Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist

Silver(I)-Mediated 2D DNA Nanostructures

Structural DNA nanotechnology enables the self-organization of matter at the nanometer scale, but approaches to expand the inorganic and electrical functionality of these scaffolds remain limited. Developments in nucleic acid metallics have enabled the incorporation of site-specific metal ions in DNA duplexes and provide a means of functionalizing the double helix with atomistic precision. Here a class of 2D DNA nanostructures that incorporate the cytosine-Ag+-cytosine (dC:Ag+:dC) base pair as a chemical trigger for self-assembly is described. It is demonstrated that Ag+-functionalized DNA can undergo programmable assembly into large arrays and rings, and can be further coassembled with guanine tetraplexes (G4). It is shown that 2D DNA lattices can be assembled with a variety of embedded nanowires at tunable spacing. These results serve as a foundation for further development of self-assembled, metalated DNA nanostructures, with potential for high-precision DNA nanoelectronics with nanometer pitch.

Circular RNA oligonucleotides: enzymatic synthesis and scaffolding for nanoconstruction

We report the efficient synthesis of monomeric circular RNAs (circRNAs) in the size range of 16-44 nt with a novel DNA dumbbell splinting plus T4 DNA ligation strategy. Such a DNA dumbbell splinting strategy was developed by one group among ours recently for near-quantitative conversion of short linear DNAs into monomeric circular ones. Furthermore, using the 44 nt circRNA as scaffold strands, we constructed hybrid RNA:DNA and pure RNA:RNA double crossover tiles and their assemblies of nucleic acid nanotubes and flat arrays.

Adoption of a Tetrahedral DNA Nanostructure as a Multifunctional Biomaterial for Drug Delivery

DNA nanostructures have been widely researched in recent years as emerging biomedical materials for drug delivery, biosensing, and cancer therapy, in addition to their hereditary function. Multiple precisely designed single-strand DNAs can be fabricated into complex, three-dimensional DNA nanostructures through a simple self-assembly process. Among all of the synthetic DNA nanostructures, tetrahedral DNA nanostructures (TDNs) stand out as the most promising biomedical nanomaterial. TDNs possess the merits of structural stability, cell membrane permeability, and natural biocompatibility due to their compact structures and DNA origin. In addition to their inherent advantages, TDNs were shown to have great potential in delivering therapeutic agents through multiple functional modifications. As a multifunctional material, TDNs have enabled innovative pharmaceutical applications, including antimicrobial therapy, anticancer treatment, immune modulation, and cartilage regeneration. Given the rapid development of TDNs in the biomedical field, it is critical to understand how to successfully produce and fine-tune the properties of TDNs for specific therapeutic needs and clinical translation. This article provides insights into the synthesis and functionalization of TDNs and summarizes the approaches for TDN-based therapeutics delivery as well as their broad applications in the field of pharmaceutics and nanomedicine, challenges, and future directions.

Diverse Chiral Nanotubes Assembled from Identical DNA Strands

DNA nanotubes with controllable geometries hold a wide range of interdisciplinary applications. When preparing DNA nanotubes of varying widths or distinct chirality, existing methods require repeatedly designing and synthesizing specific DNA sequences, which can be costly and laborious. Here, we proposed an intercalator-assisted DNA tile assembly method which enables the production of DNA nanotubes of diverse widths and chirality using identical DNA strands. Through adjusting the concentration of intercalators during assembly, the twisting direction and extent of DNA tiles could be modulated, leading to the formation of DNA nanotubes featuring controllable widths and chirality. Moreover, through introducing additional intercalators and secondary annealing, right-handed nanotubes could be reconfigured into distinct left-handed nanotubes. We expect that this method could be universally applied to modulating the self-assembly pathways of various DNA tiles and other chiral materials, advancing the landscape of DNA tile assembly.

Three-Point-Star Deoxyribonucleic Acid Tiles with the Core Arm Length at Three Half-Turns for Two-Dimensional Archimedean Tilings and Beyond

2D Archimedean tiling and complex tessellation patterns assembled from soft materials including modular DNA tiles have attracted great interest because of their specific structures and potential applications in nanofabrication, nanoelectronics, nanophotonics, biomedical sensing, drug delivery, therapeutics, etc. Traditional three- and four-point-star DNA tiles with the core arm length at two half-turns (specified as three- and four-point-star-E previously and abbreviated as 3PSE and 4PSE tiles here) have been applied to assemble intricate tessellations through tuning the size of inserted nT (n = 1-7, T is thymine) loops on helper strands at the tile center. Following our recent findings using a new type of four-point-star tiles with the core arm length at three half-turns (specified as four-point-star-O previously and abbreviated as 4PSO tiles here) to assemble DNA tubes and flat 2D arrays, we report here the cross-hybridization weaving architectures at the tile center to construct three new 3PSO tiles with circular DNA oligonucleotides of 96-nt (nucleotides) serving as the scaffolds, further the monotonous and combinatory E- and O-tilings on one type of 3PSO tiles to create 2D Archimedean tiling patterns (6.6.6) and (4.8.8), and finally, the combination of 3PSO with 4PSO as well as 2PSO tiles to tile into complex tessellation patterns. The easy realization of regular and intricate DNA tessellations with 2-4PSO tiles not only richens the fundamental DNA modules and complex DNA nanostructures in types but also broadens the potential application scopes of DNA nanostructures in nanofabrication, DNA computing, biomedicine, etc.

