Toehold-Mediated Strand Displacement in a Triplex Forming Nucleic Acid Clamp for Reversible Regulation of Polymerase Activity and Protein Expression

Triplex forming oligonucleotides are used as a tool for gene regulation and in DNA nanotechnology. By incorporating artificial nucleic acids, target affinity and biological stability superior to that of natural DNA may be obtained. This work demonstrates how a chimeric clamp consisting of acyclic (L)-threoninol nucleic acid (aTNA) and DNA can bind DNA and RNA by the formation of a highly stable triplex structure. The (L)-aTNA clamp is released from the target again by the addition of a releasing strand in a strand displacement type of reaction. It is shown that the clamp efficiently inhibits Bsu and T7 RNA polymerase activity and that polymerase activity is reactivated by displacing the clamp. The clamp was successfully applied to the regulation of luciferase expression by reversible binding to the mRNA. When targeting a sequence in the double stranded plasmid, 40 % downregulation of protein expression is achieved.     

A computational study of tert-butylbenzenium ions

A computational study of tert-butylbenzenium ions has been performed. Structures and energies of the various isomers and the transition states for their interconversions have been determined. The existence of a stable π-electron complex (called A1) between a tert-butyl cation and a benzene molecule has been confirmed. Other minimum points on the potential energy surface corresponding to π-complexes were found, but the barriers for transforming these complexes into the stable π-electron complex A1 are so low that the transformation into the stable structure can take place at all temperatures. The structures were evaluated at the DFT-B3LYP level of theory. The energies were evaluated with the Gaussian-3 (G3B3) and CBS (CBS-QB3) composite methodologies. A discussion of published experimental data in view of the computational results is given. It is pointed out that it should be possible to show the presence of the π-complex by IR spectroscopy. The computations show that the π-complex has a very strong IR band in an otherwise empty region.     

Structure, stability, and hydration of a polypeptide in AOT reverse micelles

In this communication, we provide theoretical evidence that the folded structure of a simple peptide, alanine zwitterionic octapeptide, or A8, unstable in solution, becomes stable in a reverse micelle (RM) of appropriate size. Our molecular dynamics simulations were carried out for realistic models of sodium 2-ethylhexylsulfosuccinate RM in isooctane, simulated for an extended period of time. For the RM of the smaller size, we find that a helical structure is stable for the whole length of the simulation. On the contrary, the peptide very quickly takes an extended structure in larger micelles.     

Head-to-tail self-assembly of a calix[4]arene inclusion polymer controlled by a pendant arm

A calix[4]arene functionalized at one phenolic group with a pendant ethoxy acetate group, forms an inclusion complex that is stable even in the presence of other potential guest molecules.     

The cordycepin analogue of 2,5A and its threo isomer. Chemical synthesis, conformation and biological activity

A new synthesis of the cordycepin analogue of 2,5A and its threo isomer is reported along with an assessment of their conformations by circular dichroism spectroscopy. Evidence is also presented showing that these compounds are stable against 2,5A-specific phosphodiesterase and are not able to activate the 2,5A-dependent endoribonuclease, possibly due to a reduced binding to the latter enzyme as compared to that of 2,5A.     

Gram-Scale Synthesis of Nickel(II) Norcorrole: The Smallest Antiaromatic Porphyrinoid

Small is beautiful: A ring-contracted sister of porphyrin, norcorrole, has been synthesized efficiently as a stable molecule by a nickel-templated strategy. The norcorrole complex is stable but exhibits a distinct antiaromatic character according to the Hückel rule. Oxidation of the norcorrole complex provides an aromatic oxacorrole complex.     

Stochastic transitions through unstable limit cycles in a model of bistable thermochemical system

The master equation approach is used to study transitions through an unstable limit cycle surrounding a stable focus in two-variable systems with three stationary states. The model considered describes a bistable thermochemical system. Two cases are studied. In the first one transitions occur from a basin of attraction of a stable limit cycle to a basin of attraction of a stable focus surrounded by an unstable limit cycle. In the second case, stochastic trajectories cross the unstable limit cycle going from a basin of attraction of a stable node to a basin of attraction of a stable focus. Distribution functions of the first passage time between these attractors are calculated and discussed for systems with various numbers of particles. The distribution functions in both cases exhibit a multi-peak character. A fine structure of single peaks is observed in the first case.     

Body-centered tetragonal B2N2: a novel sp3 bonding boron nitride polymorph

A novel polymorph of boron nitride (BN) with a body-centered tetragonal structure (bct-BN) has been predicted using first-principles calculations. The structural, vibrational, and mechanical calculations indicated that bct-BN is mechanically stable at zero pressure. When pressure is above 6 GPa, bct-BN becomes energetically more stable than h-BN. The bct-BN appears to be an intermediate phase between h-BN and w-BN due to a low energy barrier from h-BN to w-BN via bct-BN. Our results also indicated that the structure of unknown E-BN phase might be bct-BN.     

