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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]

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.)

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., (© 2021 Wiley-VCH GmbH.)

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., (© 2021 Wiley-VCH GmbH.)