Mass Nanotags Mediate Parallel Amplifications on Nanointerfaces for Multiplexed Profiling of RNAs

Lanthanide-Encoded Multi-functional Tetrahedral DNA for Precise Nanodevice Encoding

The encoding of precise nanodevices is undoubtedly an extremely optimal approach for information storage and multiplex detection. Undeniably, precise control over the nanostructure, composition, and morphology of these devices is of paramount importance. However, most of the tags currently used for encoding are limited by insufficient quantity and low resolution, resulting in deficiencies in accuracy, scalability, and exclusivity of the encoded structures. Here, a series of lanthanide-encoded tetrahedral DNA nanodevices are crafted as unique elemental mass spectrometry-encoded tags. These devices combine the multicomponent interference-free detection capability of elemental encoding with the spatially addressable features of DNA nanostructures. After embedding one to four distinct lanthanide tags (LnTs) and arranging them in equal stoichiometric ratios on different DNA tetrahedral frame cantilevers, the lanthanide nanotags transform into dynamic nanoprobes through combination and fine-tuning. The device can function as a 15-component element tag and generate seven signal outputs. It can respond to three different stimuli when targeting multiple objects simultaneously and is then fed into a semiquantitative analysis based on the isotope dilution method. These DNA nanodevices show strong potential for integration with biological circuits, enabling programmable signal release from their three-dimensional architecture, thereby facilitating even more sophisticated biological identification and logical output.

Hierarchical DNA Octahedral Nanoplatform for in Situ Biosensing and Clinical Monitoring of Acute Lymphoblastic Leukemia

Developing nanoscale platforms with high integration, assembly efficiency, and structural stability for performing complex computations in specific cells remains a significant challenge. To address this, the Three-dimensional Hierarchical Octahedral Robotic (THOR) DNA nanoplatform is introduced, which integrates targeting, logic computation, and sensing modules within a single framework. This nanoplatform specifically binds to cancer cell surface proteins, releasing aptamer-linked fuel chains to initiate subsequent computational processes. Three logic gates efficiently compute any arbitrary binary combination of target proteins. The sensing module employs catalytic hairpin assembly for detecting specific miRNAs with high sensitivity. THOR demonstrates robust functionality both in vitro and in situ. As a proof-of-concept, this nanoplatform to distinguish acute lymphoblastic leukemia (ALL) patients from other leukemia subtypes and healthy participants, achieving 100% accuracy is applied. Additionally, this approach reliably monitored the therapeutic progress of ALL patients, showing strong concordance with bone marrow smear results. The THOR platform highlights the feasibility of constructing a reliable, hierarchical, and multifunctional analytical system based on a single DNA polyhedron. It offers a promising auxiliary tool for clinical diagnostics and therapeutic monitoring.

Computer-Aided Design of 3D Non-Enzymatic Catalytic Cascade Systems for In Situ Multiplexed mRNA Imaging in Single-Cells

mRNA, a critical biomarker for various diseases and a promising target for cancer therapy, is central to biological and medical research. However, the development of multiplexed approaches for in situ monitoring of mRNA in live cells are limited by their reliance on enzyme-based signal amplification, challenges with in situ signal diffusion, and the complexity of nucleic acid design. In this study, we introduce a nonenzymatic catalytic DNA assembly (NEDA) technique to address these limitations. NEDA facilitates the precise in situ imaging of intracellular mRNA by assembling three free hairpin DNA amplifiers into a low-mobility, three-dimensional DNA spherical structure. This approach also enables the simultaneous detection of four distinct targets via the combination of fluorescent signals, with a detection limit as low as 141.2 pM for target mRNA. To enhance the efficiency of nucleic acid design, we employed computer-aided design (CAD) to rapidly generate feasible sequences for highly multiplexed detection. By integrating various machine learning algorithms, we achieved impressive accuracy of nearly 96.66% in distinguishing multiple cell types and 87.80% in identifying the same cell type under different drug stimulation conditions. Notably, our platform can also identify drug stimuli with similar mechanisms of action, highlighting its potential in drug development. This multiplexed 3D assembly sensing strategy with CAD not only enhances the ability to image nucleic acid sequences in situ simultaneously but also provides a novel platform for efficient molecular diagnostics and personalized therapy.

