DNA synthesis for true random number generation

A Deniable Encryption Method for Modulation-Based DNA Storage

Recent advancements in synthesis and sequencing techniques have made deoxyribonucleic acid (DNA) a promising alternative for next-generation digital storage. As it approaches practical application, ensuring the security of DNA-stored information has become a critical problem. Deniable encryption allows the decryption of different information from the same ciphertext, ensuring that the "plausible" fake information can be provided when users are coerced to reveal the real information. In this paper, we propose a deniable encryption method that uniquely leverages DNA noise channels. Specifically, true and fake messages are encrypted by two similar modulation carriers and subsequently obfuscated by inherent errors. Experiment results demonstrate that our method not only can conceal true information among fake ones indistinguishably, but also allow both the coercive adversary and the legitimate receiver to decrypt the intended information accurately. Further security analysis validates the resistance of our method against various typical attacks. Compared with conventional DNA cryptography methods based on complex biological operations, our method offers superior practicality and reliability, positioning it as an ideal solution for data encryption in future large-scale DNA storage applications.

Robust Optical Physical Unclonable Function Based on Total Internal Reflection for Portable Authentication

Physical unclonable functions (PUFs) utilize uncontrollable manufacturing randomness to yield cryptographic primitives. Currently, the fabrication of the most generally employed optical PUFs mainly depends on fluorescent, Raman, or plasmonic materials, which suffer inherent robustness issues. Herein, we construct an optical PUF with high environmental stability via total internal reflection (TIR-PUF) perturbed by randomly distributed polymer microspheres. The response image is transformed into encoded keys via an iterative binning procedure. The concentration of the polymer solution is optimized to debias the bit nonuniformity and maximize encoding capacity. The constructed TIR-PUF shows significantly high encoding capacity (2370) and markedly low total authentication error probability (1.614 × 10-23). The intra-Hamming distance is as low as 0.068, indicating the excellent readout reliability of TIR-PUF. The environmental stability of TIR-PUF has demonstrated promising results under a range of challenging conditions such as ultrasonic washing, high temperature, ultraviolet irradiation, and severe chemical environments. Moreover, the challenge-response pairs of our TIR-PUFs are demonstrated on an authentication system with low-power dissipation, lightweight components, and wireless imaging capture, rendering the possibility of portable authentication for practical applications.

Physical Unclonable Functions Based on Photothermal Effect of Gold Nanoparticles

Physical unclonable functions (PUFs) based on uncontrollable fabrication randomness are promising candidates for anticounterfeiting applications. Currently, the most popular optical PUFs are generally constructed from the scattering, fluorescent, or Raman phenomenon of nanomaterials. To further improve the security level of optical PUFs, advanced functions transparent to the above optical phenomenon have always been perused by researchers. Herein, we propose a new type of PUF based on the photothermal effect of gold nanoparticles, which shows negligible scattering, fluorescent, or Raman responses. The gold nanoparticles are randomly dispersed onto the surface of fused silica, which can enhance the photothermal effect and facilitate high contrast responses. By tuning the areal density of the gold nanoparticles, the optimized encoding capacity (2319) and the total authentication error probability (3.6428 × 10-24) are achieved from our PUF due to excellent bit uniformity (0.519) and inter Hamming distances (0.503). Moreover, the intra-Hamming distance (0.044) indicates the desired reliability. This advanced PUF with invisible features and high contrast responses provides a promising opportunity to implement authentication and identification with high security.

Chemical unclonable functions based on operable random DNA pools

Physical unclonable functions (PUFs) based on unique tokens generated by random manufacturing processes have been proposed as an alternative to mathematical one-way algorithms. However, these tokens are not distributable, which is a disadvantage for decentralized applications. Finding unclonable, yet distributable functions would help bridge this gap and expand the applications of object-bound cryptography. Here we show that large random DNA pools with a segmented structure of alternating constant and randomly generated portions are able to calculate distinct outputs from millions of inputs in a specific and reproducible manner, in analogy to physical unclonable functions. Our experimental data with pools comprising up to >1010 unique sequences and encompassing >750 comparisons of resulting outputs demonstrate that the proposed chemical unclonable function (CUF) system is robust, distributable, and scalable. Based on this proof of concept, CUF-based anti-counterfeiting systems, non-fungible objects and decentralized multi-user authentication are conceivable.

Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing

Due to its high coding density and longevity, DNA is a compelling data storage alternative. However, current DNA data storage systems rely on the de novo synthesis of enormous DNA molecules, resulting in low data editability, high synthesis costs, and restrictions on further applications. Here, we demonstrate the programmable assembly of reusable DNA blocks for versatile data storage using the ancient movable type printing principle. Digital data are first encoded into nucleotide sequences in DNA hairpins, which are then synthesized and immobilized on solid beads as modular DNA blocks. Using DNA polymerase-catalyzed primer exchange reaction, data can be continuously replicated from hairpins on DNA blocks and attached to a primer in tandem to produce new information. The assembly of DNA blocks is highly programmable, producing various data by reusing a finite number of DNA blocks and reducing synthesis costs (∼1718 versus 3000 to 30,000 US$ per megabyte using conventional methods). We demonstrate the flexible assembly of texts, images, and random numbers using DNA blocks and the integration with DNA logic circuits to manipulate data synthesis. This work suggests a flexible paradigm by recombining already synthesized DNA to build cost-effective and intelligent DNA data storage systems.

Multimodal dynamic and unclonable anti-counterfeiting using robust diamond microparticles on heterogeneous substrate

The growing prevalence of counterfeit products worldwide poses serious threats to economic security and human health. Developing advanced anti-counterfeiting materials with physical unclonable functions offers an attractive defense strategy. Here, we report multimodal, dynamic and unclonable anti-counterfeiting labels based on diamond microparticles containing silicon-vacancy centers. These chaotic microparticles are heterogeneously grown on silicon substrate by chemical vapor deposition, facilitating low-cost scalable fabrication. The intrinsically unclonable functions are introduced by the randomized features of each particle. The highly stable signals of photoluminescence from silicon-vacancy centers and light scattering from diamond microparticles can enable high-capacity optical encoding. Moreover, time-dependent encoding is achieved by modulating photoluminescence signals of silicon-vacancy centers via air oxidation. Exploiting the robustness of diamond, the developed labels exhibit ultrahigh stability in extreme application scenarios, including harsh chemical environments, high temperature, mechanical abrasion, and ultraviolet irradiation. Hence, our proposed system can be practically applied immediately as anti-counterfeiting labels in diverse fields.

Toehold-Mediated Strand Displacement in Random Sequence Pools

Toehold-mediated strand displacement (TMSD) has been used extensively for molecular sensing and computing in DNA-based molecular circuits. As these circuits grow in complexity, sequence similarity between components can lead to cross-talk, causing leak, altered kinetics, or even circuit failure. For small non-biological circuits, such unwanted interactions can be designed against. In environments containing a huge number of sequences, taking all possible interactions into account becomes infeasible. Therefore, a general understanding of the impact of sequence backgrounds on TMSD reactions is of great interest. Here, we investigate the impact of random DNA sequences on TMSD circuits. We begin by studying individual interfering strands and use the obtained data to build machine learning models that estimate kinetics. We then investigate the influence of pools of random strands and find that the kinetics are determined by only a small subpopulation of strongly interacting strands. Consequently, their behavior can be mimicked by a small collection of such strands. The equilibration of the circuit with the background sequences strongly influences this behavior, leading to up to 1 order of magnitude difference in reaction speed. Finally, we compare two established and one novel technique that speed up TMSD reactions in random sequence pools: a three-letter alphabet, protection of toeholds by intramolecular secondary structure, or by an additional blocking strand. While all of these techniques were useful, only the latter can be used without sequence constraints. We expect that our insights will be useful for the construction of TMSD circuits that are robust to molecular noise.

Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA

Using DNA as a durable, high-density storage medium with eternal format relevance can address a future data storage deficiency. The proposed storage format incorporates dehydrated particle spots on glass, at a theoretical capacity of more than 20 TB per spot, which can be efficiently retrieved without significant loss of DNA. The authors measure the rapid decay of dried DNA at room temperature and present the synthesis of encapsulated DNA in silica nanoparticles as a possible solution. In this form, the protected DNA can be readily applied to digital microfluidics (DMF) used to handle retrieval operations amenable to full automation. A storage architecture is demonstrated, which can increase the storage capacity of today's archival storage systems by more than three orders of magnitude: A DNA library containing 7373 unique sequences is encapsulated and stored under accelerated aging conditions (4 days at 70 °C, 50% RH) corresponding to 116 years at room temperature and the stored information is successfully recovered.

Encoding of non-biological information for its long-term storage in DNA

In 2019, at the World Economic Forum, DNA data storage was indicated as one of the breakthroughs expected to radically impact the global socio-economic order. Indeed, dry DNA is a relatively stable substance and an extremely capacious information carrier. One gram of DNA can hold up to 455 exabytes, provided that one nucleotide encodes two bits of information. In this critical review, the main attention is paid to nucleinography, meaning the conversion of digital data into nucleotide sequences. The evolution and diversity of approaches intended for encoding data with nucleotides are demonstrated. The most noticeable examples of storing minor as well as considerable quantities of non-biological information in DNA are given. Some issues of DNA data storage are also reported.

