DNAzyme-Based Dissipative DNA Strand Displacement for Constructing Temporal Logic Gates

ACS Nano, Journal Year: 2024, Volume and Issue: 18(3), P. 2184 - 2194

Published: Jan. 9, 2024

Toehold-mediated DNA strand displacement is the foundation of dynamic nanotechnology, encompassing a wide range tools with diverse functions, dynamics, and thermodynamic properties. However, majority these are limited to unidirectional reactions driven by thermodynamics. In response growing field dissipative we present an approach: DNAzyme-based (D-DSD), which combines principles nanotechnology nanotechnology. D-DSD introduces circular characteristics, distinguishing it from observed in conventional displacement. We investigated reaction mechanism devised temporal control elements. By substituting components, designed two distinct AND gates using fewer than 10 strands, eliminating need for complex network designs. contrast previous logic gates, our storage not through dynamics or cross-inhibition but autoregressive storage, more modular scalable approach memory storage. preserves fundamental structure toehold-mediated displacement, while offering enhanced simplicity versatility.

Language: Английский

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A Dual-Mode Colorimetric and Fluorescence Biosensor Based on a Nucleic Acid Multiplexing Platform for the Detection of Listeria monocytogenes

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Listeria monocytogenes (L. monocytogenes) is one of the most prevalent threats, capable inducing diverse illnesses and presenting a serious threat to public health. Herein, we demonstrate novel dual-mode colorimetric/fluorescence biosensor based on exponential amplification reaction strand displacement reactions (EASDR), which has multiplexing capability that significantly promotes anchoring trapping Pt nanoparticles (Pt NPs) fluorescent dyes for sensitive detection monocytogenes). The method works by targeting specific bacteria with aptamers promoting repeated EASDR affect immobilization NPs in orifice plate, could produce changes fluorescence colorimetric signals. assay achieves limit 38 CFU/mL 10 fluorescence. Furthermore, developed can be applied analysis raw food samples (milk), good recoveries were obtained spiked samples. In summary, improves accuracy simultaneously outputting two signals shows great potential identification foodborne pathogens.

Language: Английский

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DNA‐Enabled Self‐Resetting Electrochemical Sensor for microRNA Detection

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

Published: Feb. 14, 2025

Abstract Nucleic acids, such as microRNA and circulating tumor DNA, are widely utilized potential biomarkers for early disease diagnosis. Electrochemical sensors with high sensitivity play a significant role in quantitative bioanalysis, however, target molecules during detection usually bind to probes limit their reusability. Powered by DNA/RNA fuel enzyme‐based consumption unit, dissipative DNA systems can perform periodic tasks self‐resettable manner. Here, self‐resetting electrochemical sensor is reported miRNA based on networks. The microRNA‐21 (miRNA‐21) invades the incumbent strand activates displacement process. Released ferrocene‐modified strands probe electrode surface accurate detection. within RNA/DNA heteroduplex will then be digested RNase H free which replaces ferrocene restores initial state. It found that of this 0.35 p M third cycle. not only achieve lower limits, maintain repeatability stability complex matrices, but also reduce cost sensors. envisioned many real‐life applications initiated analyzing various oligonucleotide cancer diagnosis bioanalysis.

Language: Английский

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Regulation of CRISPR trans-cleavage activity by an overhanging activator

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(4)

Published: Feb. 8, 2025

Abstract The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system exhibits extraordinary capability in the field of molecular diagnosis and biosensing, attributed to its trans-cleavage ability. precise modulation performance has emerged as a significant challenge advancing CRISPR technology next stage development. Herein, we reported CRISPR/Cas12a regulation strategy based on an overhanging activator. presence domains activators creates steric hindrances that have substantial impact activity activation timing Cas12a. Cas12a can be finely tuned by adjusting position, length, complementarity domains. Moreover, specific structures exhibit characteristics automatic delayed activation. enables timely Cas12a, facilitating multifunctional applications. This effectively accomplishes dynamic regulation, programmable release cargo, logical operations, multi-enzyme detection. flexibility versatility this simple powerful regulatory will pave way for expanded applications CRISPR/Cas biotechnology, bioengineering, biomedicine.

Language: Английский

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Toehold-Mediated Strand Displacement in Random Sequence Pools

Journal of the American Chemical Society, Journal Year: 2022, Volume and Issue: 145(1), P. 634 - 644

Published: Dec. 26, 2022

Toehold-mediated strand displacement (TMSD) has been used extensively for molecular sensing and computing in DNA-based circuits. As these circuits grow complexity, sequence similarity between components can lead to cross-talk, causing leak, altered kinetics, or even circuit failure. For small non-biological circuits, such unwanted interactions be designed against. In environments containing a huge number of sequences, taking all possible into account becomes infeasible. Therefore, general understanding the impact backgrounds on TMSD reactions is great interest. Here, we investigate random DNA sequences We begin by studying individual interfering strands use obtained data build machine learning models that estimate kinetics. then influence pools find kinetics are determined only subpopulation strongly interacting strands. Consequently, their behavior mimicked collection The equilibration with background influences this behavior, leading up 1 order magnitude difference reaction speed. Finally, compare two established one novel technique speed pools: three-letter alphabet, protection toeholds intramolecular secondary structure, an additional blocking strand. While techniques were useful, latter without constraints. expect our insights will useful construction robust noise.

