Functionalizing DNA nanostructures with natural cationic amino acids

A Microfluidic Chip-Based Automated System for Whole-Course Monitoring the Drug Responses of Organoids

Tumor patients-derived organoids, as a promising preclinical prediction model, have been utilized to evaluate ex vivo drug responses for formulating optimal therapeutic strategies. Detecting adenosine triphosphate (ATP) has been widely used in existing organoid-based drug response tests. However, all commercial ATP detection kits containing the cell lysis procedure can only be applied for single time point ATP detection, resulting in the neglect of dynamic ATP variations in living cells. Meanwhile, due to the limited number of viable organoids from a single patient, it is impractical to exhaustively test all potential time points in search of optimal ones. In this work, a multifunctional microfluidic chip was developed to perform all procedures of organoid-based drug response tests, including establishment, culturing, drug treatment, and ATP monitoring of organoids. An ATP sensor was developed to facilitate the first successful attempt on whole-course monitoring the growth status of fragile organoids. To realize a clinically applicable automatic system for the drug testing of lung cancer, a microfluidic chip based automated system was developed to perform entire organoid-based drug response test, bridging the gap between laboratorial manipulation and clinical practices, as it outperformed previous methods by improving data repeatability, eliminating human error/sample loss, and more importantly, providing a more accurate and comprehensive evaluation of drug effects.

DNA-Based Nanostructured Platforms as Drug Delivery Systems

DNA nanotechnology has recently provided a novel approach for developing safe, biocompatible, biodegradable, non-immunogenic, and non-toxic drug delivery systems. DNA nanostructures have numerous advantages for deployment as drug delivery platforms, owing to programmable assembly, ease of production, reproducibility, and precise control over size, shape, and function. DNA nanostructures can dramatically improve the delivery of poorly soluble drugs, decreasing cytotoxicity to normal tissues and improving therapeutic effectiveness. Using different conjugation methods, DNA nanostructures can be precisely integrated with a wide range of functional moieties, including proteins, peptides, aptamers, polymers, lipids, inorganic nanoparticles, and targeting groups, to enhance the nanostructure stability, extend circulation, and specify drug delivery. Smart DNA nanostructures with targeting ligands or a stimuli-responsive moiety specify therapeutic delivery to target, minimize drug loss attributable to prior drug release or off-target distribution, improve target accumulation, promote cellular internalization, bypass efflux pumps, and avoid adverse effects. Target-specific delivery by smart DNA nanostructures, in turn, maximizes drug concentration, reaching the target locations at a faster rate and preventing therapeutic failure while also lowering the dose needed for therapeutic effect. This Review provides an overview of DNA nanostructures for drug encapsulation and selective delivery to the desired sites. DNA nanostructures are a novel platform for drug delivery with improved performance that may be used to treat a variety of diseases.

Size-Controlled DNA Tile Self-Assembly Nanostructures Through Caveolae-Mediated Endocytosis for Signal-Amplified Imaging of MicroRNAs in Living Cells

Signal-amplified imaging of microRNAs (miRNAs) is a promising strategy at the single-cell level because liquid biopsy fails to reflect real-time dynamic miRNA levels. However, the internalization pathways for available conventional vectors predominantly involve endo-lysosomes, showing nonideal cytoplasmic delivery efficiency. In this study, size-controlled 9-tile nanoarrays are designed and constructed by integrating catalytic hairpin assembly (CHA) with DNA tile self-assembly technology to achieve caveolae-mediated endocytosis for the amplified imaging of miRNAs in a complex intracellular environment. Compared with classical CHA, the 9-tile nanoarrays possess high sensitivity and specificity for miRNAs, achieve excellent internalization efficiency by caveolar endocytosis, bypassing lysosomal traps, and exhibit more powerful signal-amplified imaging of intracellular miRNAs. Because of their excellent safety, physiological stability, and highly efficient cytoplasmic delivery, the 9-tile nanoarrays can realize real-time amplified monitoring of miRNAs in various tumor and identical cells of different periods, and imaging effects are consistent with the actual expression levels of miRNAs, ultimately demonstrating their feasibility and capacity. This strategy provides a high-potential delivery pathway for cell imaging and targeted delivery, simultaneously offering a meaningful reference for the application of DNA tile self-assembly technology in relevant fundamental research and medical diagnostics.

Transmembrane capability of DNA origami sheet enhanced by 3D configurational changes

DNA origami-engineered nanostructures are widely used in biomedical applications involving transmembrane delivery. Here, we propose a method to enhance the transmembrane capability of DNA origami sheets by changing their configuration from two-dimensional to three-dimensional. Three DNA nanostructures are designed and constructed, including the two-dimensional rectangular DNA origami sheet, the DNA tube, and the DNA tetrahedron. The latter two are the variants of the DNA origami sheet with three-dimensional morphologies achieved through one-step folding and multi-step parallel folding separately. The design feasibility and structural stability of three DNA nanostructures are confirmed by molecular dynamics simulations. The fluorescence signals of the brain tumor models demonstrate that the tubular and the tetrahedral configurational changes could dramatically increase the penetration efficiency of the original DNA origami sheet by about three and five times, respectively. Our findings provide constructive insights for further rational designs of DNA nanostructures for transmembrane delivery.

