Alignment‐Based Approach for Durable Data Storage into Living Organisms

Yachie, Nozomu; Sekiyama, Kazuhide; Sugahara, Junichi; Ohashi, Yoshiaki; Tomita, Masaru

doi:10.1021/bp060261y

“…If certain constraints are observed, DNA can also be used to convey additional arbitrary data [1,2,4,5,6,7]. It is a key fact that information embedded within DNA will travel alongside each replication, whether it takes place in vivo or in vitro, that is, whether it happens inside or outside living organisms.…”

Section: Dna Data Embedding and Applicationsmentioning

confidence: 99%

“…By replacing or appending noncoding DNA (ncDNA) segments, which never get translated to proteins [1,2,3,4]. This amounts to transmitting an arbitrary digital signal, as one can freely establish the host segments that carry the information.…”

Section: Dna Data Embedding and Applicationsmentioning

confidence: 99%

“…Long-term storage of data in the DNA of living organisms, such as bacteria, has been actually implemented with real organisms by Wong et al [2], Yachie et al [4], and other groups of researchers.…”

Section: Dna Data Embedding and Applicationsmentioning

confidence: 99%

“…Among the methods that deal with ncDNA [1,2,3,4] the earliest one is by Clelland et al [1], who rely on a primer as a key to locate inserted data. A similar method is used by Wong et al [2].…”

Section: Brief Literature Reviewmentioning

confidence: 99%

“…A number of methods have been proposed over the last ten years for mathematically embedding information within DNA, the molecule that constitutes the building block of life [1,2,3,4,5,6,7]. However, important issues related to DNA data embedding are not elucidated yet.…”

Section: Introductionmentioning

confidence: 99%

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Image encryption by immobilized DNA molecules on chips could offer significant advantages, which include vast parallelism, immense information density, high chemical stability, and energy efficiency. Several theoretical or computer simulated models for encryption and steganography of texts have been proposed on the basis of DNA molecules, [1][2][3][4] and a few DNA-based models relevant to alphanumeric information have been realized. [5][6][7][8][9][10] DNA methods were also proposed for commercial encryption of signatures [11,12] and for information storage. [13][14][15][16][17] In contrast, image encryption has received very little attention. [18,19] Although DNA computing procedures were employed in theoretical schemes, [20][21][22] no molecular encryption of images has been tested experimentally, and certainly not by methods that involve molecular computing.Herein, we report the use of parallel computing with molecular finite-state automata and fluorescently labeled DNA molecules for deciphering two different images. Both logos of the Technion and The Scripps Research Institute were encrypted on a single DNA chip. To decipher any of these images, a mixture of input molecules was processed by a molecular finite-state automaton, which led to image visualization by fluorescent, surface-bound output molecules. The huge diversity of potentially encrypted images that is offered by this strategy stems from current DNA microarray technology, with millions of printed pixels per chip, along with a plethora of possible input molecules and a variety of DNAbased automata.Our approach to meet the challenge of image encryption was based on our two-symbol-two-state finite automata [23][24][25][26][27] as a mathematical model for information retrieval by using DNA molecules (Figure 1 A). We prepared two input mole-cules In1 and In2 in the form of a linear double-stranded (ds)DNA (Figure 1 B) that contain a string of symbols, which are six base pairs (bp) each. In1 comprises the symbols ab, whereas In2 contains the string aa. Each symbol-string was followed by a six bp terminator segment (t) and a long singlestranded (ss)DNA tail (48-56 bases). This tail was designed to be uniquely complementary to one of the connecting molecules Con1 and Con2, to avoid self-hybridization, secondary structures, and cross-hybridization with incorrect connecting molecules. The connecting molecules, in the form of ssDNA, were intended to localize the output molecules on the microarray glass slide. Again, an important part of their design considered the need to prevent self-hybridization, secondary structures and cross-hybridization with incorrect molecules.The two-symbol-two-state automata were programmed by the choice of subsets from the complete library of eight transition molecules. Each such molecule, which represents a transition rule, is comprised of three parts: a recognition site for the type II endonuclease FokI, a four-base sticky end, and a spacer of between one and five bp between them (Figure 1 C). Automaton 1 (A1, Figure 1 A) includ...

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Alignment‐Based Approach for Durable Data Storage into Living Organisms

Cited by 68 publications

References 19 publications

On the Shannon capacity of DNA data embedding

On the Shannon capacity of DNA data embedding

A Molecular Cryptosystem for Images by DNA Computing

A Molecular Cryptosystem for Images by DNA Computing

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