DNA-origami-directed virus capsid polymorphism

DNA-Origami-Based Precise Molecule Assembly and Their Biological Applications

Inspired by efficient natural biomolecule assembly with precise control on key parameters such as distance, number, orientation, and pattern, the constructions and applications of artificial precise molecule assembly are highly important in many research areas including chemistry, biology, and medicine. DNA origami, a sophisticated DNA nanotechnology with rational design, can offer a predictable, programmable, and addressable nanoscale scaffold for the precise assembly of various kinds of molecules. Herein, we summarize recent progress, particularly in the last three years, in DNA-origami-based precise molecule assembly and their emerging biological applications. We first introduce DNA origami and the progress on DNA-origami-based precise molecule assembly, including assembly of various kinds of molecules (e.g., nucleic acids, proteins, organic molecules, nanoparticles), and precise control of important parameters (e.g., distance, number, orientation, pattern). Their biological applications in sensing, imaging, therapy, bionics, biophysics, and chemical biology are then summarized, and current challenges and opportunities are finally discussed.

Bottom-up synthetic immunology

Infectious diseases and cancer evade immune surveillance using similar mechanisms. Targeting immune mechanisms using common strategies thus represents a promising avenue to improve prevention and treatment. Synthetic immunology can provide such strategies by applying engineering principles from synthetic biology to immunology. Synthetic biologists engineer cells by top-down genetic manipulation or bottom-up assembly from nanoscale building blocks. Recent successes in treating advanced tumours and diseases using genetically engineered immune cells highlight the power of the top-down synthetic immunology approach. However, genetic immune engineering is mostly limited to ex vivo applications and is subject to complex counter-regulation inherent to immune functions. Bottom-up synthetic biology can harness the rich nanotechnology toolbox to engineer molecular and cellular systems from scratch and equip them with desired functions. These are beginning to be tailored to perform targeted immune functions and should hence allow intervention strategies by rational design. In this Perspective we conceptualize bottom-up synthetic immunology as a new frontier field that uses nanotechnology for crucial innovations in therapy and the prevention of infectious diseases and cancer.

Structural stability of DNA origami nanostructures in organic solvents

DNA origami nanostructures have attracted significant attention as an innovative tool in a variety of research areas, spanning from nanophotonics to bottom-up nanofabrication. However, the use of DNA origami is often restricted by their rather limited structural stability in application-specific conditions. The structural integrity of DNA origami is known to be superstructure-dependent, and the integrity is influenced by various external factors, for example cation concentration, temperature, and presence of nucleases. Given the necessity to functionalize DNA origami also with non-water-soluble entities, it is important to acquire knowledge of the structural stability of DNA origami in various organic solvents. Therefore, we herein systematically investigate the post-folding DNA origami stability in a variety of polar, water-miscible solvents, including acetone, ethanol, DMF, and DMSO. Our results suggest that the structural integrity of DNA origami in organic solvents is both superstructure-dependent and dependent on the properties of the organic solvent. In addition, DNA origami are generally more resistant to added organic solvents in folding buffer compared to that in deionized water. DNA origami stability can be maintained in up to 25-40% DMF or DMSO and up to 70-90% acetone or ethanol, with the highest overall stability observed in acetone. By rationally selecting both the DNA origami design and the solvent, the DNA origami stability can be maintained in high concentrations of organic solvents, which paves the way for more extensive use of non-water-soluble compounds for DNA origami functionalization and complexation.

Magnetically Induced Thermal Effects on Tobacco Mosaic Virus-Based Nanocomposites for a Programmed Disassembly of Protein Cages

Protein cages are promising tools for the controlled delivery of therapeutics and imaging agents when endowed with programmable disassembly strategies. Here, we produced hybrid nanocomposites made of tobacco mosaic virus (TMV) and magnetic iron oxide nanoparticles (IONPs), designed to disrupt the viral protein cages using magnetically induced release of heat. We studied the effects of this magnetic hyperthermia on the programmable viral protein capsid disassembly using (1) elongated nanocomposites of TMV coated heterogeneously with magnetic iron oxide nanoparticles (TMV@IONPs) and (2) spherical nanocomposites of polystyrene (PS) on which we deposited presynthesized IONPs and TMV via layer-by-layer self-assembly (PS@IONPs/TMV). Notably, we found that the extent of the disassembly of the protein cages is contingent upon the specific absorption rate (SAR) of the magnetic nanoparticles, that is, the heating efficiency, and the relative position of the protein cage within the nanocomposite concerning the heating sources. This implies that the spatial arrangement of components within the hybrid nanostructure has a significant impact on the disassembly process. Understanding and optimizing this relationship will contribute to the critical spatiotemporal control for targeted drug and gene delivery using protein cages.

