Intracellular activated logic nanomachines based on framework nucleic acids for low background detection of microRNAs in living cells

Advancements in DNA computing: exploring DNA logic systems and their biomedical applications

DNA computing is regarded as one of the most promising candidates for the next generation of molecular computers, utilizing DNA to execute Boolean logic operations. In recent decades, DNA computing has garnered widespread attention due to its powerful programmable and parallel computing capabilities, demonstrating significant potential in intelligent biological analysis. This review summarizes the latest advancements in DNA logic systems and their biomedical applications. Firstly, it introduces recent DNA logic systems based on various materials such as functional DNA sequences, nanomaterials, and three-dimensional DNA nanostructures. The material innovations driving DNA computing have been summarized, highlighting novel molecular reactions and analytical performance metrics like efficiency, sensitivity, and selectivity. Subsequently, it outlines the biomedical applications of DNA computing-based multi-biomarker analysis in cellular imaging, clinical diagnosis, and disease treatment. Additionally, it discusses the existing challenges and future research directions for the development of DNA computing.

Exploring DNA Computers: Advances in Storage, Cryptography and Logic Circuits

Over the last four decades, research on DNA as a functional material has primarily focused on its predictable conformation and programmable interaction. However, its low energy consumption, high responsiveness and sensitivity also make it ideal for designing specific signaling pathways, and enabling the development of molecular computers. This review mainly discusses recent advancements in the utilization of DNA nanotechnology for molecular computer, encompassing applications in storage, cryptography and logic circuits. It elucidates the challenges encountered in the application process and presents solutions exemplified by representative works. Lastly, it delineates the challenges and opportunities within this filed.

Effective Enrichment of Free Radicals through Nanoconfinement Boosts Electrochemiluminescence of Carbon Dots Derived from Luminol

Local enrichment of free radicals at the electrode interface may open new opportunities for the development of electrochemiluminescence (ECL) applications. The sensing platform was constructed by assembling ECL-emitting luminol derived carbon dots (Lu CDs) onto the heterojunction Tungsten disulfide/Covalent organic frameworks (WS2@COF) for the first time, establishing a nanoconfinement-reactor with significantly heightened ECL intensity and stability compared to the Lu CDs-H2O2 system. This enhanced performance is credited to the COF domain's restricted pore environment, where WS2@COF exhibits a more negative adsorption energy for H2O2, effectively enriching H2O2 in the catalytic edge sites of WS2. Furthermore, the internal electric field at the WS2 and COF interface accelerates electron flow, boosting WS2's catalytic activity and achieving domain-limited catalytic enhancement of ECL. Self-designed DNA nanomachines combined with cascading molecular keypad locking mechanisms are integrated into the biosensors, effectively guaranteeing the accuracy of the sensing process while providing crucial safeguards for molecular diagnostics and information security applications. In essence, this innovative approach represents the first system to enhance local free radical concentrations by enriching co-reactants on the electrode surface through nanoconfinement catalysis, yielding heightened ECL intensity. The potential impact of this novel strategy and sensing mechanism on real-bioanalysis applications is promising.

Harnessing tetrahedral framework nucleic acids for enhanced delivery of microRNA-149-3p: A new frontier in oral squamous cell carcinoma therapy

Oral squamous cell carcinoma (OSCC), a type of malignant tumour that primarily occurs in the oral mucosa, has drawn considerable attention owing to its aggressive growth and potentially high metastatic rate. Surgical resection is the primary treatment method for OSCC and is typically combined with radiation therapy and chemotherapy. microRNA-149-3p (miR-149) is a negative regulator of the Pi3k/Akt pathway and can effectively inhibit the proliferation of tumour cells. However, the application of miR-149 is limited owing to its relatively low efficiency of cellular uptake and poor stability when used alone. To overcome these challenges, this study adopted a novel nucleic acid nanostructured material, tetrahedral framework nucleic acids (tFNAs). The use of tFNAs as carriers to assemble the T-miR-149 complex reduced the expression of Pi3k and Akt involved in tumorigenesis and alterations in proteins related to cell apoptosis. The results indicated that the bionic drug delivery system has an effective tumour suppressive effect on OSCC in mice, revealing its potential clinical value in the treatment of OSCC.

