The research field entitled structural DNA nanotechnology emerged in the beginning of the 1980s as the first immobile synthetic nucleic acid junctions were postulated and demonstrated. Since then, ...the field has taken huge leaps toward advanced applications, especially during the past decade. This Progress Report summarizes how the controllable, custom, and accurate nanostructures have recently evolved together with powerful design and simulation software. Simultaneously they have provided a significant expansion of the shape space of the nanostructures. Today, researchers can select the most suitable fabrication methods, and design paradigms and software from a variety of options when creating unique DNA nanoobjects and shapes for a plethora of implementations in materials science, optics, plasmonics, molecular patterning, and nanomedicine.
DNA nanotechnology flourishes. Here, the recent progress of structural DNA nanotechnology is reviewed by presenting versatile design strategies and computer‐aided software for design and simulation of nanoshapes. Evolution in the field is projected to lead to the development of novel biomaterials and advanced applications.
DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, ...DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.
Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms. However, their use as delivery vehicles in ...therapeutics is compromised by their low stability and poor transfection rates. This study shows that DNA origami can be coated by precisely defined one‐to‐one protein‐dendron conjugates to tackle the aforementioned issues. The dendron part of the conjugate serves as a cationic binding domain that attaches to the negatively charged DNA origami surface via electrostatic interactions. The protein is attached to dendron through cysteine‐maleimide bond, making the modular approach highly versatile. This work demonstrates the coating using two different proteins: bovine serum albumin (BSA) and class II hydrophobin (HFBI). The results reveal that BSA‐coating significantly improves the origami stability against endonucleases (DNase I) and enhances the transfection into human embryonic kidney (HEK293) cells. Importantly, it is observed that BSA‐coating attenuates the activation of immune response in mouse primary splenocytes. Serum albumin is the most abundant protein in the blood with a long circulation half‐life and has already found clinically approved applications in drug delivery. It is therefore envisioned that the proposed system can open up further opportunities to tune the properties of DNA nanostructures in biological environment, and enable their use in various delivery applications.
DNA origami nanostructures can be coated with well‐defined protein–dendron conjugates. Plain DNA origami nanostructures often suffer from poor delivery properties, stability, and immunogenicity in biological systems. Coating of the origami with inert proteins (e.g., serum albumin) can, however, alleviate these issues efficiently.
Structural DNA nanotechnology has recently gained significant momentum, as diverse design tools for producing custom DNA shapes have become more and more accessible to numerous laboratories ...worldwide. Most commonly, researchers are employing a scaffolded DNA origami technique by "sculpting" a desired shape from a given lattice composed of packed adjacent DNA helices. Albeit relatively straightforward to implement, this approach contains its own apparent restrictions. First, the designs are limited to certain lattice types. Second, the long scaffold strand that runs through the entire structure has to be manually routed. Third, the technique does not support trouble-free fabrication of hollow single-layer structures that may have more favorable features and properties compared to objects with closely packed helices, especially in biological research such as drug delivery. In this focused review, we discuss the recent development of wireframe DNA nanostructures-methods relying on meshing and rendering DNA-that may overcome these obstacles. In addition, we describe each available technique and the possible shapes that can be generated. Overall, the remarkable evolution in wireframe DNA structure design methods has not only induced an increase in their complexity and thus expanded the prevalent shape space, but also already reached a state at which the whole design process of a chosen shape can be carried out automatically. We believe that by combining cost-effective biotechnological mass production of DNA strands with top-down processes that decrease human input in the design procedure to minimum, this progress will lead us to a new era of DNA nanotechnology with potential applications coming increasingly into view.
DNA-Based Enzyme Reactors and Systems Linko, Veikko; Nummelin, Sami; Aarnos, Laura ...
Nanomaterials,
07/2016, Volume:
6, Issue:
8
Journal Article, Book Review
Peer reviewed
Open access
During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be ...exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications.
The self-assembly of the dendritic dipeptides (4-3,4-3,5)nG2-CH₂-Boc-L-Tyr-L-Ala-OMe and their achiral dendritic alcohol (4-3,4-3,5)nG2-CH₂OH precursors, both with n = 1-16, where n represents the ...number of methylenic units in the alkyl groups of the dendron, are reported. All chiral dendritic dipeptides and achiral dendritic alcohols self-assemble into helical porous columns that are stable in both solution and solid state. The pore diameter ($D_{pore}$) of the columns self-assembled from dendritic dipeptides is ≈10 Å larger than that of structures assembled from dendritic alcohols. The increase of the $D_{pore}$ at the transition from dendritic alcohol to dendritic dipeptide is accompanied by a decreased solid angle of the building block. This trend is in agreement with previous pore size-solid angle dependences observed with different protective groups of the dipeptide and primary structures of the dendron. However, within the series of dendritic alcohols and dendritic dipeptides with various n, the $D_{pore}$ increases when the solid angle increases. The results of these investigations together with those of previous studies on the role of dipeptide stereochemistry and protective groups on this self-assembly process provide the molecular principles required to program the construction of supramolecular helical pores with diameter controlled at the Å level from a single dendritic dipeptide architecture. These principles are expected to be valid for libraries of dendritic dipeptides based on dendrons and dipeptides with various primary structures.
