A Methylation-Gated DNAzyme Circuit for Spatially Controlled Imaging of MicroRNA in Cells and Animals

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(23), P. 9666 - 9675

Published: May 30, 2024

Epigenetic modification plays an indispensable role in regulating routine molecular signaling pathways, yet it is rarely used to modulate self-assembly networks. Herein, we constructed a bioorthogonal demethylase-stimulated DNA circuitry (DSC) system for high-fidelity imaging of microRNA (miRNA) live cells and mice by eliminating undesired off-site signal leakage. The simple robust DSC composed primary cell-specific regulation (CR) module ultimate signal-transducing amplifier (SA) module. After the modularly designed was delivered into target cells, DNAzyme CR site-specifically activated endogenous demethylase produce fuel strands subsequent miRNA-targeting SA Through on-site multiply guaranteed recognitions, lucid efficient realized reliably amplified vivo miRNA sensing enabled in-depth exploration demethylase-involved pathway with cells. Our bioorthogonally on-site-activated represents universal versatile biomolecular platform via various regulations shows more prospects different personalized theragnostics.

Language: Английский

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Covalent Dynamic DNA Networks to Translate Multiple Inputs into Programmable Outputs

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Inspired by naturally occurring protein dimerization networks, in which a set of proteins interact with each other to achieve highly complex input-output behaviors, we demonstrate here fully synthetic DNA-based network that enables programmable computations. Our consists DNA oligonucleotide monomers modified reactive moieties can covalently bond form dimer outputs an all-to-all or many-to-many fashion. By designing input strands specifically sequester monomers, control the size reaction and thus fine-tune yield output predictable manner. Thanks programmability specificity DNA–DNA interactions, show this approach be used different using inputs. The is also versatile networks based on two distinct covalent reactions: thiol–disulfide strain-promoted azide–alkyne cycloaddition (SPAAC) reactions. Finally, functional output, ultimately controlling assembly disassembly nanostructures. dynamic shown provide way convert multiple inputs into broader range functions, including ones mimic those living cells.

Language: Английский

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A primordial DNA store and compute engine

Nature Nanotechnology, Journal Year: 2024, Volume and Issue: 19(11), P. 1654 - 1664

Published: Aug. 22, 2024

Language: Английский

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DNA-DISK: Automated end-to-end data storage via enzymatic single-nucleotide DNA synthesis and sequencing on digital microfluidics

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(34)

Published: Aug. 15, 2024

In the age of information explosion, exponential growth digital data far exceeds capacity current mainstream storage media. DNA is emerging as a promising alternative due to its higher density, longer retention time, and lower power consumption. To date, commercially mature synthesis sequencing technologies allow for writing reading on with customization convenience at research level. However, under disconnected nonspecialized mode, encounters practical challenges, including susceptibility errors, long latency, resource-intensive requirements, elevated security risks. Herein, we introduce platform named DNA-DISK that seamlessly streamlined synthesis, storage, microfluidics coupled tabletop device automated end-to-end storage. The single-nucleotide enzymatic biocapping strategy utilized, offering an ecofriendly cost-effective approach writing. A encapsulation using thermo-responsive agarose developed on-chip solidification, not only eliminating clutter but also preventing degradation. Pyrosequencing employed in situ accurate reading. As proof concept, successfully stored retrieved musical sheet file (228 bits) write-to-read latency (4.4 min per bit) well superior automation compared other platforms, demonstrating potential evolve into Hard Disk Drive future.

Language: Английский

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DNA sequence design model for multi-scene fusion

Neural Computing and Applications, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

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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Highly Reusable Enzyme-Driven DNA Logic Circuits

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

Published: March 4, 2025

In recent years, DNA has emerged as a promising molecule for the construction of molecular computing systems. research field logic circuits, enzyme-driven which offer faster reactions and lower complexity, have become key focus in field. However, it remains significant drawback that lacks capability being reused. Reusability is essential to enhance computational capacity, correct errors, reduce costs circuits. this study, we propose method achieving high reuse circuits using exonuclease III. By selectively digesting ds-DNA while preserving gate strands, our system highly restores circuit its initial state, contains no waste-strand. This demonstrated good performance converted-input experiment single-gate, multilayer cascades. Finally, achieve four times relatively complex three multiple square root circuit.

Language: Английский

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Advanced Logic Computing and Hybrid Crypto-Steganography for Molecular Information Coding Using Gold/Silver Nanoclusters

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

Published: March 11, 2025

In the domain of digital data exchange, ensuring information security is supreme demand for storage and transmission. Interlinking cryptographic techniques with steganographic principles can enhance confidentiality. However, there have been no reports thus far to develop molecular platforms hybrid crypto-steganography systems. Using our synthesized nanoclusters (BSA-Au/Ag NCs) through bovine serum albumin (BSA) as a versatile scaffold, we fabricated platform concatenated logic circuits keypad lock. Then, integrate terrestrial direction transmission navigation, employing double block cipher by combining stego key shifting system, aimed at enhancing paradigms. Furthermore, prioritize protection developing an enhanced distress call protocol using polyalphabetic activate covert communication capabilities, thereby safeguarding against potential infiltrators.

Language: Английский

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Algorithm in chemistry: molecular logic gate-based data protection

Chemical Society Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

This review focuses on stimuli-responsive material (SRM)-based data protection, emphasizing the integration of intricate logic and algorithms in SRM-constructed hardware. It also discusses current challenges future directions field.

Language: Английский

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Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(26), P. 18041 - 18049

Published: June 20, 2024

Folding thermodynamics, quantitatively described using parameters such as ΔGfold°, ΔHfold°, and ΔSfold°, is essential for characterizing the stability functionality of noncanonical nucleic acid structures but remains difficult to measure at molecular level. Leveraging programmability dynamic deoxyribonucleic (DNA) chemistry, we introduce a DNA-based tool capable performing free energy shift assay (FESA) that directly characterizes thermodynamics DNA in their native environments. FESA operates by rational design reference probe energetically equivalent target structure series toehold-exchange reactions, yet structurally incapable folding. As result, (ΔΔGrxn°) observed when plotting reaction yield against each toehold-exchange. We mathematically demonstrated ΔSfold° analyte can be calculated based on ΔΔGrxn°. After validating six hairpins comparing measured values predictions made NUPACK software, adapted characterize structures, encompassing triplexes, G-quadruplexes, aptamers. This adaptation enabled successful characterization folding these complex under various experimental conditions. The development marks paradigm technical advancement through tools. It also opens new avenues probing fundamental chemical biophysical questions lens engineering chemistry.

Language: Английский

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