Functionalized Multichannel Fluorescence-Encoded Nanosystem on Erythrocyte-Coated Nanoparticles for Precise Cancer Subtype Discrimination

Rapid and precise cancer subtype discrimination is essential for personalized oncology. Conventional diagnostic methods often lack sufficient accuracy and speed. Here, we introduce a multichannel fluorescence-encoded nanosystem based on erythrocyte-coated polydopamine nanoparticles (PDA@EM), functionalized with multiple resurfaced fluorescent proteins. The fluorescence of these proteins is initially quenched by PDA@EM and restored upon cell addition. This multichannel fluorescence-encoded nanosystem enables highly sensitive "turn-on" fluorescence profiling of cancer cells within 30 min, achieving 100% accuracy in distinguishing various proteins and classifying a wide range of cancer cell lines, including subtypes of oral squamous cell carcinoma (OSCC). Notably, it offers rapid, label-free diagnostics of OSCC malignancy from clinical samples postsurgery. This capability was validated through histopathological and proteomic analyses, which identified protein signatures associated with tumor progression and immune suppression. Overall, our multichannel nanosensor represents an advanced molecular diagnostics platform, paving the way for personalized cancer treatment in clinical oncology.

MiRS-HF: A Novel Deep Learning Predictor for Cancer Classification and miRNA Expression Patterns

Cancer classification and biomarker identification are crucial for guiding personalized treatment. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. We propose an approach for cancer classification called MiRNA Selection and Hybrid Fusion (MiRS-HF), which consists of early fusion and intermediate fusion. The early fusion involves applying a Layer Attention Graph Convolutional Network (LAGCN) to a miRNA-disease heterogeneous network, resulting in a miRNA-disease association degree score matrix. The intermediate fusion employs a Graph Convolutional Network (GCN) in the classification tasks, weighting the expression data based on the miRNA-disease association degree score. Furthermore, MiRS-HF can identify the important miRNA biomarkers and their expression patterns. The proposed method demonstrates superior performance in the classification tasks of six cancers compared to other methods. Simultaneously, we incorporated the feature weighting strategy into the comparison algorithm, leading to a significant improvement in the algorithm's results, highlighting the extreme importance of this strategy.

DNA Nanostructure Disintegration-Assisted SPAAC Ligation for Electrochemical Biosensing

MicroRNAs (MiRNAs) are valuable biomarkers for the diagnosis and prognosis of diseases. The development of reliable assays is an urgent pursuit. We herein fabricate a novel electrochemical sensing strategy based on the conformation transitions of DNA nanostructures and click chemistry. Duplex-specific nuclease (DSN)-catalyzed reaction is first used for the disintegration of the DNA triangular pyramid frustum (DNA TPF). A DNA triangle is formed, which in turn assists strain-promoted alkyne-azide cycloaddition (SPAAC) to localize single-stranded DNA probes (P1). After SPAAC ligation, multiple DNA hairpins are spontaneously folded, and the labeled electrochemical species are dragged near the electrode interface. By recording and analyzing the responses, a highly sensitive electrochemical biosensor is established, which exhibits high sensitivity and reproducibility. Clinical applications have been verified with good stability. This sensing strategy relies on the integration of DNA nanostructures and click chemistry, which may inspire further designs for the development of DNA nanotechnology and applications in clinical chemistry.

Construction of a Spatial-Confined Self-Stacking Catalytic Circuit for Rapid and Sensitive Imaging of Piwi-Interacting RNA in Living Cells

Piwi-interacting RNAs (piRNAs) are small noncoding RNAs that repress transposable elements to maintain genome integrity. The canonical catalytic hairpin assembly (CHA) circuit relies on random collisions of free-diffused reactant probes, which substantially slow down reaction efficiency and kinetics. Herein, we demonstrate the construction of a spatial-confined self-stacking catalytic circuit for rapid and sensitive imaging of piRNA in living cells based on intramolecular and intermolecular hybridization-accelerated CHA. We rationally design a 3WJ probe that not only accelerates the reaction kinetics by increasing the local concentration of reactant probes but also eliminates background signal leakage caused by cross-entanglement of preassembled probes. This strategy achieves high sensitivity and good specificity with shortened assay time. It can quantify intracellular piRNA expression at a single-cell level, discriminate piRNA expression in tissues of breast cancer patients and healthy persons, and in situ image piRNA in living cells, offering a new approach for early diagnosis and postoperative monitoring.

