Rapid Visual Authentication Based on DNA Strand Displacement

Encapsulating Fe3O4 Nanoparticles and Carbon Dots in a Metal-Organic Framework for Magnetic Fluorescent Taggants

Magnetic fluorescent composite nanomaterials have broad application prospects in the fields of biological imaging, anticounterfeiting identification, suspicious object tracking, and identification of latent fingerprints in forensic medicine. For an effective taggant, a clearly visible identifying mark is necessary to enable observers to capture labeling information quickly and accurately, even from a distance. The preparation method of magnetic fluorescent composite materials is complicated and usually needs different surface modification and assembly processes. The limited loading capacity of fluorescent materials also limits the fluorescence properties of the composite, so it is difficult to produce obvious fluorescence as a taggant to meet the requirements of visible labeling. In this study, a core-shell structure of a magnetic fluorescent composite was prepared by using the metal-organic framework ZIF-8 as the host of fluorescent materials and an encapsulation shell coated on the Fe3O4 nanoparticles. The porous ZIF-8 is beneficial for increasing the loading capacity of fluorescent materials to ensure the fluorescence performance of the composite materials. Further modification of the composite surface prevented the desorption of fluorescent materials from the pores of ZIF-8, enabling the samples to maintain good fluorescence properties even after multiple washing cycles. The preparation method is simple, rapid, and cost-effective, and the prepared magnetic fluorescent composite nanomaterial has high magnetic separation performance and fluorescence performance, making it a promising material for identification, marking, and tracking.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Toehold clipping: A mechanism for remote control of DNA strand displacement

The ability to create stimuli-responsive DNA nanostructures has played a prominent role in dynamic DNA nanotechnology. Primary among these is the process of toehold-based strand displacement, where a nucleic acid molecule can act as a trigger to cause conformational changes in custom-designed DNA nanostructures. Here, we add another layer of control to strand displacement reactions through a 'toehold clipping' process. By designing DNA complexes with a photocleavable linker-containing toehold or an RNA toehold, we show that we can use light (UV) or enzyme (ribonuclease) to eliminate the toehold, thus preventing strand displacement reactions. We use molecular dynamics simulations to analyze the structural effects of incorporating a photocleavable linker in DNA complexes. Beyond simple DNA duplexes, we also demonstrate the toehold clipping process in a model DNA nanostructure, by designing a toehold containing double-bundle DNA tetrahedron that disassembles when an invading strand is added, but stays intact after the toehold clipping process even in the presence of the invading strand. This work is an example of combining multiple physical or molecular stimuli to provide additional remote control over DNA nanostructure reconfiguration, advances that hold potential use in biosensing, drug delivery or molecular computation.

Nanocatalyst-Enabled Physically Unclonable Functions as Smart Anticounterfeiting Tags with AI-Aided Smartphone Authentication

Counterfeiting is a worldwide issue affecting many industrial sectors, ranging from specialized technologies to retail market, such as fashion brands, pharmaceutical products, and consumer electronics. Counterfeiting is not only a huge economic burden (>$ 1 trillion losses/year), but it also represents a serious risk to human health, for example, due to the exponential increase of fake drugs and food products invading the market. Considering such a global problem, numerous anticounterfeit technologies have been recently proposed, mostly based on tags. The most advanced category, based on encryption and cryptography, is represented by physically unclonable functions (PUFs). A PUF tag is based on a unique physical object generated through chemical methods with virtually endless possible combinations, providing remarkable encoding capability. However, most methods adopted nowadays are based on expensive and complex technologies, relying on instrumental readouts, which make them not effective in real-world applications. To achieve a simple yet cryptography-based anticounterfeit method, herein we exploit a combination of nanotechnology, chemistry, and artificial intelligence (AI). Notably, we developed platinum nanocatalyst-enabled visual tags, exhibiting the properties of PUFs (encoding capability >10³⁰⁰) along with fast (1 min) ON/OFF readout and full reversibility, enabling multiple onsite authentication cycles. The development of an accurate AI-aided algorithm powers the system, allowing for smartphone-based PUF authentications.

Exponential Function Computation Based on DNA Strand Displacement Circuits

Due to its high programmability and storage, DNA circuits have been widely used in biological computing. In this paper, the addition, subtraction, multiplication, division, n-order and 1/n-order gates are built through DNA strand displacement reactions. The chemical reaction networks of the exponential function are established by using the six DNA analog computation gates. The integrated DNA strand displacement circuits are built through the chemical reaction networks. The exponential function polynomials can be computed through the integrated DNA strand displacement circuits. Finally, through visual DSD software verification, this design can realise the computation of exponential function polynomials, which provides a reference for solving exponential function equations and neural network computations in the future.

A Double-Layer Image Encryption Scheme Based on Chaotic Maps and DNA Strand Displacement

The image encryption schemes combining chaotic maps, DNA coding, and DNA sequence operation can effectively protect the image. In this paper, a double-layer image encryption scheme is proposed by combining chaotic maps with DNA strand displacement (DSD). Chaotic maps are used to generate pseudorandom sequences and perform routine scrambling and diffusion operations on the plaintext image. We propose three DSD-based encryption rules according to the diversity of DNA strand displacement, and these three encryption rules are used to encrypt the image at the DNA sequence level. The plaintext image can be transformed into the cipher image, which is difficult to be recognized without the correct keys through the double-layer encryption at the level of chaotic maps and DNA. Simulation results and security analysis show that the proposed encryption scheme can effectively protect image information and resist conventional information attacks.

Covert MOF-Based Photoluminescent Tags via Tunable Linker Energetics

Optical anticounterfeiting tags utilize the photoluminescent properties of materials to encode unique patterns, enabling identification and validation of important items and assets. These tags must combine optical complexity with ease of production and authentication to both prevent counterfeiting and to remain practical for widespread use. Metal-organic frameworks (MOFs) based on polynuclear, rare earth clusters are ideal materials platforms for this purpose, combining fine control over structure and composition, with tunable, complex energy transfer mechanisms via both linker and metal components. Here we report the design and synthesis of a set of heterometallic MOFs based on combinations of Eu, Nd, and Yb with the tetratopic linker 1,3,6,8-tetrakis(4-carboxyphenyl)pyrene. The energetics of this linker facilitate the intentional concealment of the visible emissions from Eu while retaining the infrared emissions of Nd and Yb, creating an optical tag with multiple covert elements. Unique to the materials system reported herein, we document the occurrence of a previously not observed 11-metal cluster correlated with the presence of Yb in the MOFs, coexisting with a commonly encountered 9-metal cluster. We demonstrate the utility of these materials as intricate optical tags with both rapid and in-depth screening techniques, utilizing orthogonal identifiers across composition, emission spectra, and emission decay dynamics. This work highlights the important effect of linker selection in controlling the resulting photoluminescent properties in MOFs and opens an avenue for the targeted design of highly complex, multifunctional optical tags.

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.

Solution of Simultaneous Higher Order Equations Based on DNA Strand Displacement Circuit

Currently, DNA strand displacement is often used to build neural networks or solve logical problems. While there are few studies on the use of DNA strand displacement to solve the higher order equations. In this paper, the catalysis, degradation, annihilation and adjusted reaction modules are built through DNA strand displacement. The chemical reaction networks of the corresponding higher order equations and simultaneous equations are established through these modules, and these chemical reaction networks can be used to build analog circuits to solve binary primary simultaneous equations and binary quadratic simultaneous equations. Finally, through Visual DSD software verification, this design can realize the solution of binary primary simultaneous equations and binary quadratic simultaneous equations, which provides a reference for DNA computation in the future.