BioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA

Abstract

BackgroundIn recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA. Inherently DNA is a digital medium whereby the nucleotide bases act as digital symbols, a fact which underpins all bioinformatics techniques, and which also makes trivial information encoding using DNA straightforward. However, the situation is more complex in methods which aim at embedding information in the genomes of living organisms. DNA is susceptible to mutations, which act as a noisy channel from the point of view of information encoded using DNA. This means that the DNA data embedding field is closely related to digital communications. Moreover it is a particularly unique digital communications area, because important biological constraints must be observed by all methods. Many DNA data embedding algorithms have been presented to date, all of which operate in one of two regions: non-coding DNA (ncDNA) or protein-coding DNA (pcDNA).ResultsThis paper proposes two novel DNA data embedding algorithms jointly called BioCode, which operate in ncDNA and pcDNA, respectively, and which comply fully with stricter biological restrictions. Existing methods comply with some elementary biological constraints, such as preserving protein translation in pcDNA. However there exist further biological restrictions which no DNA data embedding methods to date account for. Observing these constraints is key to increasing the biocompatibility and in turn, the robustness of information encoded in DNA.ConclusionThe algorithms encode information in near optimal ways from a coding point of view, as we demonstrate by means of theoretical and empirical (in silico) analyses. Also, they are shown to encode information in a robust way, such that mutations have isolated effects. Furthermore, the preservation of codon statistics, while achieving a near-optimum embedding rate, implies that BioCode pcDNA is also a near-optimum first-order steganographic method.

Reversible Data Hiding for DNA Sequence Using Multilevel Histogram Shifting

“…The coding DNA of a gene is transcribed by codons of three nucleotide bases that specify amino acids to encode proteins. The watermark should be embedded into coding DNA by considering codon degeneracy, to preserve the protein sequence, and codon optimization, including codon usage and GC content [10,11]. Codon degeneracy and optimization make it difficult to embed a large number of bits into coding DNA.…”

“…Recently, it has been shown that the genome of a genetically tractable organism can be used as a medium for data hiding depending on the required application [1][2][3][4][5][6][7][8][9][10][11][12][13][14]. The coding DNA of a gene is transcribed by codons of three nucleotide bases that specify amino acids to encode proteins.…”

“…In addition to DNA storage [1][2][3], DNA steganography for secret communication or encryption using noncoding DNA sequences [4][5][6] has been widely studied for decades. Recent years have witnessed the use of coding DNA sequences to investigate DNA watermarking for tracking parent genes in offspring or genetically modified organisms and for protecting DNA copyright [7][8][9][10][11][12][13][14]. In silico and in vitro/in vivo tracking of offspring by watermarking has been easily realized in bacteria and other genetically modified genomes.…”

“…Furthermore, reversible data hiding for DNA storage, steganography, or watermarking is necessary to recover an original DNA sequence without loss of information. However, most methods [1][2][3][4][5][6][7][8][9][10][11][12][13][14] are irreversible. In addition to facilitating original DNA recovery, reversible DNA data hiding can prevent DNA forgery and mutations from external data, and the mutation process can be analyzed using the iterative process of embedding, detecting, and recovering the information.…”

Improving Dependability and Precision of Data Encoding in DNA

“…The potential of DNA has been realized for various information-theoretic protocols, including DNA steganography for the identification of genetically modified organisms [12,21,23] hiding of messages in DNA [9,11,16,20] and long-term data storage in DNA [3,7,8,10,14,21]. These applications require mechanisms to validate, ensure, and possibly verify message accuracy.…”