Search

Fold‐change detection is widespread in sensory systems of various organisms. Dynamic DNA nanotechnology provides an important toolbox for reproducing structures and responses of cellular circuits. In this work, we construct an enzyme‐free nucleic acid circuit based on the incoherent feed‐forward loop using toehold‐mediated DNA strand displacement reactions and explore its dynamic behaviors. The mathematical model based on ordinary differential equations is used to evaluate the parameter regime required for fold‐change detection. After selecting appropriate parameters, the constructed synthetic circuit exhibits approximate fold‐change detection for multiple rounds of inputs with different initial concentrations. This work is anticipated to shed new light on the design of DNA dynamic circuits in the enzyme‐free environment. [ABSTRACT FROM AUTHOR]

Developing smart material systems for performing different tasks in diverse environments remains challenging. Here, we show that by integrating stimuli‐responsive soft materials with multi‐mode reconfigurable DNA‐based chemical reaction circuits (D‐CRCs), it can control size change of microgels with multiple reaction pathways and adapt expansion behaviors to meet diverse environments. We first use pH‐responsive intramolecular conformational switches for regulating DNA strand displacement reactions (SDRs). The ability to regulate SDRs with tunable pH‐dependence allows to build dynamic chemical reaction networks with diverse reaction pathways. We confirm that the designed DNA switching circuits are reconfigurable at different pH and perform different logic operations, and the swelling of DNA switching circuit‐integrated microgel systems can be programmably directed by D‐CRCs. Our approach provides insight into building smart responsive materials and fabricating autonomous soft robots. [ABSTRACT FROM AUTHOR]

Precise control of DNA‐circuit functions facilitates the construction of complex DNA networks to perform sophisticated functions. Inspired by optochemical genetics with high precision for controlling and studying neural networks by photoregulation of membrane receptors, we herein report optochemically controlled DNA switching circuits for regulating computation functions. The DNA‐switching circuits involve a CG–C+ triplex‐based DNA switch that undergoes structural transition from triplex to duplex states after exposure to UV irradiation due to proton transfer, showing optochemical control. We demonstrate that the DNA‐switching circuits enable the regulation of computation functions by optochemical control of the state of the DNA switch, including multiple logic computations and probabilistic computation. We hope this work will broaden DNA‐circuit functions and facilitate the construction of complex DNA networks. [ABSTRACT FROM AUTHOR]

DNA nanotechnology, fluorescence, fold-change detection, nucleic acid circuits, strand displacement Front Cover: Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection (ChemPlusChem 9/2023) Keywords: DNA nanotechnology; fluorescence; fold-change detection; nucleic acid circuits; strand displacement EN DNA nanotechnology fluorescence fold-change detection nucleic acid circuits strand displacement 1 1 1 09/28/23 20230901 NES 230901 B The cover picture shows b an enzyme-free nucleic acid synthetic circuit constructed by the toehold-mediated DNA strand displacement reaction, where a fold-change input (top left) elicits a similar response (bottom right). [Extracted from the article]

Titelbild: Optochemical Control of DNA-Switching Circuits for Logic and Probabilistic Computation (Angew. Keywords: chemical reaction networks; DNA circuits; DNA switches; logic computations; probabilistic computations EN chemical reaction networks DNA circuits DNA switches logic computations probabilistic computations 3353 3353 1 02/10/21 20210215 NES 210215 B Ein molekularer Computer b aus optochemischen DNA-Schaltkreisen wurde entwickelt, der digitale Rechenoperationen einschließlich Boolescher Logik (dargestellt durch 0 und 1) und Wahrscheinlichkeitsrechnungen (dargestellt durch die Würfel), ausführen kann. Chemical reaction networks, DNA circuits, DNA switches, logic computations, probabilistic computations. [Extracted from the article]

Nanomaterials-based enzymatic mimics have recently received considerable attention due to their superior properties over natural enzymes. Particularly, great efforts have been made to the fabrication of enzymatic mimics based on carbon matrix-based hybrid nanocomposites because of their improved dispersion, stability and catalytic activity compared with naomaterials alone. In this work, a new peroxidase mimic based on carbon coated magnetite nanoparticle (Fe 3 O 4 @C) with improved water-dispersion and peroxidase-like activity was presented for the first time. Unlike conventional hybrid nanocomposites, Fe 3 O 4 @C is a typical core–shell structure in the nanoscale regime and possesses the properties of easy preparation, super water-dispersion and excellent stability. Owing to the presence of carbon shell, Fe 3 O 4 @C showed an enhanced peroxidase-like activity as compared with its two components. As a peroxidase mimic, the catalytic kinetic of Fe 3 O 4 @C follows Michaelis–Menten behaviors and shows stronger affinity to peroxidase substrates than horseradish peroxidase. On the basis of these findings, a simple colorimetric method for glucose detection was developed by combining the catalytic reactions of Fe 3 O 4 @C and glucose oxidase. Additionally, the proposed method was successfully applied to determine the levels of glucose in serum and urine samples and showed a satisfactory result. [ABSTRACT FROM AUTHOR]

In this study, a deep learning model based on quantum chemistry is introduced to enhance the accuracy and efficiency of predicting DNA reaction parameters. By integrating quantum chemical calculations with self-designed descriptor matrices, the model offers a comprehensive description of energy variations and considers a broad range of relevant factors. To overcome the challenge of limited labeled data, an active learning method is employed. The results demonstrate that this model outperforms existing methods in predicting DNA hybridization free energies and strand displacement rate constants, thus advancing the understanding of DNA molecular interactions, and aiding in the precise design and optimization of DNA-based systems., (© 2024 The Author(s). Advanced Science published by Wiley‐VCH GmbH.)

DNA computing harnesses the immense potential of DNA molecules to enable sophisticated and transformative computational processes but is hindered by low computing speed. Here, we propose freeze-thaw cycling as a simple yet powerful method for high-speed DNA computing without complex procedures. Through iterative cycles, we achieve a substantial 20-fold speed enhancement in basic strand displacement reactions. This acceleration arises from the utilization of eutectic ice phase as a medium, temporarily increasing the effective local concentration of molecules during each cycle. In addition, the acceleration effect follows the Hofmeister series, where kosmotropic anions such as sulfate (SO 4 2- ) reduce eutectic phase volume, leading to a more notable enhancement in strand displacement reaction rates. Leveraging this phenomenon, freeze-thaw cycling demonstrates its generalizability for high-speed DNA computing across various circuit sizes, achieving up to a remarkable 120-fold enhancement in reaction rates. We envision its potential to revolutionize molecular computing and expand computational applications in diverse fields.