A Multi‐Input Molecular Classifier Based on Digital DNA Strand Displacement for Disease Diagnostics

Advanced Materials, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

DNA-based molecular computing systems for biomarkers have emerged as powerful tools intelligent diagnostics. However, with the variety of feature expanding, current suffer from use a large number oligonucleotides and limited encoding capability. Here, study develops an alternative approach termed Digital DNA Strand Displacement (DDSD) which recognizes targets operates target valence through polymerase-based extension strand release. DDSD significantly reduced used oligonucleotide species, provided robust classifiers. In clinical blood samples, 96% accuracy rate is achieved DDSD-based binary classifier distinguishing bacterial viral infections, 100% multiclass identifying pathogen types, surpassing existing systems. Moreover, can be readily expanded. Cascade developed, enabling simultaneous up to 14 states maximum 25. Multiway junction implemented achieve high-valence by compact nanostructures rather than split units, reducing potential leakage. The implementation enhances capability valence-based diagnostics multiplexed biomarker detection.

Language: Английский

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Agarose Gel‐Coated Nanochannel Biosensor for Detection of Prostate‐Specific Antigen in Unprocessed Whole Blood Samples

Small, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

Abstract Solid‐state nanopore/nanochannel biosensors have rapidly advanced due to their high sensitivity, label‐free detection, and fast response. However, detecting biomarkers directly in complex biological environments, particularly whole blood, remains challenging because of nonspecific protein adsorption clogging. Here, a DNA aptamer functionalized nanochannel biosensor is developed with excellent antifouling properties, achieved by coating the surface agarose gel. This gel effectively mitigates fouling diverse environments while maintaining comparable sensitivity uncoated nanochannels for prostate‐specific antigen (PSA) buffer solutions within 20 min. The exhibits detection limit 1 ng mL −1 PSA human serum, matching performance commercial enzyme‐linked immunosorbent assay (ELISA) kits. Importantly, it successfully differentiates blood samples from prostate cancer patients healthy individuals. superior behavior attributed electrically neutral, highly hydrophilic nature, porous structure gel, which prevents large biomolecules facilitating diffusion aptamer‐based capture. offers reliable showing great promise biomedical applications.

Language: Английский

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Two-dimensional nanomaterials-based optical biosensors empowered by machine learning for intelligent diagnosis

TrAC Trends in Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 118162 - 118162

Published: Feb. 1, 2025

Language: Английский

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Scalable acoustic virtual stirrer for enhanced interfacial enzymatic nucleic acid reactions

Science Advances, Journal Year: 2025, Volume and Issue: 11(10)

Published: March 5, 2025

Enzymatic nucleic acid reaction is a fundamental tool in molecular biology. However, high-complexity enzymatic DNA reactions and assays are still challenging due to the difficulties integrating scaling up microscale units mixing tools. Here, we present scalable acoustofluidic platform featuring acoustic virtual stirrer (AVS) arrays, serving as stirrers increase efficiency of interfacial reactions. Analogous magnetic stirrers, AVS arrays perturb fluid through oscillating pressure nodes, controllable terms speeds amplitudes via modulation. By optimizing kinetics surface-tethered enzymes AVS, achieve 7.74% improvement stepwise yield synthesis. In addition, enhanced logic gate architecture can complete responses within 2 minutes, achieving average speed enhancement 8.58 times compared non-AVS configuration. With its tunability, ease integration, efficiency, this technology holds promises for applications biology chemistry.