Bimodal DNA self-origami material with nucleic acid function enhancement

BACKGROUND

The design of DNA materials with specific nanostructures for biomedical tissue engineering applications remains a challenge. High-dimensional DNA nanomaterials are difficult to prepare and are unstable; moreover, their synthesis relies on heavy metal ions. Herein, we developed a bimodal DNA self-origami material with good biocompatibility and differing functions using a simple synthesis method. We simulated and characterized this material using a combination of oxDNA, freeze-fracture electron microscopy, and atomic force microscopy. Subsequently, we optimized the synthesis procedure to fix the morphology of this material.

RESULTS

Using molecular dynamics simulation, we found that the bimodal DNA self-origami material exhibited properties of spontaneous stretching and curling and could be fixed in a single morphology via synthesis control. The application of different functional nucleic acids enabled the achievement of various biological functions, and the performance of functional nucleic acids was significantly enhanced in the material. Consequently, leveraging the various functional nucleic acids enhanced by this material will facilitate the attainment of diverse biological functions.

CONCLUSION

The developed design can comprehensively reveal the morphology and dynamics of DNA materials. We thus report a novel strategy for the construction of high-dimensional DNA materials and the application of functional nucleic acid-enhancing materials.

Structural Description of Chiral E-Tiling DNA Nanotubes with the Chiral Indices (n,m) and Handedness Defined by Microscopic Imaging

In structural DNA nanotechnology, E-tiling DNA nanotubes are evidenced to be homogeneous in diameter and thus have great potential in biomedical applications such as cellular transport and communication, transmembrane ion/molecule channeling, and drug delivery. However, a precise structural description of chiral DNA nanotubes with chiral parameters was lacking, thus greatly hindering their application breadth and depth, until we recently raised and partly solved this problem. In this perspective, we summarize recent progress in defining the chiral indices and handedness of E-tiling DNA nanotubes by microscopic imaging, especially atomic force microscopy (AFM) imaging. Such a detailed understanding of the chiral structures of E-tiling DNA nanotubes will be very helpful in the future, on the one hand for engineering DNA nanostructures precisely, and, on the other, for realizing specific physicochemical properties and biological functions successfully.

Construction of DNA Bilayer Tiles and Arrays Using Circular DNA Molecules as Scaffolds

Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi-arm junction (mAJ) tiles and arrays is well-known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E-tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface-mediated assembly.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Tuning the Roundabout of Four-Point-Star Tiles with the Core Arm Length of Three Half-Turns for 2D DNA Arrays

By rationally adjusting the weaving modes of point-star tiles, the curvature inherent in the tiles can be changed, and various DNA nanostructures can be assembled, such as planar wireframe meshes, perforated wireframe tubes, and curved wireframe polyhedra. Based on the weaving and tiling architectures for traditional point-star tiles with the core arm length at two DNA half-turns, we improved the weaving modes of our newly reported four-point-star tiles with the core arm length at three half-turns to adjust their curvature and rigidity for assembling 2D arrays of DNA grids and tubes. Following our previous terms and methods to analyze the structural details of E-tiling tubes, we used the chiral indices (n,m) to describe the most abundant tube of typical assemblies; especially, we applied both one-locus and/or dual-locus biotin/streptavidin (SA) labelling strategies to define the configurations of two specific tubes, along with the absolute conformations of their component tiles. Such structural details of the DNA tubes composed of tiles with addressable concave and convex faces and packing directions should help us understand their physio-chemical and biological properties, and therefore promote their applications in drug delivery, biocatalysis, biomedicine, etc.

Highly Symmetric, Self-Assembling 3D DNA Crystals with Cubic and Trigonal Lattices

The rational design of nanoscopic DNA tiles has yielded highly ordered crystalline matter in 2D and 3D. The most well-studied 3D tile is the DNA tensegrity triangle, which is known to self-assemble into macroscopic crystals. However, contemporary rational design parameters for 3D DNA crystals nearly universally invoke integer numbers of DNA helical turns and Watson-Crick (WC) base pairs. In this study, 24-bp edges are substituted into a previously 21-bp (two helical turns of DNA) tensegrity triangle motif to explore whether such unconventional motif can self-assemble into 3D crystals. The use of noncanonical base pairs in the sticky ends results in a cubic arrangement of tensegrity triangles with exceedingly high symmetry, assembling a lattice from winding helical axes and diamond-like tessellation patterns. Reverting this motif to sticky ends with Watson-Crick pairs results in a trigonal hexagonal arrangement, replicating this diamond arrangement in a hexagonal context. These results showcase that the authors can generate unexpected, highly complex, pathways for materials design by testing modifications to 3D tiles without prior knowledge of the ensuing symmetry. This study expands the rational design toolbox for DNA nanotechnology; and it further illustrates the existence of yet-unexplored arrangements of crystalline soft matter.

Chiral DNA Nanotubes Self-Assembled from Building Blocks with Tailorable Curvature and Twist

DNA nanotubes with prescribed geometry could allow for nanomaterial organization with designed optical or electrical function. As one of the dominating driving forces for DNA nanotube assembly, intrinsic curvature and twist of building blocks can be induced by bending deformation and twisting deformation. However, it is still unknown that how bending and twisting design on nanoscale building blocks affects the geometry of DNA tubes with micrometer length. Here, through targeted base pair deletion or insertion, the amount of bending deformation in building blocks is modulated by length gradient and the amount of twisting deformation is modulated by average twist density. This work systematically explores the independent effect and synergistic effect of two types of deformation on tube geometry, including diameter, chirality, and helical angles, via a streptavidin-labeling technique. The design rules enable the construction of DNA nanotubes with prescribed chirality and tailored diameters.