Run-length encoding graphic rules, biochemically editable designs and steganographical numeric data embedment for DNA-based cryptographical coding system

Discrete Biochemistry of DNA: Arithmetic DNA Molecules for Binary Additions, Naturally Found Genetic Logic Circuits for Plant Sensing, and DNA-Based Animation

To date, a number of researchers are seeking for and/or designing novel molecules which function as arithmetic molecular engines. Biomolecules such as deoxyribonucleic acid (DNA) and proteins are examples of promising candidate molecules. In the present article, we showed our view that DNA-based molecules could be used as a novel class of platforms for discrete mathematical operations or tools for natural computation. Here, we report on a novel molecular logic circuit combining exclusive disjunction (XOR) gate and conjunction (AND) gate implemented on a single DNA molecule performing arithmetic operations with simple binary numbers through polymerase chain reactions (PCR); which was inspired by previously developed protein-based computing model allowing simple polynomial algebra over fields through algebraic representation of cyclic inter-conversions in the catalytic modes of a plant enzyme as a cyclic additive group. In addition, we showed that DNA can be used as the platform for image coding and processing leading to DNA-coded animation by using novel PCR-based protocols. Lastly, we discussed the significance of recent attempts in the stream of natural computing and synthetic biological research, by handling DNA and related biomolecules as the media for discrete mathematical operations.

Multiplexed Sequence Encoding: A Framework for DNA Communication

Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA.

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.

Run-Length Encoding Graphic Rules Applied to DNA-Coded Images and Animation Editable by Polymerase Chain Reactions

We previously proposed novel designs for artificial genes as media for storing digitally compressed image data, specifically for biocomputing by analogy to natural genes mainly used to encode proteins. A run-length encoding (RLE) rule had been applied in DNA-based image data processing, to form coding regions, and noncoding regions were created as space for designing biochemical editing. In the present study, we apply the RLE-based image-coding rule to creation of DNAbased animation. This article consisted of three parts: (i) a theoretical review of RLE-based image coding by DNA, (ii) a technical proposal for biochemical editing of DNA-coded images using the polymerase chain reaction, and (iii) a minimal demonstration of DNAbased animation using simple model images encoded on short DNA molecules.