Nucleic acid based molecular devices

In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major "historical" influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology.     

Rearrangement of lithiated S-alkyl O,O-dialkyl thiophosphates: scope and stereochemistry of the thiophosphate-mercaptophosphonate rearrangement

S-Alkyl O,O-dialkyl thiophosphates are prepared by alkylation of the triethylammonium salt of O,O-diisopropyl thiophosphoric acid. S-Benzyl thiophosphate was metallated at temperatures of ≥-45 °C by trityllithium and LiTMP (lithium 2,2,6,6-tetramethylpiperidide) and S-alkyl thiophosphates only by LiTMP to give dipole-stabilised carbanions which rearrange to α-mercaptophosphonates in yields of up to 45%. Metallation occurs with a high primary kinetic isotope effect (k(H)/k(D) up to ≈50). When the lithium (R)-N-isopropyl-1-phenylethylamide was used to induce the isomerisation of S-pentyl thiophosphate an α-mercaptophosphonate with an ee of 22% was isolated. (R)-S-[1-D(1)]hexyl O,O-diisopropyl thiophosphate was rearranged to a dextrorotary α-mercapto-[1-D(1)]hexylphosphonate, whose (R)-configuration was determined by chemical correlation. The thiophosphate-mercaptophosphonate rearrangement proceeds with retention of configuration.     

Low-temperature chemistry in helium droplets: reactions of aluminum atoms with O2 and H2O

The doping of He droplets by Al atoms and their reactions with H(2)O and O(2) at T = 0.37 K was investigated. It was found that at high doping concentrations, the incorporated Al atoms do not aggregate to form clusters. They rather remain as separated atoms inside of the He droplets. Mass spectrometry and the recently developed depletion method have been applied to study the reactions. It was found that single Al atoms react with single O(2) molecules. The dominant product of this reaction occurring inside of the He droplets is AlO(2). The reaction between Al and O(2) clusters has also been detected. The Al clusters react with single H(2)O molecules or clusters. While single Al atoms react with H(2)O clusters, no reaction of single Al atoms with a single water molecule was found.     

Effect of alkylimidazolium based ionic liquids on the structure of UV-irradiated cellulose

In this paper, the influence of three alkylimidazolium-based ionic liquids with the same cation (1-ethyl-3-methylimidazolium) and different anions (chloride, tetrafluoroborate and hexafluorophosphate) on the structure and properties of cellulose, have been studied by using Fourier transform infrared spectroscopy measurements, fluorescence microscopy imaging, viscometric and methylene blue sorption tests. Cellulose treated with ionic liquids showed better stability to UV light, as demonstrated by the lower variations of the polymerization degree, carboxyl groups content, moisture index, crystallinity index, lateral order index and allomorph index, with the increase of the UV exposure period, by comparing to non-treated cellulose. The results show that the tested ionic liquids could be effective as “green” plasticizers and UV stabilizers for cellulose-based materials.     

Synthesis and Characterization of PEG‐Based Drug‐Responsive Biohybrid Hydrogels

Interactive materials being responsive to a biocompatible stimulus represent a promising approach for future therapeutic applications. In this study, we present a novel biohybrid material synthesized from biocompatible components being stimulus‐responsive to the pharmaceutically approved small‐molecule novobiocin. The hydrogel design is based on the gyrase B (GyrB) protein, which is covalently grafted to multi‐arm polyethylene glycol (PEG) using a Michael‐type addition reaction. Upon addition of the GyrB‐dimerizing substance coumermycin, stable hydrogels form which can be dissolved in a dose‐adjustable manner by the antibiotic novobiocin. The switchable properties of this PEG‐based hydrogel are favorable for future applications in tissue engineering and as externally controlled drug depot.     

Perturbation Theory of Polymer Chains Revisited, 2—Intermolecular Excluded Volume of Random and Self‐Avoiding Walks

The intermolecular compatibility of 10⁷–10⁸ independent pair configurations of linear chains (chain length 64 ≤ N ≤ 8192) with and without intramolecular interaction on various lattices is checked and the intermolecular excluded volume u evaluated. From the (average) number of possible i‐tuples of overlaps in the pair configurations the parameters C_k of the perturbation theory are calculated. Differences between the various lattice types at finite N vanish completely for N → ∞. While the theoretical values of C₁ and C₂ were recovered within very narrow limits for chains without intramolecular interaction, markedly higher figures apply to self‐avoiding walks. The excluded volume u itself and higher C_k parameters are called upon to test several classical and renormalized perturbation theories.

     

Toward a Universal Behavior of Linear Athermal Model Chains in the Limit of Infinite Chain‐length

Athermal chains of various stiffness embedded in several types of lattices were analyzed with respect to their pair distribution function G(R). Extrapolation to infinite chain‐length on a reduced distance scale made all the G(R) data coincide within extremely narrow limits, thus suggesting the existence of a universal pair distribution function for polymers in good solvents in the long‐chain limit. The ratio –ln(G(R))/Z(R) with Z(R) being the reduced distribution of overlaps is also universal in type and varies only little with distance R. Further, a likewise universal function could be established that allows the construction of Z(R) from the Flory–Krigbaum expression taking into account not only the deviations from Gaussian behavior but also the effect of intramolecular repulsion present in athermal chains.

     

Surface and Bulk Structure of Thin Spin Coated and Plasma-Polymerized Polystyrene Films

Polystyrene (PS) spin coated thin films were modified by O₂ and Ar plasma as well as by UV irradiation treatments. The modified PS samples were compared with plasma polymerized and commercial polystyrene. The effects of plasma (O₂ and Ar) and UV irradiation treatments on the surface and the bulk properties of the polymer layers were discussed. The surface properties were evaluated by X-ray Photoelectron Spectroscopy and Contact angle measurements and the bulk properties were investigated by FTIR and dielectric relaxation spectroscopy. As a result only one second treatment time was sufficient to modify the surface. However, this study was also dedicated to understand the effect of plasma and plasma irradiation on the deposited layers of plasma polymers. The dielectric measurements showed that the plasma deposited films were not thermally stable and underwent an undesired post-plasma chemical oxidation.