Engineered Protein Copolymers for Heparin Neutralization and Detection

Heparin is a widely applied anticoagulant agent. However, in clinical practice, it is of vital importance to reverse its anticoagulant effect to restore the blood-clotting cascade and circumvent side effects. Inspired by protein cages that can encapsulate and protect their cargo from surroundings, we utilize three designed protein copolymers to sequester heparin into inert nanoparticles. In our design, a silk-like sequence provides cooperativity between proteins, generating a multivalency effect that enhances the heparin-binding ability. Protein copolymers complex heparin into well-defined nanoparticles with diameters below 200 nm. We also develop a competitive fluorescent switch-on assay for heparin detection, with a detection limit of 0.01 IU mL^-1 in plasma that is significantly below the therapeutic range (0.2-8 IU mL^-1). Moreover, moderate cytocompatibility is demonstrated by in vitro cell studies. Therefore, such engineered protein copolymers present a promising alternative for neutralizing and sensing heparin, but further optimization is required for in vivo applications.

Robotic DNA Nanostructures

Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.

Increasing Complexity in Wireframe DNA Nanostructures

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.

High-Generation Amphiphilic Janus-Dendrimers as Stabilizing Agents for Drug Suspensions

Pharmaceutical nanosuspensions are formed when drug crystals are suspended in aqueous media in the presence of stabilizers. This technology offers a convenient way to enhance the dissolution of poorly water-soluble drug compounds. The stabilizers exert their action through electrostatic or steric interactions, however, the molecular requirements of stabilizing agents have not been studied extensively. Here, four structurally related amphiphilic Janus-dendrimers were synthesized and screened to determine the roles of different macromolecular domains on the stabilization of drug crystals. Physical interaction and nanomilling experiments have substantiated that Janus-dendrimers with fourth generation hydrophilic dendrons were superior to third generation analogues and Poloxamer 188 in stabilizing indomethacin suspensions. Contact angle and surface plasmon resonance measurements support the hypothesis that Janus-dendrimers bind to indomethacin surfaces via hydrophobic interactions and that the number of hydrophobic alkyl tails determines the adsorption kinetics of the Janus-dendrimers. The results showed that amphiphilic Janus-dendrimers adsorb onto drug particles and thus can be used to provide steric stabilization against aggregation and recrystallization. The modular synthetic route for new amphiphilic Janus-dendrimers offers, thus, for the first time a versatile platform for stable general-use stabilizing agents of drug suspensions.

Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems

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.

Evolution of Structural DNA Nanotechnology

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 nanostructure-directed assembly of metal nanoparticle superlattices

Structural DNA nanotechnology provides unique, well-controlled, versatile, and highly addressable motifs and templates for assembling materials at the nanoscale. These methods to build from the bottom-up using DNA as a construction material are based on programmable and fully predictable Watson-Crick base pairing. Researchers have adopted these techniques to an increasing extent for creating numerous DNA nanostructures for a variety of uses ranging from nanoelectronics to drug-delivery applications. Recently, an increasing effort has been put into attaching nanoparticles (the size range of 1-20 nm) to the accurate DNA motifs and into creating metallic nanostructures (typically 20-100 nm) using designer DNA nanoshapes as molds or stencils. By combining nanoparticles with the superior addressability of DNA-based scaffolds, it is possible to form well-ordered materials with intriguing and completely new optical, plasmonic, electronic, and magnetic properties. This focused review discusses the DNA structure-directed nanoparticle assemblies covering the wide range of different one-, two-, and three-dimensional systems.

Protein Coating of DNA Nanostructures for Enhanced Stability and Immunocompatibility

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.

Modular synthesis of self-assembling Janus-dendrimers and facile preparation of drug-loaded dendrimersomes

Materials and methods aimed at the next generation of nanoscale carriers for drugs and other therapeutics are currently in great demand. Yet, creating these precise molecular arrangements in a feasible and straightforward manner represents a remarkable challenge. Herein we report a modular synthetic route for amphiphilic Janus-dendrimers via a copper-catalyzed click reaction (CuAAC) and a facile procedure, using simple injection, to obtain highly uniform dendrimersomes with efficient loading of the model drug compound propranolol. The resulting assemblies were analyzed by dynamic light scattering and cryogenic transmission electron microscopy revealing the formation of unilamellar and multilamellar dendrimersomes. The formation of a bilayer structure was confirmed using cryo-TEM and confocal microscopy visualization of an encapsulated solvatochromic dye (Nile Red). The dendrimersomes reported here are tunable in size, stable over time and display robust thermal stability in aqueous media. Our results expand the scope of dendrimer-based supramolecular colloidal systems and offer the means for one-step fabrication of drug-loaded dendrimersomes in the size range of 90-200 nm, ideal for biomedical applications.

