In vitro selection and characterization of cellulose-binding DNA aptamers

Many nucleic acid enzymes and aptamers have modular architectures that allow them to retain their functions when combined with other nucleotide sequences. This modular function facilitates the engineering of RNAs and DNAs that have more complex functions. We sought to create new DNA aptamers that bind cellulose to provide a module for immobilizing DNAs. Cellulose has been used in a variety of applications ranging from coatings and films to pharmaceutical preparations, and therefore DNA aptamers that bind cellulose might enable new applications. We used in vitro selection to isolate aptamers from a pool of random-sequence DNAs and subjected two distinct clones to additional rounds of mutagenesis and selection. One aptamer (CELAPT 14) was chosen for sequence minimization and more detailed biochemical analysis. CELAPT 14 aptamer variants exhibit robust binding both to cellulose powder and paper. Also, an allosteric aptamer construct was engineered that exhibits ATP-mediated cellulose binding during paper chromatography

Influence of nano-mechanical properties on single electron tunneling: A vibrating Single-Electron Transistor

We describe single electron tunneling through molecular structures under the influence of nano-mechanical excitations. We develop a full quantum mechanical model, which includes charging effects and dissipation, and apply it to the vibrating C$_{60}$ single electron transistor experiment by Park {\em et al.} {[Nature {\bf 407}, 57 (2000)].} We find good agreement and argue vibrations to be essential to molecular electronic systems. We propose a mechanism to realize negative differential conductance using local bosonic excitations.Comment: 7 pages, 6 figure

Thermoelectric effects in Kondo correlated quantum dots

In this Letter we study thermoelectric effects in ultra small quantum dots. We study the behaviour of the thermopower, Peltier coefficient and thermal conductance both in the sequencial tunneling regime and in the regime where Kondo correlations develope. Both cases of linear response and non-equilibrium induced by strong temperature gradients are considered. The thermopower is a very sensitive tool to detect Kondo correlations. It changes sign both as a function of temperature and temperature gradient. We also discuss violations of the Wiedemann-Franz law.Comment: 7 pages; 5 figure

Mechanical Cooper pair transportation as a source of long distance superconducting phase coherence

Transportation of Cooper-pairs by a movable single Cooper-pair-box placed between two remote superconductors is shown to establish coherent coupling between them. This coupling is due to entanglement of the movable box with the leads and is manifested in the supression of quantum fluctuations of the relative phase of the order parameters of the leads. It can be probed by attaching a high resistance Josephson junction between the leads and measuring the current through this junction. The current is suppressed with increasing temperature.Comment: 4 pages, 4 figures, RevTeX; Updated version, typos correcte

Thermopower of Kondo Effect in Single Quantum Dot Systems with Orbital at Finite Temperatures

We investigate the thermopower due to the orbital Kondo effect in a single quantum dot system by means of the noncrossing approximation. It is elucidated how the asymmetry of tunneling resonance due to the orbital Kondo effect affects the thermopower under gate-voltage and magnetic-field control.Comment: 4 pages, 4 figures, proceeding of Second International Symposium on Nanometer-Scale Quantum Physic

Phonon distributions of a single bath mode coupled to a quantum dot

The properties of an unconventional, single mode phonon bath coupled to a quantum dot, are investigated within the rotating wave approximation. The electron current through the dot induces an out of equilibrium bath, with a phonon distribution qualitatively different from the thermal one. In selected transport regimes, such a distribution is characterized by a peculiar selective population of few phonon modes and can exhibit a sub-Poissonian behavior. It is shown that such a sub-Poissonian behavior is favored by a double occupancy of the dot. The crossover from a unequilibrated to a conventional thermal bath is explored, and the limitations of the rotating wave approximation are discussed.Comment: 21 Pages, 7 figures, to appear in New Journal of Physics - Focus on Quantum Dissipation in Unconventional Environment

Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria

AbstractRiboswitches are metabolite binding domains within certain messenger RNAs that serve as precision sensors for their corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression. We have identified a class of riboswitches that selectively recognizes guanine and becomes saturated at concentrations as low as 5 nM. In Bacillus subtilis, this mRNA motif is located on at least five separate transcriptional units that together encode 17 genes that are mostly involved in purine transport and purine nucleotide biosynthesis. Our findings provide further examples of mRNAs that sense metabolites and that control gene expression without the need for protein factors. Furthermore, it is now apparent that riboswitches contribute to the regulation of numerous fundamental metabolic pathways in certain bacteria

1,3-Difluoro­benzene

The weak electrostatic and dispersive forces between C(δ+)—F(δ−) and H(δ+)—C(δ−) are at the borderline of the hydrogen-bond phenomenon and are poorly directional and further deformed in the presence of other dominant inter­actions, e.g. C—H⋯π. The title compound, C6H4F2, Z′ = 2, forms one-dimensional tapes along two homodromic C—H⋯F hydrogen bonds. The one-dimensional tapes are connected into corrugated two-dimensional sheets by further bi- or trifrucated C—H⋯F hydrogen bonds. Packing in the third dimension is controlled by C—H⋯π inter­actions

2,9,16,23-Tetra­kis(1-methyl­eth­yl)-5,6,11,12,13,14,19,20,25,26,27,28-dodecadehydro­tetra­benzo[a,e,k,o]cyclo­eicosene1

The title compound, C48H40, is a tetra­isopropyl-substituted polyannulenoenyne. The unsubstituted polyannulenoenyne, C36H16 (CSD: RICVEE; CAS: 186494-87-1), has quasi-D 2 (222) symmetry, as determined by least-squares fit (excluding H atoms) to a model optimized in D 2 symmetry by mol­ecular mechanics (r.m.s. deviation = 0.239 Å). The least-squares fits of 36 common C atoms of the title compound (at 90 K) to the parent (at 295 K) and to the optimized model show r.m.s. deviations of 0.419 and 0.426 Å, respectively

Engineering of an octupolar non-linear optical crystal: tribenzyl isocyanurate

The title compound has a C-H···O hydrogen bond-mediated trigonal network structure that leads to octupolar NLO behaviour in the solid state