Endogenous AND Logic DNA Nanomachine for Highly Specific Cancer Cell Imaging

Intracellular cancer-related biomarker imaging strategy has been used for specific identification of cancer cells, which was of great importance to accurate cancer clinical diagnosis and prognosis studies. Localized DNA circuits with improved sensitivity showed great potential for intracellular biomarkers imaging. However, the ability of localized DNA circuits to specifically image cancer cells is limited by off-site signal leakage associated with a single-biomarker sensing strategy. Herein, we integrated the endogenous enzyme-powered strategy with logic-responsive and localized signal amplifying capability to construct a self-assembled endogenously AND logic DNA nanomachine (EDN) for highly specific cancer cell imaging. When the EDN encountered a cancer cell, the overexpressed DNA repairing enzyme apurinic/apyrimidinic endonuclease 1 (APE1) and miR-21 could synergistically activate a DNA circuit via cascaded localized toehold-mediated strand displacement (TMSD) reactions, resulting in amplified fluorescence resonance energy transfer (FRET) signal. In this strategy, both endogenous APE1 and miR-21, served as two "keys" to activate the AND logic operation in cancer cells to reduce off-tumor signal leakage. Such a multiplied molecular recognition/activation nanomachine as a powerful toolbox realized specific capture and reliable imaging of biomolecules in living cancer cells.

Logic Signal Amplification System for Sensitive Electrochemiluminescence Detection and Subtype Identification of Cancer Cells

Achieving sensitive detection and accurate identification of cancer cells is vital for diagnosing and treating the disease. Here, we developed a logic signal amplification system using DNA tetrahedron-mediated three-dimensional (3D) DNA nanonetworks for sensitive electrochemiluminescence (ECL) detection and subtype identification of cancer cells. Specially designed hairpins were integrated into DNA tetrahedral nanostructures (DTNs) to perform a catalytic hairpin assembly (CHA) reaction in the presence of target microRNA, forming hyperbranched 3D nanonetworks. Benefiting from the "spatial confinement effect," the DNA tetrahedron-mediated catalytic hairpin assembly (DTCHA) reaction displayed significantly faster kinetics and greater cycle conversion efficiency than traditional CHA. The resulting 3D nanonetworks could load a large amount of Ru(phen)32+, significantly enhancing its ECL signal, and exhibit detection limits for both miR-21 and miR-141 at the femtomolar level. The biosensor based on modular logic gates facilitated the distinction and quantification of cancer cells and normal cells based on miR-21 levels, combined with miR-141 levels, to further identify different subtypes of breast cancer cells. Overall, this study provides potential applications in miRNA-related clinical diagnostics.

Simulation-Assisted DNA Nanodevice Serve as a General Optical Platform for Multiplexed Analysis of Micrornas

Small frame nucleic acids (FNAs) serve as excellent carrier materials for various functional nucleic acid molecules, showcasing extensive potential applications in biomedicine development. The carrier module and function module combination is crucial for probe design, where an improper combination can significantly impede the functionality of sensing platforms. This study explores the effect of various combinations on the sensing performance of nanodevices through simulations and experimental approaches. Variances in response velocities, sensitivities, and cell uptake efficiencies across different structures are observed. Factors such as the number of functional molecules loaded, loading positions, and intermodular distances affect the rigidity and stability of the nanostructure. The findings reveal that the structures with full loads and moderate distances between modules have the lowest potential energy. Based on these insights, a multisignal detection platform that offers optimal sensitivity and response speed is developed. This research offers valuable insights for designing FNAs-based probes and presents a streamlined method for the conceptualization and optimization of DNA nanodevices.

Remotely Activated DNA Probe System for the Detection and Imaging of Dual miRNAs

Cancers remain the leading cause of mortality worldwide. It is crucial to detect cancer at an early stage for improving survival rates. Biomarkers have precise implications for cancer progression. Here, we built a straightforward DNA probe system that could be activated by near-infrared light to detect dual miRNAs with a high specificity. This probe is built on the basis of upconversion nanoparticles, which could emit ultraviolet light and activate DNA probes adsorbed on the outer layer. The DNA probe system is remotely controlled through manipulation of the near-infrared (NIR) light, enabling simultaneous detection of dual miRNAs. The DNA nanosystem could be effectively endocytosed by cancer cells and reflect expression levels of dual miRNAs. Overall, this study demonstrates a promising remote-controlled DNA nanoplatform for the simultaneous detection of dual miRNAs, which has tremendous potential for precise cancer diagnostics and therapies.