Language: Английский

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High-Security Data Encryption Enabled by DNA Multi-Strand Solid-Phase Hybridization and Displacement in Inkjet-Printed Microarrays

ACS Applied Materials & Interfaces, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

Multicolor fluorescent encryption systems that respond to specific stimuli have drawn widespread attention data storage and due their low cost facile access. However, existing are limited by materials, restricting depth. This study uses DNA molecules as materials offer exceptional specificity depth within sequences. With inkjet-printed microarrays on a solid-phase interface, multicolor system based hybridization strand displacement is developed, achieving an with high flexibility. strands, modified different labels, delivered onto interfaces containing self-assembled monolayer (SAM) via inkjet printing, forming microarrays. Data achieved through the of strands for presentation interference SAM at interface between solid phase droplets. Interference can be removed decryption. The this determined design sequences combination multiple showcasing its outstanding ability. Meanwhile, high-throughput printing accelerates writing process, further enhancing efficiency. reaction in microarrays, provides scalable robust strategy high-depth efficient encryption.

Language: Английский

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Logical Analysis of Multiple miRNAs with Isothermal Molecular Classifiers Based on LATE-RCA

Nano Letters, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 30, 2025

Logical analysis of multiple-miRNA expression information and immediate output diagnostic results facilitates early cancer detection. In this work, we constructed an isothermal molecular classifier capable performing computations on multiple miRNAs directly providing diagnosis results. First, developed linear-after-the-exponential rolling circle amplification (LATE-RCA), a nearly linear that does not destroy the original quantitative about miRNAs. By designing different numbers weighted coding sequences circular template, naturally implemented multiplication in LATE-RCA process. Summation, subtraction, reporting were then carried out by strand displacement reactions. The entire workflow was validated using synthetic gastric healthy miRNA samples with accuracy 100%, demonstrating its robustness accuracy. Compared existing classifiers, our approach performs under conditions, streamlines computational procedures, simplifies probe design. We believe has promising prospects personalized precision medicine.

Language: Английский

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Fast DNA‐Based Molecular Classifier for Cancer Diagnosis Using Freeze‐Thaw Cycling^†

Chinese Journal of Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 11, 2025

Comprehensive Summary Monitoring and analyzing expression levels of multiple biomarkers in biological samples can improve disease risk prediction guide precision medicine but suffers from high cost being time‐consuming. Here, we construct a fast molecular classifier based on freeze‐thaw cycling that implements an silico support vector machine (SVM) model at the level with panel disease‐related patterns for rapid diagnosis. The employs DNA reaction networks as computing module repeated dehydration concentration process driving force to implement set simplified mathematical operations (such multiplication, summation subtraction) efficient classification complex input patterns. We demonstrate DNA‐based enables precise cancer diagnosis within short turnaround time synthetic compared those free diffusion classifiers. envision this all‐in‐one will create more opportunities inexpensive, accurate, diagnosis, prognosis therapy, particularly emergency departments or point care.

Language: Английский

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DNA Nanoframework-Confined Well-Organized Catalytic Hairpin Assembly for Highly Sensitive and Specific Detection of MiRNA

Talanta, Journal Year: 2025, Volume and Issue: 290, P. 127788 - 127788

Published: Feb. 21, 2025

Language: Английский

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A Localized Scalable DNA Logic Circuit System Based on the DNA Origami Surface

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 2043 - 2043

Published: Feb. 26, 2025

DNA (Deoxyribonucleic Acid) logic circuit systems provide a powerful arithmetic architecture for the development of molecular computations. nanotechnology, particularly origami, provides nanoscale addressable surface systems. Although computations based on origami surfaces have received significant attention in research, there are still obstacles to constructing localized scalable Here, we developed elementary circuits by employing strand displacement reaction (SDR) realize We showed that constructed can be scaled up perform arbitrary digital computing tasks, including square root functions, full adder and subtractor. used 50% reduction number components, compared threshold strategy. further demonstrated three-satisfiability (3-SAT) problem solving disease classification implemented using circuits. expect our approach new design paradigm their applications complex mathematical diagnosis.

Language: Английский

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DNA logic circuit coupled with enzymatic amplification for signal-enhanced, AND-gated imaging of inflammation-associated mRNAs

Nano Today, Journal Year: 2025, Volume and Issue: 62, P. 102700 - 102700

Published: Feb. 28, 2025

Language: Английский

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