A specific and low background nucleic acids sensing strategy based on rolling circle amplification coupled with a magnetic DNA machine

One-step strand displacement-mediated nucleic acids signal-amplified analytical strategy based on superparamagnetism-functionalized DNA arrays

DNA nanostructure, as polymeric material with remarkable molecular recognition property, has been widely used in bioassay. However, it still faces some challenges to overcome complexity of signal-amplified strategies and to realize efficient separation of reaction products. Herein, we present an innovative signal-amplified approach by integrating the toehold-mediated strand displacement reaction with DNA tile self-assembly technology to construct superparamagnetism-functionalized DNA polymeric materials, establishing a new signal-amplified analytical strategy for nucleic acids. This strategy enables highly sensitive, rapid, and efficient nucleic acid detection, making it a promising candidate for point-of-care testing (POCT). The analytical performance of this strategy was validated using target DNA (tDNA) and PIWI-interacting RNA-36026 (piRNA-36026), achieving limits of detection (LOD) of 2.4 × 10-10 M and 2.7 × 10-10 M. Moreover, it successfully detected single-base mutations and demonstrated stability over seven days. Comparative experiments confirmed the superior signal-amplified efficiency of DNA arrays. Recovery experiments yielded recoveries of 88.53 %-101.89 % for tDNA and 87.58 %-108.61 % for piRNA-36026. Ultimately, the feasibility of this strategy for real-world applications was validated through detecting piRNA-36026 in cell lysates. In conclusion, this work introduces an innovative and efficient signal-amplified method, while expanding the application prospects of multifunctional DNA polymeric materials in biomedical diagnostics.

Point-of-need species identification using non-PCR DNA-based approaches to combat wildlife crime

Wildlife crime, defined as any unlawful exploitation and trade of wildlife, is a lucrative illegal global industry, along with narcotics and weapons trafficking. It encompasses the harvest, transport, exchange, and end use of wildlife or wildlife-derived products. Regulated internationally by the Convention on the International Trade in Endangered Species of Flora and Fauna (CITES, 1973), wildlife crime is primarily detected using morphological or DNA sequencing methods. However, there is a growing demand for rapid, portable, and cost-effective screening tools to bypass time-consuming workflows and specialist laboratory equipment. Point-of-need testing, particularly at wildlife hotspots like international borders, offers a promising solution for the swift detection of illegal activities. Isothermal amplification methods such as loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), and recombinase polymerase amplification (RPA), are favoured for their low resource needs compared to traditional PCR. These methods can be combined with target detection methods such as clustered regularly interspaced short palindromic repeats (CRISPR) and aptamers to enhance sensitivity. Integrating these methods with others, such as lateral flow assays (LFA) and microfluidic devices, simplifies sample preparation and visualisation. Already established in disease diagnosis and food safety, these innovations in genetic testing provide rapid, on-site detection. When applied to wildlife crime, they can serve as tools to complement traditional PCR and sequencing methods. This review explores how non-PCR based approaches could offer faster, simpler, and more cost-effective solutions to combat wildlife crime.

A novel photoelectrochemical biosensor for sensitive detection of nucleic acids based on recombinase polymerase amplification and 3D-array titania nanorods

Nucleic acids detection is essential for diagnosing pathogens; however, traditional methods usually face challenges such as low sensitivity, lengthy reaction times, and strict temperature requirements. This study develops a novel photoelectrochemical (PEC) biosensor that integrates recombinase polymerase amplification (RPA) with a 3D-array titania (TiO2) nanorods nanorod electrode, addressing the challenge of achieving sensitive detection of RPA-amplified nucleic acids products, thereby enabling earlier and more reliable pathogen detection. The biosensor utilizes a triple-binding mode involving FITC antibodies, target nucleic acids, and an HRP-streptavidin sandwich structure, significantly improving the bio-functionalization of the electrode surface. The isothermal RPA process amplifies DNA at 37 °C within 20 min, while the TiO2 nanorods ensure efficient photoelectric conversion. The oxidation of 4-chloro-1-naphthol (4-CN) generates a signal-reducing benzo-4-chlorohexadienone (4-CD), enabling precise and sensitive detection. This PEC-RPA biosensor successfully detects Orientia tsutsugamushi (Ot) nucleic acids with a detection limit of 15 copies/μL within 60 min, demonstrating robust performance. The study provides a promising strategy for advancing pathogen nucleic acids diagnostic platforms and offers a versatile approach adaptable for detecting diverse pathogens.

