DNA watermarks: A proof of concept

<p>Abstract</p> <p>Background</p> <p>DNA-based watermarks are helpful tools to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. <it>In silico </it>analyses showed that in coding regions synonymous codons can be used to insert encrypted information into the genome of living organisms by using the DNA-Crypt algorithm.</p> <p>Results</p> <p>We integrated an authenticating watermark in the Vam7 sequence. For our investigations we used a mutant <it>Saccharomyces cerevisiae </it>strain, called CG783, which has an amber mutation within the Vam7 sequence. The CG783 cells are unable to sporulate and in addition display an abnormal vacuolar morphology. Transformation of CG783 with pRS314 Vam7 leads to a phenotype very similar to the wildtype yeast strain CG781. The integrated watermark did not influence the function of Vam7 and the resulting phenotype of the CG783 cells transformed with pRS314 Vam7-TB shows no significant differences compared to the CG783 cells transformed with pRS314 Vam7.</p> <p>Conclusion</p> <p>From our experiments we conclude that the DNA watermarks produced by DNA-Crypt do not influence the translation from mRNA into protein. By analyzing the vacuolar morphology, growth rate and ability to sporulate we confirmed that the resulting Vam7 protein was functionally active.</p

Capacity of DNA Data Embedding Under Substitution Mutations

A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of quaternary symbols (bases), DNA data embedding (diversely called DNA watermarking or DNA steganography) can be seen as a digital communications problem where channel errors are tantamount to mutations of DNA bases. Depending on the use of coding or noncoding DNA hosts, which, respectively, denote DNA segments that can or cannot be translated into proteins, DNA data embedding is essentially a problem of communications with or without side information at the encoder. In this paper the Shannon capacity of DNA data embedding is obtained for the case in which DNA sequences are subject to substitution mutations modelled using the Kimura model from molecular evolution studies. Inferences are also drawn with respect to the biological implications of some of the results presented.Comment: 22 pages, 13 figures; preliminary versions of this work were presented at the SPIE Media Forensics and Security XII conference (January 2010) and at the IEEE ICASSP conference (March 2010

Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors

DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction problem, which is applicable whenever multiple reads of noisy data are available. This strategy is uniquely suited to the medium, which inherently replicates stored data in multiple distinct ways, caused by mutations. We consider noise introduced solely by uniform tandem-duplication, and utilize the relation to constant-weight integer codes in the Manhattan metric. By bounding the intersection of the cross-polytope with hyperplanes, we prove the existence of reconstruction codes with greater capacity than known error-correcting codes, which we can determine analytically for any set of parameters.Comment: 11 pages, 2 figures, Latex; version accepted for publicatio

DNA watermarks in non-coding regulatory sequences

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DNA nanotechnology: new adventures for an old warhorse

As the blueprint of life, the natural exploits of DNA are admirable. However, DNA should not only be viewed within a biological context. It is an elegantly simple yet functionally complex chemical polymer with properties that make it an ideal platform for engineering new nanotechnologies. Rapidly advancing synthesis and sequencing technologies are enabling novel unnatural applications for DNA beyond the realm of genetics. Here we explore the chemical biology of DNA nanotechnology for emerging applications in communication and digital data storage. Early studies of DNA as an alternative to magnetic and optical storage mediums have not only been promising, but have demonstrated the potential of DNA to revolutionize the way we interact with digital data in the future.United States. Defense Advanced Research Projects Agency (Contract FA8721-05-C-0002)National Institutes of Health (U.S.) (Grant 1R01EB017755)National Institutes of Health (U.S.) (Grant 1DP2OD008435)National Institutes of Health (U.S.) (Grant 1P50GM098792

Data Encryption in Communication Using DNA Sequences

cryptography is a field which makes the transmitted message unreadable to unauthorised users. In this work we take inspiration from DNA encryption schemes and use of biological alphabets to manipulate information by employing the DNA sequence reaction to autonomously make a copy of its threads as an extended encryption key. Information is converted from plain text to several formats and then follows the stages of protein formation from DNA sequences to generate an extended key using chemical property and attributes to be used in encryption mechanism. This technique will enhance the security of the encryption mechanism by substitution, manipulation, and complexity. Furthermore this technique can be used in many applications of information and communication systems as well as adding more complexity to existing encryption algorithms

Stabilizing synthetic data in the DNA of living organisms

Data-encoding synthetic DNA, inserted into the genome of a living organism, is thought to be more robust than the current media. Because the living genome is duplicated and copied into new generations, one of the merits of using DNA material is long-term data storage within heritable media. A disadvantage of this approach is that encoded data can be unexpectedly broken by mutation, deletion, and insertion of DNA, which occurs naturally during evolution and prolongation, or laboratory experiments. For this reason, several information theory-based approaches have been developed as an error check of broken DNA data in order to achieve data durability. These approaches cannot efficiently recover badly damaged data-encoding DNA. We recently developed a DNA data-storage approach based on the multiple sequence alignment method to achieve a high level of data durability. In this paper, we overview this technology and discuss strategies for optimal application of this approach

Noise and Uncertainty in String-Duplication Systems

Duplication mutations play a critical role in the generation of biological sequences. Simultaneously, they have a deleterious effect on data stored using in-vivo DNA data storage. While duplications have been studied both as a sequence-generation mechanism and in the context of error correction, for simplicity these studies have not taken into account the presence of other types of mutations. In this work, we consider the capacity of duplication mutations in the presence of point-mutation noise, and so quantify the generation power of these mutations. We show that if the number of point mutations is vanishingly small compared to the number of duplication mutations of a constant length, the generation capacity of these mutations is zero. However, if the number of point mutations increases to a constant fraction of the number of duplications, then the capacity is nonzero. Lower and upper bounds for this capacity are also presented. Another problem that we study is concerned with the mismatch between code design and channel in data storage in the DNA of living organisms with respect to duplication mutations. In this context, we consider the uncertainty of such a mismatched coding scheme measured as the maximum number of input codewords that can lead to the same output