Crystal structure of [tris-(4,4'-bi-pyridine)]-diium bis-(1,1,3,3-tetra-cyano-2-eth-oxy-propenide) trihydrate

The title hydrated salt, C30H26N62+·2C9H5N4O-·3H2O, was obtained as an unexpected product from the hydro-thermal reaction between potassium 1,1,3,3-tetra-cyano-2-eth-oxy-propenide, 4,4'-bi-pyridine and iron(II) sulfate hepta-hydrate. The cation lies across a twofold rotation axis in the space group I2/a with the other components all in general positions. In the cation, the H atom linking the pyridine units is disordered over two adjacent sites having occupancies of 0.66 (4) and 0.36 (4), i.e. as N-H⋯N and N⋯H-N. The water mol-ecules of crystallization are each disordered over two sets of atomic sites, having occupancies of 0.522 (6) and 0.478 (6) for one, and 0.34 (3) and 0.16 (3) for the other, and it was not possible to reliably locate the H atoms associated with these partial-occupancy sites. In the crystal, four independent C-H⋯N hydrogen bonds link the ionic components into a three-dimensional network.

DNA-Based Enzyme Reactors and Systems

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.

Crystal structures of 2,2'-bipyridin-1-ium 1,1,3,3-tetracyano-2-ethoxyprop-2-en-1-ide and bis(2,2'-bipyridin-1-ium) 1,1,3,3-tetracyano-2-(dicyanomethylene)propane-1,3-diide

In each of the title compounds, the anion shows evidence of extensive electronic delocalization. A combination of N—H⋯N and X—H⋯N hydrogen bonds links the ions in (I) into a ribbon of alternating centrosymmetric (18) and (26) rings, and those in (II) into simple (7) chains of alternating cations and anion with further cations pendent from the chain.

In 2,2′-bipyridin-1-ium 1,1,3,3-tetra­cyano-2-eth­oxy­prop-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-tetra­cyano-2-(di­cyano­methyl­ene)propane-1,3-diide [alternative name bis­(2,2′-bipyridin-1-ium) tris­(di­cyano­methyl­ene)methane­diide], 2C₁₀H₉N₂⁺·C₁₀N₆²⁻ (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 C₃ 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 R₄⁴(18) and R₄⁴(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 C₂¹(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.

Janus-Dendrimer-Mediated Formation of Crystalline Virus Assemblies

Amphiphilic dendrimers have been shown to self-assemble with nanosized protein particles (viruses) to form highly ordered hierarchical assemblies. Here we present Janus-type dendrimers that have been synthesized from Newkome-type dendrons with hydrophilic spermine groups and hydrophobic Percec-type dendrons. These amphiphilic dendrimers bind electrostatically on the surface of virus particles and co-assemble into crystalline complexes with a lattice constant (a = 42 nm) comparable to the size of the virus particles. Small-angle X-ray scattering and cryogenic transmission electron microscopy show that the complexes have a face-centered cubic structure (space group Fm3̅m) and remarkable long-range order. Results indicate that amphiphilic dendrimers can be utilized to create inclusion body mimicking nanostructures.

3,4-Dimeth-oxy-4'-methyl-biphen-yl

In the title compound, C₁₅H₁₆O₂, the dihedral angle between the planes of the aromatic rings is 30.5 (2)°. In the crystal, mol­ecules are linked via C—H⋯O hydrogen bonds and C—H⋯π inter­actions, forming a two-dimensional network lying parallel to (100).

3,5-Dimeth-oxy-4'-methyl-biphen-yl

The title compound, C₁₅H₁₆O₂, crystallizes with three independent mol­ecules in the asymmetric unit. The intra­molecular torsion angle between the aromatic rings of each mol­ecule are −36.4 (3), 41.3 (3) and −37.8 (3)°. In the crystal, the complicated packing of the mol­ecules forms wave-like layers along the b and c axes. The mol­ecules are connected via extensive meth­oxy–phenyl C—H⋯π inter­actions. A weak C—H⋯O hydrogen-bonding network also exists between meth­oxy O atoms and aromatic or meth­oxy H atoms.

Methyl 3',5'-dimeth-oxy-biphenyl-4-carboxyl-ate

In the title compound, C16H16O4, the dihedral angle between the benzene rings is 28.9 (2)°. In the crystal, mol-ecules are packed in layers parallel to the b axis in which they are connected via weak inter-molecular C-H⋯O contacts. Face-to-face π-π inter-actions also exist between the benzene rings of adjacent mol-ecules, with centroid-centroid and plane-to-plane shift distances of 3.8597 (14) and 1.843 (2) Å, respectively.

Methyl 3',4',5'-trimeth-oxy-biphenyl-4-carboxyl-ate

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.

