Smart Sensing Based on DNA-Metal Interaction Enables a Label-Free and Resettable Security Model of Electrochemical Molecular Keypad Lock

Photocleavable DNA Nanotube-Based Dual-Amplified Resonance Rayleigh Scattering System for MicroRNA Detection Incorporating Molecular Computing-Cascaded Keypad Lock Functionality

Cascade molecular events in complex systems are of vital importance for enhancing molecular diagnosis and information processing. However, the conversion of a cascaded biosensing system into a multilayer encrypted molecular keypad lock remains a significant challenge in the development of molecular logic devices. In this study, we present a photocleavable DNA nanotube-based dual-amplified resonance Rayleigh scattering (RRS) system for detecting microRNA-126 (miR-126). The cascading dual-amplification biosensing system provides a multilayer-encrypted prototype with the functionality of a molecular computing cascade keypad lock. RRS signals were greatly amplified by using photocleavable DNA nanotubes and enzyme-assisted strand displacement amplification (SDA). In the presence of miR-126, enzyme-assisted SDA produced numerous identical nucleotide fragments as the target, which were then specifically attached to magnetic beads through the DNA nanotube by using a Y-shaped DNA scaffold. Upon ultraviolet irradiation, the DNA nanotube was released into the solution, resulting in an increase in the intensity of the RRS signal. This strategy demonstrated a low limit of detection (0.16 fM) and a wide dynamic range (1 fM to 1 nM) for miR-126. Impressively, the enzyme-assisted SDA offers a molecular computing model for generating the target pool, which serves as the input element for unlocking the system. By cascading the molecular computing process, we successfully constructed a molecular keypad lock with a multilevel authentication technique. The proposed system holds great potential for applications in molecular diagnosis and information security, indicating significant value in integrating molecular circuits for intelligent sensing.

Biomolecule-Driven Two-Factor Authentication Strategy for Access Control of Molecular Devices

The rise of DNA nanotechnology is promoting the development of molecular security devices and marking an essential change in information security technology, to one that can resist the threats resulting from the increase in computing power, brute force attempts, and quantum computing. However, developing a secure and reliable access control strategy to guarantee the confidentiality of molecular security devices is still a challenge. Here, a biomolecule-driven two-factor authentication strategy for access control of molecular devices is developed. Importantly, the two-factor is realized by applying the specificity and nicking properties of the nicking enzyme and the programmable design of the DNA sequence, endowing it with the characteristic of a one-time password. To demonstrate the feasibility of this strategy, an access control module is designed and integrated to further construct a role-based molecular access control device. By constructing a command library composed of three commands (Ca, Cb, Ca and Cb), the authorized access of three roles in the molecular device is realized, in which the command Ca corresponds to the authorization of role A, Cb corresponds to the authorization of role B, and Ca and Cb corresponds to the authorization of role C. In this way, when users access the device, they not only need the correct factor but also need to apply for role authorization in advance to obtain secret information. This strategy provides a highly robust method for the research on access control of molecular devices and lays the foundation for research on the next generation of information security.

Colorimetric multi-channel sensing of metal ions and advanced molecular information protection based on fish scale-derived carbon nanoparticles

Some nanosystems based on carbon nanomaterials have been used for fluorescent chemical/biosensing, elementary information processing, and textual coding. However, little attention has been paid to utilizing biowaste-derived carbon nanomaterials for colorimetric multi-channel sensing and advanced molecular information protection (including text and pattern information). Herein, fish scale-derived carbon nanoparticles (FSCN) were prepared and used for colorimetric detection of metal ions, encoding, encrypting and hiding text- and pattern-based information. The morphology and composition of FSCN were analyzed by TEM, XRD, FTIR, and XPS, and it was found that the FSCN-based multi-channel colorimetric sensing system can detect Cr⁶⁺ (detection limit of 56.59 nM and 13.32 nM) and Fe³⁺ (detection limit of 81.55 nM) through the changes of absorption intensity at different wavelengths (272, 370, and 310 nm). Moreover, the selective responses of FSCN to 20 kinds of metal ions can be abstracted into a series of binary strings, which can encode, hide, and encrypt traditional text-based and even two-dimensional pattern-based information. The preparation of carbon nanomaterials derived from waste fish scales can stimulate other researcheres' enthusiasm for the development and utilization of wastes and promoting resource recycling. Inspired by this work, more researches will continue to explore the world of molecular information technology.

A renewable platform based on the entropy-driven catalytic amplification and element labeling inductively coupled plasma mass spectrometry for microRNA analysis

The element labeling inductively coupled plasma mass spectrometry (ICP-MS) strategy has been increasingly applied to the bioanalysis for various bio-targets. Herein, a renewable analysis platform with element labeling ICP-MS was firstly proposed for microRNA (miRNA) analysis. The analysis platform was established on the magnetic bead (MB) with entropy-driven catalytic (EDC) amplification. When the EDC reaction was initiated by target miRNA, numerous strands labeled with Ho element were released from MBs, and ¹⁶⁵Ho in the supernatant detected by ICP-MS could reflect the amount of target miRNA. After detection, the platform was easily regenerated by adding strands to reassemble EDC complex on MBs. This MB platform could be used four times, and the limit of detection for miRNA-155 was 8.4 pmol L^-1. Moreover, the developed regeneration strategy based on EDC reaction can be easily expanded to other renewable analysis platforms, such as, the renewable platform involving EDC and rolling circle amplification technology. Overall, this work proposed a novel regenerated bioanalysis strategy to reduce the consumption of reagent and time for probe preparation, profiting the development of bioassay based on element labeling ICP-MS strategy.