A two-layer circuit cascade-based DNA machine for highly sensitive miRNA imaging in living cells

Sensitive detection of microRNA (miRNA), one of the most promising biomarkers, plays crucial roles in cancer diagnosis. However, the low expression level of miRNA makes it extremely urgent to develop ultrasensitive and highly selective strategies for quantification of miRNA. Herein, a DNA machine is rationally constructed for amplified detection and imaging of low-abundance miRNA in living cells based on the toehold-mediated strand displacement reaction (TMSDR). The isothermal and enzyme-free DNA machine with low background leakage is fabricated by integrating two DNA circuits into a cascade system, in which the output of one circuit serves as the input of the other one. Once the DNA machine is transfected into breast cancer cells, the overexpressed miRNA-203 initiates the first-layer circuit through TMSDR, leading to the concentration variation of fuel strands, which further influences the assembly of hairpin DNA in the second-layer circuit and the occurrence of fluorescence resonance energy transfer (FRET) for fluorescence imaging. Benefiting from the cascade of the two-layer amplification reaction, the proposed DNA machine acquires a detection limit down to 4 fM for quantification of miR-203 and a 10 000-fold improvement in amplification efficiency over the single circuit. Therefore, the two-layer circuit cascade-based DNA machine provides an effective platform for amplified analysis of low-abundance miRNA with high sensitivity, which holds great promise in biomedical and clinical research.

A Single Electrochemical Biosensor Designed to Detect Any Virus

Viruses are the primary cause of many infectious diseases in both humans and animals. Various testing methods require an amplification step of the viral RNA sample before detection, with quantitative reverse transcription polymerase chain reaction (RT-qPCR) being one of the most widely used along with lesser-known methods like Nucleic Acid Sequence-Based Amplification (NASBA). NASBA offers several advantages, such as isothermal amplification and high selectivity for specific sequences, making it an attractive option for low-income facilities. In this research, we employed a single electrochemical biosensor (E-Biosensor) designed for potentially detecting any virus by modifying the NASBA protocol. In this modified protocol, a reverse primer is designed with an additional 22-nucleotide sequence (tag region) at the 5'-end, which is added to the NASBA process. This tag region becomes part of the final amplicon generated by NASBA. It can hybridize with a single specific E-Biosensor probe set, enabling subsequent virus detection. Using this approach, we successfully detected three different viruses with a single E-Biosensor design, demonstrating the platform's potential for virus detection.

A cascade signal-amplified fluorescent biosensor combining APE1 enzyme cleavage-assisted target cycling with rolling circle amplification

A cascade signal-amplified fluorescent biosensor was developed for miRNA-21 detection by combining APE1 enzyme-assisted target recycling and rolling circle amplification strategy. A key feature of this biosensor is its dual-trigger mechanism, utilizing both tumor-endogenous miRNA-21 and the APE1 enzyme in the initial amplification step, followed by a second rolling circle amplification reaction. This dual signal amplification cascade significantly enhanced sensitivity, achieving a detection limit of 3.33 pM. Furthermore, this biosensor exhibited excellent specificity and resistance to interference, allowing it to effectively distinguish and detect the target miRNA-21 in the presence of multiple interfering miRNAs. Moreover, the biosensor maintained its robust detection capabilities in a 10% serum environment, demonstrating its potential for clinical disease diagnosis applications.