Synthetic DNA applications in information technology

Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold displacement and polymerase chain reaction (PCR) capabilities. In this review, we provide an overview of the most prevalent applications of synthetic DNA that could shape the future of information technology. We emphasize the reasons why the biomolecule can be a valuable alternative for conventional electronic-based media, and give insights on where the DNA-analog technology stands with respect to its electronic counterparts.

A flexible and stretchable bionic true random number generator

The volume of securely encrypted data transmission increases continuously in modern society with all things connected. Towards this end, true random numbers generated from physical sources are highly required for guaranteeing security of encryption and decryption schemes for exchanging sensitive information. However, majority of true random number generators (TRNGs) are mechanically rigid, and thus cannot be compatibly integrated with some specific flexible platforms. Herein, we present a flexible and stretchable bionic TRNG inspired by the uniqueness and randomness of biological architectures. The flexible TRNG film is molded from the surface microstructures of natural plants (e.g., ginkgo leaf) via a simple, low-cost, and environmentally friendly manufacturing process. In our proof-of-principle experiment, the TRNG exhibits a fast generation speed of up to 1.04 Gbit/s, in which random numbers are fully extracted from laser speckle patterns with a high extraction rate of 72%. Significantly, the resulting random bit streams successfully pass all randomness test suites including NIST, TestU01, and DIEHARDER. Even after 10,000 times cyclic stretching or bending tests, or during temperature shock (-25-80 °C), the bionic TRNG still reveals robust mechanical reliability and thermal stability. Such a flexible TRNG shows a promising potential in information security of emerging flexible networked electronics.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (light path diagram of transmitted laser speckle, pseudo random pattern, statistical distribution of bionic microstructures, haze of the bionic TRNG film, multi-layer circular laser intensity pattern, percentage of bit 0/1 for different hashed images, Pearson correlation coefficient between 100 different speckle images, the whole process of randomness extraction, SEM images of the flexible TRNG film after 10,000 times stretching and bending, continuous work stability of the TRNG at low or high temperature, light path diagram of reflective laser speckle, and detailed randomness test results of NIST, TestU01, and DIEHARDER) is available in the online version of this article at 10.1007/s12274-022-4109-9.

A Machine Learning Attack Resilient True Random Number Generator Based on Stochastic Programming of Atomically Thin Transistors

A true random number generator (TRNG) is a critical hardware component that has become increasingly important in the era of Internet of Things (IoT) and mobile computing for ensuring secure communication and authentication schemes. While recent years have seen an upsurge in TRNGs based on nanoscale materials and devices, their resilience against machine learning (ML) attacks remains unexamined. In this article, we demonstrate a ML attack resilient, low-power, and low-cost TRNG by exploiting stochastic programmability of floating gate (FG) field effect transistors (FETs) with atomically thin channel materials. The origin of stochasticity is attributed to the probabilistic nature of charge trapping and detrapping phenomena in the FG. Our TRNG also satisfies other requirements, which include high entropy, uniformity, uniqueness, and unclonability. Furthermore, the generated bit-streams pass NIST randomness tests without any postprocessing. Our findings are important in the context of hardware security for resource constrained IoT edge devices, which are becoming increasingly vulnerable to ML attacks.

Position Matters: Fluorescent Positional Isomers for Reliable Multichannel Encryption Devices

Fluorescence signals have been widely used in information encryption for a few decades, but still suffer from limited reliability. Here, reversible multichannel fluorescent devices with encrypted information were constructed, based on two fluorescent positional isomers of a diphenylquinoxaline derivative. Possessing the same core fluorescent group and acid-/pH-responsive mechanism, the two isomers showed different fluorescence colors in an acidic environment; this allowed us to realize stepwise encryption of information in orthogonal fluorescence channels. Because the protonation was reversible, the revealed information could be re-encrypted simply by heating. This approach highlights the value of positional isomers to build multichannel encryption devices, improving their reliability on the molecular level.

Storing and Reading Information in Mixtures of Fluorescent Molecules

The rapidly increasing use of digital technologies requires the rethinking of methods to store data. This work shows that digital data can be stored in mixtures of fluorescent dye molecules, which are deposited on a surface by inkjet printing, where an amide bond tethers the dye molecules to the surface. A microscope equipped with a multichannel fluorescence detector distinguishes individual dyes in the mixture. The presence or absence of these molecules in the mixture encodes binary information (i.e., "0" or "1"). The use of mixtures of molecules, instead of sequence-defined macromolecules, minimizes the time and difficulty of synthesis and eliminates the requirement of sequencing. We have written, stored, and read a total of approximately 400 kilobits (both text and images) with greater than 99% recovery of information, written at an average rate of 128 bits/s (16 bytes/s) and read at a rate of 469 bits/s (58.6 bytes/s).

Uncertainties in synthetic DNA-based data storage

Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.