Language: Английский

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Timed Pulses in DNA Strand Displacement Reactions

Journal of the American Chemical Society, Journal Year: 2023, Volume and Issue: 145(38), P. 20968 - 20974

Published: Sept. 15, 2023

Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays, we demonstrate here a strategy to achieve temporally programmed output signals in DNA-based strand displacement reactions (SDRs). To this, rationally designed input strands that, once bound their target duplex, can be gradually degraded, resulting signal. We also blocker suppress and determine the time at which reaction is generated. show controlling degradation rate of strands, finely control delayed over range 10 h. prove it possible orthogonally delay two different same solution taking advantage specificity for strands. Finally, applications such SDRs: time-programmed decoration DNA nanostructures sequentially appearing self-erasing formation patterns.

Language: Английский

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Decorated DNA‐Based Scaffolds as Lateral Flow Biosensors

Angewandte Chemie International Edition, Journal Year: 2023, Volume and Issue: 62(47)

Published: Oct. 7, 2023

Abstract Here we develop Lateral Flow Assays (LFAs) that employ as functional elements DNA‐based structures decorated with reporter tags and recognition elements. We have rationally re‐engineered tile‐based DNA tubular can act scaffolds be of different nature (i.e. antigens, aptamers or proteins) orthogonal fluorescent dyes. As a proof‐of‐principle developed sandwich competitive multiplex lateral flow platforms for the detection several targets, ranging from small molecules (digoxigenin, Dig dinitrophenol, DNP), to antibodies (Anti‐Dig, Anti‐DNP Anti‐MUC1/EGFR bispecific antibodies) proteins (thrombin). Coupling advantages together simplicity LFAs, our approach offers opportunity detect wide range targets nanomolar sensitivity high specificity.

Language: Английский

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Temporally controlled multistep division of DNA droplets for dynamic artificial cells

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 27, 2024

Abstract Synthetic droplets mimicking bio-soft matter formed via liquid-liquid phase separation (LLPS) in living cells have recently been employed nanobiotechnology for artificial cells, molecular robotics, computing, etc. Temporally controlling the dynamics of synthetic is essential developing such bio-inspired systems because maintain their functions based on temporally controlled biomolecular reactions and assemblies. This paper reports temporal control DNA-based LLPS (DNA droplets). We demonstrate timing-controlled division DNA time-delayed triggers regulated by chemical reactions. Controlling release order multiple results multistep droplet division, i.e., pathway-controlled a reaction landscape. Finally, we apply into computing element to compare microRNA concentrations. believe that will promote design dynamic cells/molecular robots sophisticated biomedical applications.

Language: Английский

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Switching from Molecules to Functional Materials: Breakthroughs in Photochromism With MOFs

Advanced Materials, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 7, 2024

Abstract Photochromic materials with properties that can be dynamically tailored as a function of external stimuli are rapidly expanding field driven by applications in areas ranging from molecular computing, nanotechnology, or photopharmacology to programable heterogeneous catalysis. Challenges arise, however, when translating the rapid, solution‐like response stimuli‐responsive moieties solid‐state due intermolecular interactions imposed through close packing bulk solids. As result, integration photochromic compounds into synthetically porous matrices, such metal‐organic frameworks (MOFs), has come forefront an emerging strategy for material development. This review highlights how core principles reticular chemistry (on example MOFs) play critical role performance, surpassing limitations previously observed solution solid state. The symbiotic relationship between photoresponsive and focus on synthesis creates avenues toward tailorable photoisomerization kinetics, directional energy charge transfer, switchable gas sorption, synergistic chromophore communication is discussed. not only focuses recent cutting‐edge advancements development, but also novel, vital‐to‐pursue pathways multifaceted functional realms energy, technology, biomedicine.

Language: Английский

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Dynamic and Reversible Decoration of DNA‐Based Scaffolds

Advanced Materials, Journal Year: 2023, Volume and Issue: 35(18)

Published: Feb. 5, 2023

An approach to achieving dynamic and reversible decoration of DNA-based scaffolds is demonstrated here. To do this, rationally engineered DNA tiles containing enzyme-responsive strands covalently conjugated different molecular labels are employed. These designed be recognized degraded by specific enzymes (i.e., Ribonuclease H, RNase or Uracil Glycosylase, UDG) inducing their spontaneous de-hybridization from the assembled tile replacement a new strand label. Multiple that specifically respond allow for dynamic, orthogonal, structures. As proof-of-principle strategy, possibility orthogonally control distribution fluorophores small molecules) on same scaffold without crosstalk demonstrated. By doing so, display antibody recognition patterns obtained. The offers higher-order supramolecular assemblies (including origami) with several functional moieties achieve biomaterials improved adaptability, precision, sensing capabilities.

Language: Английский

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