DNA origami: a quantum leap for self-assembly of complex structures

The spatially controlled positioning of functional materials by self-assembly is one of the fundamental visions of nanotechnology. Major steps towards this goal have been achieved using DNA as a programmable building block. This tutorial review will focus on one of the most promising methods: DNA origami. The basic design principles, organization of a variety of functional materials and recent implementation of DNA robotics are discussed together with future challenges and opportunities.     

Controlled self-assembly of re-engineered insulin by Fe(II)

Self-assembly of proteins mediated by metal ions is crucial in biological systems and a better understanding and novel strategies for its control are important. An abiotic metal ion ligand in a protein offers the prospect of control of the oligomeric state, if a selectivity over binding to the native side chains can be achieved. Insulin binds Zn(II) to form a hexamer, which is important for its storage in vivo and in drug formulations. We have re-engineered an insulin variant to control its self-assembly by covalent attachment of 2,2'-bipyridine. The use of Fe(II) provided chemoselective binding over the native site, forming a homotrimer in a reversible manner, which was easily followed by the characteristic color of the Fe(II) complex. This provided the first well-defined insulin trimer and the first insulin variant for which self-assembly can be followed visually.     

Magnetic Flux Lines in Complex Geometry Type-II Superconductors Studied by the Time Dependent Ginzburg-Landau Equation

The time-dependent Ginzburg-Landau equation is solved numerically for type-II superconductors of complex geometry using the finite element method. The geometry has a marked influence on the magnetic vortex distribution and the vortex dynamics. We have observed generation of giant vortices at boundary defects, suppressing the superconducting state far into the superconductor.     

The combination of living radical polymerization and click chemistry for the synthesis of advanced macromolecular architectures

Since its introduction, click chemistry has received a considerable amount of interest. In this contribution, the term click chemistry and the reactions that fall under this term are briefly explained. The main focus of this review is on the application of click chemistry in conjunction with living radical polymerization for the synthesis of advanced macromolecular architectures. Therefore the most powerful living radical polymerization (LRP) techniques are discussed and an overview of click chemistry in the different synthetic schemes is given. A large number of examples are shown that include the synthesis of block copolymers, star-shaped polymers, surface modified particles, and polymer-protein conjugates. The enormous potential of LRP/click chemistry is probably best exemplified by the synthesis of different miktoarm star copolymers, to which a separate section is dedicated.     

Atomic interactions in the p-type clathrate I Ba8Au5.3Ge40.7

Single crystals of Ba(8)Au(5.3)Ge(40.7) [space group Pm(3)n (No. 223), a = 10.79891(8) ?] were prepared by a Bridgman technique. The crystal structure refinement based on single-crystal X-ray diffraction data does not reveal any vacancies in the Au/Ge framework or in the cages. In addition to the ionic bonding between Ba and the anionic framework, a direct interaction between Ba and Au atoms was identified in Ba(8)Au(5.3)Ge(40.7) by applying the electron localizability indicator. As expected by the chemical-bonding picture, Ba(8)Au(5.3)Ge(40.7) is a diamagnet and shows p-type electrical conductivity with a hole carrier concentration of 7.14 × 10(19) cm(-3) at 300 K and very low lattice thermal conductivity of ≈0.6 W m(-1) K(-1) at 500 K. The thermoelectric figure of merit ZT of single crystals of Ba(8)Au(5.3)Ge(40.7) attains 0.3 at 511 K and reaches 0.9 at 680 K in a polycrystalline sample of closely similar composition. This opens up an opportunity for tuning of the thermoelectric properties of materials in the Ba-Au-Ge clathrate system by changing the chemical composition.     

5-(Indol-2-yl)pyrazolo[3,4-b]pyridines as a New Family of TASK-3 Channel Blockers: A Pharmacophore-Based Regioselective Synthesis

