Parallel biomolecular computation on surfaces with advanced finite automata

A biomolecular, programmable 3-symbol-3-state finite automaton is reported. This automaton computes autonomously with all of its components, including hardware, software, input, and output being biomolecules mixed together in solution. The hardware consisted of two enzymes: an endonuclease, BbvI, and T4 DNA ligase. The software (transition rules represented by transition molecules) and the input were double-stranded (ds) DNA oligomers. Computation was carried out by autonomous processing of the input molecules via repetitive cycles of restriction, hybridization, and ligation reactions to produce a final-state output in the form of a dsDNA molecule. The 3-symbol-3-state deterministic automaton is an extension of the 2-symbol-2-state automaton previously reported, and theoretically it can be further expanded to a 37-symbol-3-state automaton. The applicability of this design was further amplified by employing surface-anchored input molecules, using the surface plasmon resonance technology to monitor the computation steps in real time. Computation was performed by alternating the feed solutions between endonuclease and a solution containing the ligase, ATP, and appropriate transition molecules. The output detection involved final ligation with one of three soluble detection molecules. Parallel computation and stepwise detection were carried out automatically with a Biacore chip that was loaded with four different inputs.     

Copper‐Mediated Aromatic Radiofluorination Revisited: Efficient Production of PET Tracers on a Preparative Scale

Two novel methods for copper‐mediated aromatic nucleophilic radiofluorination were recently reported. Evaluation of these methods reveals that, although both are efficient in small‐scale experiments, they are inoperative for the production of positron emission tomography (PET) tracers. Since high base content turned out to be responsible for low radiochemical conversions, a “low base” protocol has been developed which affords ¹⁸F‐labeled arenes from diaryliodonium salts and aryl pinacol boronates in reasonable yields. Furthermore, implementation of our “minimalist” approach to the copper‐mediated [¹⁸F]‐fluorination of (mesityl)(aryl)iodonium salts allows the preparation of ¹⁸F‐labeled arenes in excellent RCCs. The novel radiofluorination method circumvents time‐consuming azeotropic drying and avoids the utilization of base and other additives, such as cryptands. Furthermore, this procedure enables the production of clinically relevant PET tracers; [¹⁸F]FDA, 4‐[¹⁸F]FPhe, and [¹⁸F]DAA1106 are obtained in good isolated radiochemical yields. Additionally, [¹⁸F]DAA1106 has been evaluated in a rat stroke model and demonstrates excellent potential for visualization of translocator protein 18 kDa overexpression associated with neuroinflammation after ischemic stroke.     

A Barrel-Shaped Metal–Organic Blue-Box Analogue with Photo-/Redox-Switchable Behavior

Donor–acceptor interactions are ubiquitous in the design and understanding of host–guest complexes. Despite their non-covalent nature, they can readily dictate the self-assembly of complex architectures. Here, a photo-/redox-switchable metal–organic nanocapsule is presented, which was assembled by using lanthanide ions and viologen building blocks, by relying on such donor–acceptor interactions. The potential of this unique barrel-shaped structure is highlighted for the encapsulation of suitable electron donors, akin to the well-investigated “blue-box” macrocycles. The light-triggered reduction of the viologen units has been investigated by single-crystal-to-single-crystal X-ray diffraction experiments, complemented by magnetic, optical, and solid-state electrochemical characterizations. Density functional theory (DFT) calculations were employed to suggest the most likely electron donor in the light-triggered reduction of the viologen-based ligand.     

