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DNA logic circuits have gained great success in the past, thanks to their distinct performance regarding the scalability and correctness of computation. However, there are still two challenges often considered for DNA logic circuit-based computation. First, the mainstream optical probes are often subject to spectral overlapping interference for complex multitask analysis and outputs. Second, absolute quantification results traceable to the primary international system of units are mission impossible, especially for interlaboratory comparisons and quality assurances. Herein, we constructed DNA logic circuits encoded with lanthanide isotopes and decoded by elemental mass spectrometry. The Gd-enriched isotope and Nd-enriched isotope were incorporated in the DNA logic circuits for the isotope dilution-based absolute quantification of microRNAs. The proposed isotopic DNA logic circuits greatly enhance the multiplexity and computation accuracy, which poses a great potential for cancer biomarker-related diagnosis.
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http://dx.doi.org/10.1021/acs.analchem.4c06637 | DOI Listing |
ACS Synth Biol
September 2025
Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.
Cell-free biosensing systems are being engineered as versatile and programmable diagnostic technologies. A core component of cell-free biosensors is programmable molecular circuits that improve biosensor speed, sensitivity, and specificity by performing molecular computations such as logic evaluation and signal amplification. In previous work, we developed one such circuit system called Polymerase Strand Recycling (PSR), which amplifies cell-free molecular circuits by using T7 RNA polymerase off-target transcription to recycle nucleic acid inputs.
View Article and Find Full Text PDFAdv Drug Deliv Rev
September 2025
Department of Chemistry, Purdue University, West Lafayette 47907, IN 47907, USA. Electronic address:
DNA nanotechnology, a cutting-edge field that constructs sophisticated DNA-based nanostructures by harnessing the unparalleled programmability of DNA, has evolved into a powerful tool for applications in therapy, biosensing, logic computation, and more. This review outlines the fundamental strategies for constructing DNA nanostructures, beginning with the design of basic building blocks such as small, symmetric tiles (e.g.
View Article and Find Full Text PDFTalanta
August 2025
School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China.
G-Quadruplex (G4) DNA structures play a crucial role in regulating various biological processes, rendering them attractive targets for diagnostic and therapeutic applications. The development of G4-targeted fluorescent probes will significantly enhance our understanding of G4 DNA biology in vivo and improve the precision of diagnosing and treating genetic diseases. Herein, we report on a regioisomer of a thiazole orange derivative (SQ2) as a promising fluorescent dye for G4 DNA structures and demonstrate its application in both cell and tumor tissue imaging.
View Article and Find Full Text PDFJ Nanobiotechnology
September 2025
State Key Laboratory of Organic-Inorganic Composites, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
Conventional miRNA-based diagnostic methods often treat all biomarkers equally, overlooking the fact that each miRNA contributes differently to disease classification. This differential diagnostic importance is captured by the concept of Cancerous Diagnostic Valence (CDV)-a metric that quantifies both the direction (oncogenic or protective) and magnitude of each miRNA's association with cancer. Here, we introduce a polymerase-based DNA molecular computing system that directly encodes and integrates CDVs to perform weighted molecular classification of non-small cell lung cancer (NSCLC).
View Article and Find Full Text PDFNPJ Sci Food
August 2025
Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia.
Ensuring halal food integrity requires detecting porcine DNA, as contamination may occur during processing despite the use of halal-certified ingredients. This study presents a fuzzy logic (FL) framework to determine the presence of porcine DNA in processed meat by analyzing cycle threshold (Ct) values of four target genes: Cytochrome B, 18 s RNA, 12 s RNA, and D-loop mitochondria. The framework utilizes 12 fuzzy rules, 12 input functions, and 5 output functions, validated with 48 data points from laboratory and historical analyses.
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