 / 783,489, filed May 19, 2010, each of which is incorporated by reference in its entirety.FIELD OF THE INVENTION[0002]The presently disclosed application relates generally to the field of molecular biology. More specifically, this application relates to synthetic nucleic acid sequences comprising non-genetic information.REFERENCE TO SEQUENCE LISTING[0003]This application contains references to amino acid sequences and / or nucleic acid sequences which have been submitted concurrently herewith as the sequence listing text file “SGI1450-1_ST25.txt”, file size 09.02 KiloBytes (KB), created on Oct. 29, 2010. The aforementioned sequence listing is hereby incorporated by reference in its entirety pursuant to 37 C.F.R. §1.52(e)(5).BACKGROUND OF THE INVENTION[0004]Biological organisms comprise nucleic acid seque...

AI Technical Summary

Benefits of technology

[0017]The present application is directed to generating an encoding scheme configured to translate human readable symbols into codon identifiers (i.e., discrete sequences of preferably three elements, where each element contains one of four selected nucleotide bases). In this manner, sequences of human readable symbols can be used to convey non-genetic messages (for example, text messages, trademarks, copyright notices, unique identifying information, etc.) by encoding the message into sequences of codon identifiers. These sequences of codon identifiers may then be used to generate synthetic nucleic acid sequences that are introduced into a living cell or organism as free DNA or incorporated into other various types of cellular nucleic acid materials (e.g., plasmids, chromosomes, mitochondrial DNA, genomes, etc.). The resulting set of codons or codon identifiers effectively serves as a memory source for the encoded sequences of human readable symbols.

[0018]Unlike conventional methods of encoding such nucleic acid sequences, embodiments described herein utilize an encoding scheme with a remarkably low probability of biological impact. That is to say, a low probability exists that a synthetic nucleic acid sequence created using invention methods and schemes will be transcribed or translated by a cell's internal biological processes. As a result, the non-genetic message created using invention methods and schemes may be innocuously carried and replicated by cells comprising the message, but may be decoded to provide the human readable symbols, i.e., the message carried therein. Advance knowledge of a gene's structure and / or function is not required in order to decode a given sequence of nucleotides. This greatly simplifies the decoding process, enabling a message recipient to decode one or more messages using a simple human readable symbol map.

[0019]Also, since the encoding scheme is configured to translate each human readable symbol of an input message into a three-nucleotide codon identifier, efficiency gains are realized over many conventional encoding systems. Therefore, significantly less storage space is required to store an encoded message, both within a cell or a cell within an organism, and within the transcoder itself or the memory of the transcoder itself.

Problems solved by technology

Unfortunately, conventional encoding schemes suffer from a one of two serious drawbacks, either they run the risk of causing a negative biological impact on a cell harboring nucleic acid sequences made using such encoding schemes, or they rely upon codon-redundancy in a carrier-gene of known function.

Methods using a carrier-gene are characterized by extreme inefficiency of encoded information and are further limited by their requirement of encoding a message inside a carrier gene of known sequence and limited length.

This imposes a limit on the length of the message that can be encoded that is further exacerbated by the inefficiency of the encoding scheme.

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