Kinetics-accelerated one-step detection of MicroRNA through spatially localized reactions based on DNA tile self-assembly

The localization of isothermal amplification systems has elicited extensive attention due to the enhanced reaction kinetics when detecting ultra-trace small-molecule nucleic acids. Therefore, the seek for an appropriate localization cargo of spatially confined reactions is urgent. Herein, we have developed a novel approach to localize the catalytic hairpin assembly (CHA) system into the DNA tile self-assembly nanostructure. Thanks to the precise programming and robust probe loading capacity, this strategy achieved a 2.3 × 10⁵-fold higher local reaction concentration than a classical CHA system with enhanced reaction kinetics in theory. From the experimental results, this strategy could reach the reaction plateau faster and get access to a magnified effect of 1.57-6.99 times higher in the linear range of microRNA (miRNA) than the simple CHA system. Meanwhile, this strategy satisfied the demand for the one-step detection of miRNA in cell lysates at room temperature with good sensitivity and specificity. These features indicated its excellent potential for ultra-trace molecule detection in clinical diagnosis and provided new insights into the field of bioassays based on DNA tile self-assembly nanotechnology.

Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures

Nucleic acid-based biomolecular self-assembly enables the creation of versatile functional architectures. Electrostatic screening of the negative charges of nucleic acids is essential for their folding and stability; thus, ions play a critical role in nucleic acid self-assembly in both biology and nanotechnology. However, the ion-DNA interplay and the resulting ion-specific structural integrity and responsiveness of DNA constructs are underexploited. Here, we harness a wide range of mono- and divalent ions to control the structural features of DNA origami constructs. Using atomic force microscopy and Förster resonance energy transfer (FRET) spectroscopy down to the single-molecule level, we report on the global and local structural performance and responsiveness of DNA origami constructs following self-assembly, upon post-assembly ion exchange and post-assembly ion-mediated reconfiguration. We determined the conditions for highly efficient DNA origami folding in the presence of several mono- (Li⁺, Na⁺, K⁺, Cs⁺) and divalent (Ca²⁺, Sr²⁺, Ba²⁺) ions, expanding the range where DNA origami structures can be exploited for custom-specific applications. We then manipulated fully folded constructs by exposing them to unfavorable ionic conditions that led to the emergence of substantial disintegrity but not to unfolding. Moreover, we found that poorly assembled nanostructures at low ion concentrations undergo substantial self-repair upon ion addition in the absence of free staple strands. This reconfigurability occurs in an ion type- and concentration-specific manner. Our findings provide a fundamental understanding of the ion-mediated structural responsiveness of DNA origami at the nanoscale enabling applications under a wide range of ionic conditions.

Engineering the Surface Properties of DNA Nanostructures by Tuning the Valency of Assembling Species for Biomedical Applications

Self-assembled DNA nanostructures hold great potentials in biomedical applications. Nevertheless, the negatively charged DNA backbone and susceptivity to enzyme degradation pose challenges to this regard. Engineering the surface properties of DNA nanostructures by assembling DNA with guest molecules in magnesium-free system is promising to solve these issues. In this study, the polyamines-mediated DNA self-assembly with an emphasis on the valency of polyamines is investigated. Both spermine, spermidine, and putrescine can assemble DNA tetrahedron under appropriate concentrations. The cytotoxicity and cellular uptake efficiencies vary with the polyamine valency. Compared with magnesium-assembled DNA tetrahedron, polyamine-assembled DNA tetrahedron exhibits higher cellular uptake efficiency and serum stability. Circular dichroism spectrum results indicate that polyamines induce DNA conformation slightly shifting from B form to A form. The improved performances of polyamine-assembled DNA tetrahedrons under physiological settings are attributed to the surface properties that altered by guest molecules polyamine. The current study suggests that engineering the surface properties of DNA nanostructures by assembling them with guest cationic species is promising to further their biomedical applications.

An mTOR siRNA-Loaded Spermidine/DNA Tetrahedron Nanoplatform with a Synergistic Anti-Inflammatory Effect on Acute Lung Injury

Acute lung injury (ALI) is characterized by severe inflammation and damage to the lung air-blood barrier, resulting in respiratory function damage and life-threatening outcomes. Macrophage polarization plays an essential role in the occurrence, development, and outcome of ALI. As drug carriers, self-assembled DNA nanostructures can potentially overcome the drawbacks and limitations of traditional anti-inflammatory agents owing to their nontoxicity, programmability, and excellent structural control at the nanoscale. A small interfering RNA (siRNA) and drug dual therapy nanoplatform are proposed and constructed here to combat ALI. The nanoplatform consists of a spermidine-assembled DNA tetrahedron and four mammalian target of rapamycin siRNAs. Spermidine serves as a mediator of drug delivery vehicle synthesis and a drug that alters macrophage polarization. Both spermidine and siRNA exert anti-inflammatory effects in vitro and in vivo by regulating the macrophage phenotype. More importantly, these factors exhibit a synergistic anti-inflammatory effect by promoting macrophage autophagy. For the first time, an anti-inflammatory dual therapy strategy that uses self-assembled DNA nanostructures as nontoxic, programmable delivery vehicles is proposed and demonstrated through this work. Future work on utilizing DNA nanostructures for the treatment of noncancerous diseases such as ALI is highly promising and desirable.

Protein-mediated DNA self-assembly by controlling the surface charge in a molecular crowding environment

Designing and building artificial nanodevices and nanoarchitectures in living systems are extremely intriguing subjects in nanotechnology and synthetic biology. Taking advantage of cellular machinery and endogenous biomacromolecules, such as proteins,...