TASK channels belong to the two-pore-domain potassium (K_2P) channels subfamily. These channels modulate cellular excitability, input resistance, and response to synaptic stimulation. TASK-channel inhibition led to membrane depolarization. TASK-3 is expressed in different cancer cell types and neurons. Thus, the discovery of novel TASK-3 inhibitors makes these bioactive compounds very appealing to explore new cancer and neurological therapies. TASK-3 channel blockers are very limited to date, and only a few heterofused compounds have been reported in the literature. In this article, we combined a pharmacophore hypothesis with molecular docking to address for the first time the rational design, synthesis, and evaluation of 5-(indol-2-yl)pyrazolo[3,4-b]pyridines as a novel family of human TASK-3 channel blockers. Representative compounds of the synthesized library were assessed against TASK-3 using Fluorometric imaging plate reader—Membrane Potential assay (FMP). Inhibitory properties were validated using two-electrode voltage-clamp (TEVC) methods. We identified one active hit compound (MM-3b) with our systematic pipeline, exhibiting an IC₅₀ ≈ 30 μM. Molecular docking models suggest that compound MM-3b binds to TASK-3 at the bottom of the selectivity filter in the central cavity, similar to other described TASK-3 blockers such as A1899 and PK-THPP. Our in silico and experimental studies provide a new tool to predict and design novel TASK-3 channel blockers.     

An effective force field for molecular dynamics simulations of dimethyl sulfone

A rigid five-site united atom model for dimethyl sulfone (DMSO₂) compatible with the GROMOS force field is parametrized and tested. The parameters were optimized with respect to experimental quantities such as liquid density, heat of vaporization, shear viscosity and excess free energy. Good agreement with pure component properties is achieved except for the static dielectric permittivity which is calculated too low. Together with the SPC model for water the new DMSO₂ model was used to study aqueous mixtures at low concentrations and compared to aqueous mixtures of DMSO. It is concluded that interaction parameters for sulfoxide oxygen are not directly transferable to sulfonyl oxygen.     

An Aldehyde Responsive,Cleavable Linker for Glucose Responsive Insulins

A glucose responsive insulin (GRI) that responds to changes in blood glucose concentrations has remained an elusive goal. Here we describe the development of glucose cleavable linkers based on hydrazone and thiazolidine structures. We developed linkers with low levels of spontaneous hydrolysis but increased level of hydrolysis with rising concentrations of glucose, which demonstrated their glucose responsiveness in vitro. Lipidated hydrazones and thiazolidines were conjugated to the LysB29 side-chain of HI by pH-controlled acylations providing GRIs with glucose responsiveness confirmed in vitro for thiazolidines. Clamp studies showed increased glucose infusion at hyperglycemic conditions for one GRI indicative of a true glucose response. The glucose responsive cleavable linker in these GRIs allow changes in glucose levels to drive the release of active insulin from a circulating depot. We have demonstrated an unprecedented, chemically responsive linker concept for biopharmaceuticals.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

Preparation and Evaluation of [18F]AlF-NOTA-NOC for PET Imaging of Neuroendocrine Tumors: Comparison to [68Ga]Ga-DOTA/NOTA-NOC

Background: The somatostatin receptors 1–5 are overexpressed on neuroendocrine neoplasms and, as such, represent a favorable target for molecular imaging. This study investigates the potential of [¹⁸F]AlF-NOTA-[1-Nal³]-Octreotide and compares it in vivo to DOTA- and NOTA-[1-Nal³]-Octreotide radiolabeled with gallium-68. Methods: DOTA- and NOTA-NOC were radiolabeled with gallium-68 and NOTA-NOC with [¹⁸F]AlF. Biodistributions of the three radioligands were evaluated in AR42J xenografted mice at 1 h p.i and for [¹⁸F]AlF at 3 h p.i. Preclinical PET/CT was applied to confirm the general uptake pattern. Results: Gallium-68 was incorporated into DOTA- and NOTA-NOC in yields and radiochemical purities greater than 96.5%. NOTA-NOC was radiolabeled with [¹⁸F]AlF in yields of 38 ± 8% and radiochemical purity above 99% after purification. The biodistribution in tumor-bearing mice showed a high uptake in tumors of 26.4 ± 10.8 %ID/g for [⁶⁸Ga]Ga-DOTA-NOC and 25.7 ± 5.8 %ID/g for [⁶⁸Ga]Ga-NOTA-NOC. Additionally, [¹⁸F]AlF-NOTA-NOC exhibited a tumor uptake of 37.3 ± 10.5 %ID/g for [¹⁸F]AlF-NOTA-NOC, which further increased to 42.1 ± 5.3 %ID/g at 3 h p.i. Conclusions: The high tumor uptake of all radioligands was observed. However, [¹⁸F]AlF-NOTA-NOC surpassed the other clinically well-established radiotracers in vivo, especially at 3 h p.i. The tumor-to-blood and -liver ratios increased significantly over three hours for [¹⁸F]AlF-NOTA-NOC, making it possible to detect liver metastases. Therefore, [¹⁸F]AlF demonstrates promise as a surrogate pseudo-radiometal to gallium-68.