Electrochemical DNA Scaffold-Based Sensing Platform for Multiple Modes of Protein Assay and a Keypad Lock System

Development of a flexible, easy-to-use, and well-controllable DNA-based sensing platform would provide enormous opportunities to boost molecular diagnosis and signal transduction or information processing. Herein, a duplex DNA scaffold containing a bulge was deployed for the fabrication of a simple and general DNA-based electrochemical sensing platform. It could be harnessed for different signal output behaviors (one signal-off and two signal-on modes) toward a single-step analysis of the target protein. The detection limit toward the target protein could reach about 0.1 nM. Also, it could be used as a streamlined electrochemical workflow for the successive monitoring of protein binding. Furthermore, such an electrochemical sensing platform could be explored for the operation of the concatenated AND logic gates as a molecular keypad lock system. The current sensing platform based on only one duplex DNA scaffold presented features such as simple biosensor design and fabrication, flexible operation for different signal outputs, sensitive and selective protein detection, and expandable logic operation. It thus would pave a broad road toward the development of high-performance biosensors or logic devices to be applied for molecular diagnosis or computing.

Tuning the Redox Chemistry of Copper Oxide Nanoarchitectures Integrated with rGOP via Facet Engineering: Sensing H2S toward SRB Detection

The ultrasensitive determination of sulfate reducing bacteria (SRB) is of great significance for their crucial roles in environmental and industrial harms together with the early detection of microbial corrosion. In this work, we report the development of highly efficient electrocatalysts, i.e., Cu₂O-CuO extended hexapods (EHPs), which are wrapped on homemade freestanding graphene paper to construct a flexible paper electrode in the electrochemical sensing of the biomarker sulfide for SRB detection. Herein Cu₂O-CuO EHPs have been synthesized via a highly controllable and facile approach at room temperature, where the redox centers of copper oxide nanoarchitectures are tuned via facet engineering, and then they are deposited on the graphene paper surface through an electrostatic adsorption to enable homogeneous and highly dense distribution. Owing to the synergistic contribution of high electrocatalytic activity from the Cu mixed oxidation states and abundant catalytically active facets of Cu₂O-CuO EHPs and high electrical conductivity of the graphene paper electrode substrate, the resultant nanohybrid paper electrode has exhibited superb electrochemical sensing properties for H₂S with a wide linear range up to 352 μM and an extremely low detection limit (LOD) of 0.1 nM with a signal-to-noise ratio of 3 (S/N = 3), as well as high sensitivity, stability, and selectivity. Furthermore, taking advantage of the good biocompatibility and mechanical flexibility, the electrochemical sensing platform based on the proposed electrode has been applied in the sensitive detection of SRB in environmental samples through the sensing of sulfide from SRB, which holds great promise for on-site and online corrosion and environmental monitoring.

Peptide-Based Sensing, Logic Computing, and Information Security on the Antimonene Platform

Peptides have higher information density than DNA and equivalent molecular recognition ability and durability. However, there are currently no reports on the comprehensive use of peptides' recognition ability and structural diversity for sensing, logic computing, information coding, and protection. Herein, we, for the first time, demonstrate peptide-based sensing, logic computing, and information security on the antimonene platform. The molecular recognition capability and structural diversity (amino acid sequence) of peptides (Pb²⁺-binding peptide DHHTQQHD as a model) adsorbed on the antimonene universal fluorescence quenching platform were comprehensively utilized to sense targets (Pb²⁺) and give a response (fluorescence turn-on) and then to encode, encrypt, and hide information. Fluorescently labeled peptides used as the recognition probe and the information carrier were quenched and hidden by the large-plane two-dimensional material antimonene and specifically bound by Pb²⁺ as the stego key, resulting in fluorescence recovery. The above interaction and signal change can be considered as a peptide-based sensing and steganographic process to further implement quantitative detection of Pb²⁺, complex logic operation, information coding, encrypting, and hiding using a peptide sequence and the binary conversion of its selectivity. This research provides a basic paradigm for the construction of a molecular sensing and informatization platform and will inspire the development of biopolymer-based molecular information technology (processing, communication, control, security).

Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement

Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.

A molecular device: A DNA molecular lock driven by the nicking enzymes

As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.

Biocomputing for Portable, Resettable, and Quantitative Point-of-Care Diagnostics: Making the Glucose Meter a Logic-Gate Responsive Device for Measuring Many Clinically Relevant Targets

It is recognized that biocomputing can provide intelligent solutions to complex biosensing projects. However, it remains challenging to transform biomolecular logic gates into convenient, portable, resettable and quantitative sensing systems for point-of-care (POC) diagnostics in a low-resource setting. To overcome these limitations, the first design of biocomputing on personal glucose meters (PGMs) is reported, which utilizes glucose and the reduced form of nicotinamide adenine dinucleotide as signal outputs, DNAzymes and protein enzymes as building blocks, and demonstrates a general platform for installing logic-gate responses (YES, NOT, INHIBIT, NOR, NAND, and OR) to a variety of biological species, such as cations (Na+ ), anions (citrate), organic metabolites (adenosine diphosphate and adenosine triphosphate) and enzymes (pyruvate kinase, alkaline phosphatase, and alcohol dehydrogenases). A concatenated logical gate platform that is resettable is also demonstrated. The system is highly modular and can be generally applied to POC diagnostics of many diseases, such as hyponatremia, hypernatremia, and hemolytic anemia. In addition to broadening the clinical applications of the PGM, the method reported opens a new avenue in biomolecular logic gates for the development of intelligent POC devices for on-site applications.