DNA Walker-Driven Mass Nanotag Assembly System for Simultaneously Profiling Dual Markers of Oxidative Stress at Different Cellular Locations

Simultaneous profiling of redox-regulated markers at different cellular sublocations is of great significance for unraveling the upstream and downstream molecular mechanisms of oxidative stress in living cells. Herein, by synchronizing dual target-triggered DNA machineries in one nanoentity, we engineered a DNA walker-driven mass nanotag (MNT) assembly system (w-MNT-AS) that can be sequentially activated by oxidative stress-associated mucin 1 (MUC1) and apurinic/apyrimidinic endonuclease 1 (APE1) from plasma membrane to cytoplasm and induce recycled assembly of MNTs for multiplex detection of the two markers by matrix-assisted laser desorption ionization mass spectrometry (MALDI MS). In the working cascade, the sensing process governs the separate activation of w-MNT-AS by MUC1 and APE1 in diverse locations, while the assembly process contributes to the parallel amplification of the ion signal of the characteristic mass tags. In this manner, the differences between MCF-7, HeLa, HepG2, and L02 cells in membrane MUC1 expression and cytoplasmic APE1 activation were fully characterized. Furthermore, the oxidative stress level and dynamics caused by exogenous H2O2, doxorubicin, and simvastatin were comprehensively demonstrated by tracking the fate of the two markers across different cellular locations. The proposed w-MNT-AS coupled MS method provides an effective route to probe multiple functional molecules that lie at different locations while participating in the same cellular event, facilitating the mechanistic studies on cellular response to oxidative stress and other disease-related cellular processes.

Quality Control of Mass-Encoded Nanodevices by Compartmented DNA Origami Frames for Precision Information Coding and Logic Mapping

Encoded nanostructures afford an ideal platform carrying multi-channel signal components for multiplexed assay and information security. However, with the demand on exclusivity and reproducibility of coding signals, precise control on the structure and composition of nanomaterials featuring fully distinguishable signals remains challenging. By using the multiplexing capability of mass spectrometry (MS) and spatial addressability of DNA origami nanostructures, we herein propose a quality control methodology for constructing mass-encoded nanodevices (namely MNTs-TDOFs) in the scaffold of compartmented tetrahedral DNA origami frames (TDOFs), in which the arrangement and stoichiometry of four types of mass nanotags (MNTs) can be finely regulated and customized to generate characteristic MS patterns. The programmability of combinatorial MNTs and orthogonality of individual compartments allows further evolution of MNTs-TDOFs to static tagging agents and dynamic nanoprobes for labeling and sensing of multiple targets. More importantly, structure control at single TDOF level ensures the constancy of prescribed MS outputs, by which a high-capacity coding system was established for secure information encryption and decryption. In addition to the multiplexed outputs in parallel, the nanodevices could also map logic circuits with interconnected complexity and logic events of c-Met recognition and dimerization on cell surface for signaling regulation by MS interrogation.

Multifunctional dumbbell probes-based logic circuits: microRNAs logic detection and tumor cells identification

BACKGROUND

The powerful logic processing capability of DNA logic circuits over multiple input signals perfectly meets the demands of multi-biomarker-based clinical diagnostics. As important biomarkers for cancer diagnosis and treatment, the orthogonal differential expression of microRNAs (miRNAs) in different diseases and different cancer cells makes the precise logical detection of multiple miRNAs particularly critical.

RESULTS

Therefore, we constructed two fundamental "AND" and "OR" logic gates and one "AND-OR" logic gate on the basis of our proposed multifunctional dumbbell probes. These logic gates allowed for the logical profiling of multiple cancer-associated miRNAs. In addition, by making simple adjustments to the functional modules of multifunctional dumbbell probes, the three logic gates we proposed could be easily transformed without the use of sophisticated probe design. Remarkably, these logic gates, in particular the "AND-OR" logic gate, were able to compute several miRNAs simultaneously, demonstrating excellent cell identification capabilities.

SIGNIFICANCE

Overall, this work provided a new idea for accurately distinguishing multiple cell types and showed great application prospects.