DNA Framework-Guided Self-Limiting Aggregation for Highly Luminescent Metal Cluster Nanoaggregates

The photoluminescent properties of atomically precise metal nanoclusters (MCs) have garnered significant attention in the fields of chemical sensing and biological imaging. However, the limited brightness of single-component nanoclusters hinders their practical applications, and the conventional ligand engineering approaches have proven insufficient in enhancing the emission efficiency of MCs. Here, we present a DNA framework-guided strategy to prepare highly luminescent metal cluster nanoaggregates. Our approach involves an amphiphilic DNA framework comprising a hydrophobic alkyl core and a rigid DNA framework shell, serving as a nucleation site and providing well-defined nanoconfinements for the self-limiting aggregation of MCs. Through this method, we successfully produced homogeneous MC nanoaggregates (10.1 ± 1.2 nm) with remarkable nanoscale precision. Notably, this strategy proves adaptable to various MCs, leading to a substantial enhancement in emission and quantum yield, up to 3011- and 87-fold, respectively. Furthermore, our investigation using total internal reflection fluorescence microscopy at the single-particle level uncovered a more uniform photon number distribution and higher photostability for MC nanoaggregates compared to template-free counterparts. This DNA-templating strategy introduces a conceptually innovative approach for studying the photoluminescent properties of aggregates with nanoscale precision and holds promise for constructing highly luminescent MC nanoparticles for diverse applications.

DNA-based nanostructures for RNA delivery

RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases, including cancer, genetic disorders, and infectious diseases. However, the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake. To overcome these hurdles, DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics. Due to its excellent characteristics such as programmability and biocompatibility, these DNA-based nanostructures, composed of DNA molecules assembled into precise and programmable structures, have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations. In this review, we highlight the current progress in the design and application of three DNA-based nanostructures: DNA origami, lipid-nanoparticle (LNP) technology related to frame guided assembly (FGA), and DNA hydrogel for the delivery of RNA molecules. Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.

Harnessing DNA origami's therapeutic potential for revolutionizing cardiovascular disease treatment: A comprehensive review

DNA origami is a cutting-edge nanotechnology approach that creates precise and detailed 2D and 3D nanostructures. The crucial feature of DNA origami is how it is created, which enables precise control over its size and shape. Biocompatibility, targetability, programmability, and stability are further advantages that make it a potentially beneficial technique for a variety of applications. The preclinical studies of sophisticated programmable nanomedicines and nanodevices that can precisely respond to particular disease-associated triggers and microenvironments have been made possible by recent developments in DNA origami. These stimuli, which are endogenous to the targeted disorders, include protein upregulation, pH, redox status, and small chemicals. Oncology has traditionally been the focus of the majority of past and current research on this subject. Therefore, in this comprehensive review, we delve into the intricate world of DNA origami, exploring its defining features and capabilities. This review covers the fundamental characteristics of DNA origami, targeting DNA origami to cells, cellular uptake, and subcellular localization. Throughout the review, we emphasised on elucidating the imperative for such a therapeutic platform, especially in addressing the complexities of cardiovascular disease (CVD). Moreover, we explore the vast potential inherent in DNA origami technology, envisioning its promising role in the realm of CVD treatment and beyond.

Transformation of a Viral Capsid from Nanocages to Nanotubes and Then to Hydrogels: Redirected Self-Assembly and Effects on Immunogenicity

The ability to manipulate the self-assembly of proteins is essential to understanding the mechanisms of life and beneficial to fabricating advanced nanomaterials. Here, we report the transformation of the MS2 phage capsid from nanocages to nanotubes and then to nanotube hydrogels through simple point mutations guided by interfacial interaction redesign. We demonstrate that site 70, which lies in the flexible FG loop of the capsid protein (CP), is a "magic" site that can largely dictate the final morphology of assemblies. By varying the amino acid at site 70, with the aid of a cysteine-to-alanine mutation at site 46, we achieved the assembly of double-helical or single-helical nanotubes in addition to nanocages. Furthermore, an additional cysteine substitution on the surface of nanotubes mediated their cross-linking to form hydrogels with reducing agent responsiveness. The hierarchical self-assembly system allowed for the investigation of morphology-related immunogenicity of MS2 CPs, which revealed dramatic differences among nanocages, nanotubes, and nanotube hydrogels in terms of immune response types, antibody levels and T cell functions. This study provides insights into the assembly manipulation of protein nanomaterials and the customized design of nanovaccines and drug delivery systems.

Dominant Analytical Techniques in DNA Nanotechnology for Various Applications

DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.

From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y

The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.

Assembly and optically triggered disassembly of lipid-DNA origami fibers

The co-assembly of lipids and other compounds has recently gained increasing interest. Here, we report the formation of stimuli-responsive lipid-DNA origami fibers through the electrostatic co-assembly of cationic lipids and 6-helix bundle (6HB) DNA origami. The photosensitive lipid degrades when exposed to UV-A light, which allows a photoinduced, controlled release of the 6HBs from the fibers. The presented complexation strategy may find uses in developing responsive nanomaterials e.g. for therapeutics.

Recent Advances in DNA Nanomaterials

Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.