Generic method for modular surface modification of cellulosic materials in aqueous medium by sequential "click" reaction and adsorption

A generic approach for heterogeneous surface modification of cellulosic materials in aqueous medium, applicable for a wide range of functionalizations, is presented. In the first step, carboxymethyl cellulose (CMC) modified with azide or alkyne functionality, was adsorbed on a cellulosic substrate, thus, providing reactive sites for azide-alkyne cycloaddition click reactions. In the second step, functional units with complementary click units were reacted on the cellulose surface, coated by the click-modified CMC. Selected model functionalizations on diverse cellulosic substrates are shown to demonstrate the generality of the approach. The concept by sequentially combining the robust physical adsorption ("physical click") and robust chemical reaction ("chemical click") allows versatile, simple, and environmentally friendly modification of a cellulosic substrate with virtually any azide- or alkyne-modified molecule and even functionalization with several types of units.

Self-assembly of hybrid dendrons with complex primary structure into functional helical pores

The synthesis of three libraries of self-assembling hybrid dendrons containing a primary structure based on the sequence (4-3,4-3,5)12G2-CO(2)CH(3) generated from benzyl ether, biphenyl-4-methyl ether, and AB(2) repeat units constructed from (AB)(y)--AB(2) combinations of benzyl ethers, is reported. The structural and retrostructural analysis of their supramolecular dendrimers facilitated the discovery of new architectural principles that lead to the assembly of functional helical pores. The self-assembly of an example of hybrid dendron containing -H, -CO(2)CH(3), -CH(2)OH, -COOH, -COOK, -CONH(2), -CONHCH(3), -CO(2)(CH(2))(2)OCH(3), -(R) and -(S)-CONHCH(CH(3))C(2)H(5) as X-groups at the apex demonstrated that these self-assembling dendrons provide the simplest strategy for the design and synthesis of porous columns containing a diversity of hydrophilic and hydrophobic functional groups in the inner part of the pore. The results reported here expand the scope and limitations of dendrons available for the self-assembly of functional pores that previously were generated mostly from dendritic dipeptides, to simpler architectures based on hybrid dendrons.

Exploring and Expanding the Structural Diversity of Self-Assembling Dendrons through Combinations of AB, Constitutional Isomeric AB2, and AB3 Biphenyl-4-Methyl Ether Building Blocks

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 Ni(II)-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-Assembly, Structural, and Retrostructural Analysis of Dendritic Dipeptide Pores Undergoing Reversible Circular to Elliptical Shape Change

The synthesis of dendritic dipeptides (4-3,4-3,5-4)12G2-CH(2)-Boc-L-Tyr-L-Ala-OMe and (4-3, 4-3,5-4)12G2-CH(2)-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.

Principles of self-assembly of helical pores from dendritic dipeptides

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 approximately 10 A 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 A 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.

Self-assembly of amphiphilic dendritic dipeptides into helical pores

Natural pore-forming proteins act as viral helical coats and transmembrane channels, exhibit antibacterial activity and are used in synthetic systems, such as for reversible encapsulation or stochastic sensing. These diverse functions are intimately linked to protein structure. The close link between protein structure and protein function makes the design of synthetic mimics a formidable challenge, given that structure formation needs to be carefully controlled on all hierarchy levels, in solution and in the bulk. In fact, with few exceptions, synthetic pore structures capable of assembling into periodically ordered assemblies that are stable in solution and in the solid state have not yet been realized. In the case of dendrimers, covalent and non-covalent coating and assembly of a range of different structures has only yielded closed columns. Here we describe a library of amphiphilic dendritic dipeptides that self-assemble in solution and in bulk through a complex recognition process into helical pores. We find that the molecular recognition and self-assembly process is sufficiently robust to tolerate a range of modifications to the amphiphile structure, while preliminary proton transport measurements establish that the pores are functional. We expect that this class of self-assembling dendrimers will allow the design of a variety of biologically inspired systems with functional properties arising from their porous structure.

Alkoxy-, Acyloxy-, and Bromomethylation of Resorcinarenes

Reaction of resorcinarene octols with tris-hydroxymethylmethylamine (TRIS), formaldehyde, and alcohols results in tetraalkoxymethylation of the resorcinol rings. Harsh acylation of aminomethylated resorcinarenes with acid anhydrides leads to the complete acylation of eight hydroxyls and substitution of the amino versus acyloxy groups. Acyloxymethylated resorcinarene 6b can be transformed into a tetrabromomethylated derivative 7 through the reaction with HBr in acetic acid.

Bisfunctionalized Janus Molecules

[reaction: see text] Bisfunctionalized dendritic multiester molecules were synthesized by combined protection-deprotection and divergent-convergent-divergent sequences in high yields leading to dendritic molecules that combine two functionally different surfaces, polar aliphatic arborol and nonpolar gallate ether moieties, resulting in a two-faced Janus molecule.