Comparative analysis of sensory rhodopsin II structures in complex with a transducer and without it

Sensory rhodopsin II (NpSRII) is a heptahelical transmembrane protein containing the retinal chromophore. In complex with another membrane protein, i.e., NpHtrII transducer, NpSRII transmits a signal into a cell, initiating negative phototaxis of Natronobacterium pharaonis. In the absence of a transducer, rhodopsin II can work as a proton pump similar to bacteriorhodopsin. The main objective of this study is to comparatively analyze receptor structures in complex with the transducer and without it to understand the mechanism of the protein switching function. Diffraction data for sensory rhodopsin II crystals grown in the lipidic cubic phase were obtained at the synchrotron x-ray source. In this paper, we present a new NpSRII structure with a resolution of 2.1 Å and the results of a comparative analysis of the obtained NpSRII structure with our previously published data on the NpSRII/NpHtrII complex structure and with two NpSRII structures without a transducer, previously published in the literature.     

Structure of organosilicon dendrimers of higher generations

The structure of organosilicon dendrimers of the ninth generation with the four-functional core and butyl terminal groups has been studied by small-angle neutron scattering. It has been demonstrated that the dendrimers are monodisperse objects with an anisometric shape. The partial volume and the average scattering density have been determined using the contrast variation technique. It has been shown that the dendrimers under study are identical in overall sizes and scattering density distribution. It has been revealed that 20% of the overall volume of the dendrimer is accessible for the penetration of the solvent. The distribution of the scattering length density in the dendrimers has been simulated and reconstructed using the Monte Carlo method, and a change in the excluded volume for different contrasts has been revealed. The specific features of the spatial structure of organosilicon dendrimers of higher generations have been discussed.     

Magnetic and structural anomalies of Na<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>C<Subscript>60</Subscript> (n = 2, 3)

Sodium fullerides Na _n C60 (n = 2, 3) have been synthesized by a liquid phase reaction and investigated with X-ray diffraction (XRD), nuclear magnetic resonance (NMR), electron paramagnetic resonance, and differential thermal analysis. XRD data indicate that the crystal structure of Na₂C₆₀ at 300 K is face centered cubic (FCC). A phase transition from primitive cubic to FCC crystal structure has been observed in this work in Na₂C₆₀ fulleride at 290 K. The transition is accompanied by the step-like change of paramagnetic susceptibility. The crystal structure of Na₃C₆₀ is more complicated than, and different from, what has been reported in the literature. A nearly seven-fold increase of paramagnetic susceptibility with increasing temperature has been observed in the Na₃C₆₀ fulleride at 240–260 K. In the same temperature range, a new line at about 255 ppm appears in the ²³Na NMR spectrum, indicating a significant increase of electron density near the Na nucleus. The observed effect can be explained by a metal-insulator transition caused by a structural transition.     

Hybrid vertical‐cavity laser with lateral emission into a silicon waveguide

We experimentally demonstrate an optically‐pumped III‐V/Si vertical‐cavity laser with lateral emission into a silicon waveguide. This on‐chip hybrid laser comprises a distributed Bragg reflector, a III‐V active layer, and a high‐contrast grating reflector, which simultaneously funnels light into the waveguide integrated with the laser. This laser has the advantages of long‐wavelength vertical‐cavity surface‐emitting lasers, such as low threshold and high side‐mode suppression ratio, while allowing integration with silicon photonic circuits, and is fabricated using CMOS compatible processes. It has the potential for ultrahigh‐speed operation beyond 100 Gbit/s and features a novel mechanism for transverse mode control.

     

Regioselective Heteroannelation in 4-Cyanomethyl-3,5-pyridinedicarbonitriles. Synthesis of 6-Alkoxy-3-dialkylamino-1,8-diamino-2,7-naphthyridine-4-carbonitriles

Summary.  The title naphthyridines were found to be the sole products obtained after treatment of 2-amino-4-cyanomethyl-6-dialkylamino-3,5-pyridinedicarbonitriles with alkoxides. The starting pyridine derivatives were prepared by amination of the readily available 2-amino-6-chloro-4-cyanomethyl-3,5-pyridinedicarbonitrile in quantitative yields. Corresponding author. E-mail: atver@mail.univ.kiev.ua Received November 4, 2002; accepted November 22, 2002 Published online May 6, 2003