The synthesis of dendritic dipeptides (4-3,4-3,5-4)12G2-CH2-Boc-l-Tyr-l-Ala-OMe and (4-3, 4-3,5-4)12G2-CH2-Boc-d-Tyr-d-Ala-OMe is described. These dendritic dipeptides self-assemble into porous ...elliptical and circular columns that in turn self-organize into centered rectangular columnar and hexagonal columnar periodic arrays. The transition from porous elliptical to porous circular columns is mediated in a reversible or irreversible way by the thermal history of the sample. A method to determine the dimensions of hollow elliptical and circular columns by the reconstruction of the small-angle powder X-ray diffractograms of the centered rectangular or hexagonal columnar lattices was elaborated. This technique together with wide-angle X-ray experiments performed on aligned fibers provided access to the structural and retrostructural analysis of elliptical supramolecular pores. This procedure is general and can be adapted for the determination of the dimensions of pores of any columnar shape.
General, efficient and inexpensive methods for the synthesis of dendritic building blocks methyl 3′,4′‐dihydroxybiphenyl‐4‐carboxylate, 3′,5′‐dihydroxybiphenyl‐4‐carboxylate, and methyl ...3′,4′,5′‐trihydroxybiphenyl‐4‐carboxylate were elaborated. In all syntheses the major step involved an inexpensive NiII‐catalyzed Suzuki cross‐coupling reaction. These three building blocks were employed together with methyl 4′‐hydroxybiphenyl‐4‐carboxylate in a convergent iterative strategy to synthesize seven libraries containing up to three generations of 3′,4′‐, 3′,5′‐, and 3′,4′,5′‐substituted biphenyl‐4‐methyl ether based amphiphilic dendrons. These dendrons self‐assemble into supramolecular dendrimers that self‐organize into periodic assemblies. Structural and retrostructural analysis of their assemblies demonstrated that these dendrons self‐assemble into hollow and non‐hollow supramolecular dendrimers exhibiting dimensions of up to twice those reported for architecturally related dendrons based on benzyl ether repeat units. These new dendrons expand the structural diversity and demonstrate the generality of the concept of self‐assembling dendrons based on amphiphilic arylmethyl ethers.
Self‐assembling amphiphilic dendrons generated from combinations of AB, constitutional isomeric AB2, and AB3 biphenyl‐4‐methyl ether building blocks (see scheme) were used to explore and expand the structural diversity of non‐hollow and hollow supramolecular dendrimers, and to demonstrate the generality of the concept of self‐assembling dendrons based on amphiphilic arylmethyl ethers.
In the title compound, C17H18O5, the dihedral angle between the benzene rings is 31.23 (16)°. In the crystal, the molecules are packed in an antiparallel fashion in layers along the a axis. In each ...layer, very weak C-H...O hydrogen bonds occur between the methoxy and methyl ester groups. Weak C-H...π interactions between the 4′- and 5′-methoxy groups and neighbouring benzene rings methoxy-C-ring centroid distances = 4.075 and 3.486 Å, respectively connect the layers.
In 2,2'-bipyridin-1-ium 1,1,3,3-tetra-cyano-2-eth-oxy-prop-2-en-1-ide, C10H9N2 (+)·C9H5N4O(-), (I), the ethyl group in the anion is disordered over two sets of atomic sites with occupancies 0.634 (9) ...and 0.366 (9), and the dihedral angle between the ring planes in the cation is 2.11 (7)°. The two independent C(CN)2 groups in the anion make dihedral angles of 10.60 (6) and 12.44 (4)° with the central propenide unit, and the bond distances in the anion provide evidence for extensive electronic delocalization. In bis-(2,2'-bipyridin-1-ium) 1,1,3,3-tetra-cyano-2-(di-cyano-methyl-ene)propane-1,3-diide alternative name bis-(2,2'-bipyridin-1-ium) tris-(di-cyano-methyl-ene)methane-diide, 2C10H9N2 (+)·C10N6 (2-) (II), the dihedral angles between the ring planes in the two independent cations are 7.7 (2) and 10.92 (17)°. The anion exhibits approximate C 3 symmetry, consistent with extensive electronic delocalization, and the three independent C(CN)2 groups make dihedral angles of 23.8 (2), 27.0 (3) and 27.4 (2)° with the central plane. The ions in (I) are linked by an N-H⋯N hydrogen bond and the resulting ion pairs are linked by two independent C-H⋯N hydrogen bonds, forming a ribbon containing alternating R 4 (4)(18) and R 4 (4)(26) rings, where both ring types are centrosymmetric. The ions in (II) are linked by two independent N-H⋯N hydrogen bonds and the resulting ion triplets are linked by a C-H⋯N hydrogen bond, forming a C 2 (1)(7) chain containing anions and only one type of cation, with the other cation linked to the chain by a further C-H⋯N hydrogen bond.
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