Molecular logic gates play an important role in many fields and DNA-based logic gates are the basis of DNA computers. A dynamically NAND gate system on the DNA origami template is established in this paper. Naturally, the system is stable in solution without any reaction. Different logical values are mapped into different DNA input strands. When logical values are entered into the system, the corresponding DNA input strands undergo a directed hybridization chain reaction (HCR) at corresponding positions on the DNA origami template. The operation results are identified by disassembly between the nanogold particles (AuNPs) and DNA origami template. The nanogold particles remain on the DNA origami template, indicating that the result is true; The nanogold particles are dynamically separated from the DNA origami template, indicating that the result is false. The simulation of the system through Visual DSD shows that the reaction strictly followed the designed direction, and no error products are generated during the reaction. These simulation results show that the system has the advantages of feasibility, stability and intelligence.
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http://dx.doi.org/10.1016/j.compbiomed.2019.04.026 | DOI Listing |
ACS Appl Nano Mater
June 2024
Department of Chemistry, College of Arts and Sciences, Case Western Reserve University, Cleveland, Ohio 44106, United States.
DNA nanotechnology has made initial progress toward developing gene-encoded DNA origami nanoparticles (NPs) that display potential utility for future gene therapy applications. However, due to the challenges involved with gene delivery into cells including transport through the membrane, intracellular targeting, and inherent expression of nucleases along with interference from other active proteins, it can be difficult to more directly study the effect of DNA NP design on subsequent gene expression. In this work, we demonstrate an approach for studying the expression of gene-encoding DNA origami NPs without the use of cells.
View Article and Find Full Text PDFACS Appl Bio Mater
January 2025
Department of Biomedical Engineering, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada.
Synthetic ssDNA oligonucleotides hold great potential for various applications, including DNA aptamers, DNA digital data storage, DNA origami, and synthetic genomes. In these contexts, precise control over the synthesis of the ssDNA strands is essential for generating combinatorial sequences with user-defined parameters. Desired features for creating synthetic DNA oligonucleotides include easy manipulation of DNA strands, effective detection of unique DNA sequences, and a straightforward mechanism for strand elongation and termination.
View Article and Find Full Text PDFSmall Methods
January 2025
Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated system has displayed promise in visualizing the dynamics of target loci in living cells, which is important for studying genome regulation. However, developing a cell-friendly and rapid transfection method for achieving dynamic and long-term genomic imaging in living cells with high specificity and accuracy is still challenging. Herein, a robust and versatile method is presented that employs a barrel-shaped DNA nanostructure (TUBE) modified with aptamers for loading, protecting, and delivering CRISPR-Cas9 to visualize specific genomic loci in living cells.
View Article and Find Full Text PDFACS Nano
January 2025
State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
Higher-order DNA nanomaterials have emerged as programmable tools for probing biological processes, constructing metamaterials, and manipulating mechanically active nanodevices with the multifunctionality and high-performance attributes. However, their utility is limited by intricate mixtures formed during hierarchical multistage assembly, as standard techniques like gel electrophoresis lack the resolution and applicability needed for precise characterization and enrichment. Thus, it is urgent to develop a sorter that provides high separation resolution, broad scope, and bioactive functionality.
View Article and Find Full Text PDFNat Biotechnol
January 2025
Institute for Intelligent Biotechnologies (iBIO), Helmholtz Center Munich, Neuherberg, Germany.
Efficient and accurate nanocarrier development for targeted drug delivery is hindered by a lack of methods to analyze its cell-level biodistribution across whole organisms. Here we present Single Cell Precision Nanocarrier Identification (SCP-Nano), an integrated experimental and deep learning pipeline to comprehensively quantify the targeting of nanocarriers throughout the whole mouse body at single-cell resolution. SCP-Nano reveals the tissue distribution patterns of lipid nanoparticles (LNPs) after different injection routes at doses as low as 0.
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