We demonstrate a strategy to trigger and finely control the assembly of supramolecular DNA nanostructures with pH. Control is achieved via a rationally designed strand displacement circuit that responds to pH and activates a downstream DNA tile self-assembly process. We observe that the DNA structures form under neutral/basic conditions, while the self-assembly process is suppressed under acidic conditions. The strategy presented here demonstrates a modular approach toward building systems capable of processing biochemical inputs and finely controlling the assembly of DNA-based nanostructures under isothermal conditions. In particular, the presented architecture is relevant for the development of complex DNA devices able to sense and respond to molecular markers associated with abnormal metabolism.
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http://dx.doi.org/10.1021/jacs.6b07676 | DOI Listing |
Int J Biol Macromol
December 2024
Institute for Complex Systems, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy; Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy. Electronic address:
Polyelectrolyte complexes (PECs), formed via the self-assembly of oppositely charged polysaccharides, are highly valued for their biocompatibility, biodegradability, and hydrophilicity, offering significant potential for biotechnological applications. However, the complex nature and lack of insight at a molecular level into polyelectrolytes conformation and aggregation often hinders the possibility of achieving an optimal control of PEC systems, limiting their practical applications. To address this problem, an in-depth investigation of PECs microscopic structural organization is required.
View Article and Find Full Text PDFJ Struct Biol
December 2024
Instituto Andaluz de Ciencias de la Tierra (IACT-CSIC), Armilla 18100, Granada, Spain. Electronic address:
The nacre formation process is a fascinating phenomenon involving mineral phase transformations, self-assembly processes, and protein-mineral interactions, resulting in a hierarchical structure that exhibits outstanding mechanical properties. However, this process is only partially known, and many aspects of nacre structure are not well understood, especially at the molecular scale. To understand the interplay between components-aragonite, protein and chitin-of the structure of nacre observed experimentally, we investigate the interactions of a peptide that is part of the protein lustrin A, identified in the nacreous layer of the shell of the abalone Haliotis rufescens, with the (001) crystal surface of aragonite and the chitin molecule.
View Article and Find Full Text PDFFood Chem
December 2024
College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China. Electronic address:
Amyloid fibrils (AFs) are highly ordered nanostructures formed through the self-assembly of proteins under specific conditions. Due to their unique properties, AFs have garnered significant attention as biomaterials over the past decade. Nevertheless, the increasing reliance on animal proteins for AFs production raises sustainability concerns, highlighting the need for a transition to plant-based proteins as more environmentally friendly feedstocks.
View Article and Find Full Text PDFACS Nano
December 2024
Faculty of Materials Science, Shenzhen MSU-BIT University, Shenzhen 518100, P. R. China.
Protein hydrolysis targeted chimeras (PROTACs) represent a different therapeutic approach, particularly relevant for overcoming challenges associated with traditional small molecule inhibitors. These challenges include targeting difficult proteins that are often deemed "undruggable" and addressing issues of acquired resistance. PROTACs employ the body's own E3 ubiquitin ligases to induce the degradation of specific proteins of interest (POIs) through the ubiquitin-proteasome pathway.
View Article and Find Full Text PDFJ Phys Chem A
December 2024
State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering, Chinese Academy of Science s, Beijing 100190, China.
To understand the mechanism of self-assembly and to predict the evolutionary pattern of the fusion-fission system over a long period of time, studying the dynamics of these processes is of great significance. The trajectories from molecular dynamics (MD) simulations of self-assembly processes contain numerous latent fusion and fission events. To analyze the fusion and fission events from the simulated trajectory, in this article, a dynamic clustering approach was developed by comparing the changes of monomer composition within clusters over simulated time.
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