Numerically stable optimized effective potential method with balanced Gaussian basis sets

A solution to the long-standing problem of developing numerically stable optimized effective potential (OEP) methods based on Gaussian basis sets is presented by introducing an approach consisting of an exact exchange OEP method with an accompanying construction and balancing scheme for the involved auxiliary and orbital Gaussian basis sets that is numerically stable and that properly represents an exact exchange Kohn-Sham method. The method is a purely analytical method that does not require any numerical grid, scales like Hartree-Fock or B3LYP procedures, is straightforward to implement, and is easily generalized to take into account orbital-dependent density functionals other than the exact exchange considered in this work. Thus, the presented OEP approach opens the way to the development and application of novel orbital-dependent exchange-correlation functionals. It is shown that adequately taking into account the continuum part of the Kohn-Sham orbital spectrum is crucial for numerically stable Gaussian basis set OEP methods. Moreover, it is mandatory to employ orbital basis sets that are converged with respect to the used auxiliary basis representing the exchange potential. OEP calculations in the past often did not meet the latter requirement and therefore may have led to erroneously low total energies.     

In vivo absorption spectra of the two stable states of the Euglena photoreceptor photocycle

Euglena gracilis possesses a simple but sophisticated light detecting system, consisting of an eyespot formed by carotenoids globules and a photoreceptor. The photoreceptor of Euglena is characterized by optical bistability, with two stable states. In order to provide important and discriminating information on the series of structural changes that Euglena photoreceptive protein(s) undergoes inside the photoreceptor in response to light, we measured the in vivo absorption spectra of the two stable states A and B of photoreceptor photocycle. Data were collected using two different devices, i.e. a microspectrophotometer and a digital microscope. Our results show that the photocycle and the absorption spectra of the photoreceptor possess strong spectroscopic similarities with a rhodopsin-like protein. Moreover, the analysis of the absorption spectra of the two stable states of the photoreceptor and the absorption spectrum of the eyespot suggests an intriguing hypothesis for the orientation of microalgae toward light.     

Stability of the Front of Filtration Combustion of Bidisperse Fuel Mixture in an Inclined Rotating Gas Generator

To characterize the stability of the filtration combustion (FC) front, a dimensionless coefficient that describes the spatial distortions of the combustion front and is equal to the ratio between the maximum and minimum front width is suggested. It was shown for the example of bidisperse fuel mixtures of hard coal that, with an inclined rotating reactor, the gasification process can be stabilized as compared with the vertical reactor. A stable combustion front was observed at any content of the fine fraction in experiments of gasification of a fuel composed of 5–7- and 3–5-mm fractions. A stable combustion front was observed in experiments with a fine (1–2 mm) fraction up to its content of 60%.     

Monitoring i-motif transitions through the exciplex emission of a fluorescent probe incorporating two (Py)A units

Pairs of pyrene-modified deoxyadenosine ((Py)A) units induce a stable interstrand i-motif structure, which can be characterized by a change in the fluorescence λ(max), with an exciplex emission that is not observable in its single-strand structure.     

A Kinetically Stabilized Nitrogen-Doped Triangulene Cation: Stable and NIR Fluorescent Diradical Cation with Triplet Ground State

A kinetically-stabilized nitrogen-doped triangulene cation derivative has been synthesized and isolated as the stable diradical with a triplet ground state that exhibits near-infrared emission. As was the case for a triangulene derivative we previously synthesized, the triplet ground state with a large singlet-triplet energy gap was experimentally confirmed by magnetic measurements. In contrast to the triangulene derivative, the nitrogen-doped triangulene cation derivative is highly stable even in solution under air and exhibits near-infrared absorption and emission because the alternancy symmetry of triangulene is broken by the nitrogen cation. Breaking the alternancy symmetry of triplet alternant hydrocarbon diradicals by a nitrogen cation would therefore be an effective strategy to create stable diradicals possessing magnetic properties similar to the parent hydrocarbons but with different electrochemical and photophysical properties.     

Deracemization in a Complex Quaternary System with a Second-Order Asymmetric Transformation by Using Phase Diagram Studies

A productive deracemization process based on a quaternary phase diagram study of a naphthamide derivative is reported. New racemic compounds of an atropisomeric naphthamide derivative have been discovered, and a quaternary phase diagram has been constructed that indicated that four solids are stable in a methanol/H₂O solution. Based on the results of a heterogeneous equilibria study showing the stable domain of the conglomerate, a second-order asymmetric transformation was achieved with up to 97 % ee. Furthermore, this methodology showcases the chiral separation of a stable racemic compound forming system and does not suffer from any of the typical limitations of deracemization, although application is still limited to conglomerate-forming systems. We anticipate that this present study will serve as a fundamental model for the design of sophisticated chiral separation processes.     

Synthesis and Reactivity of a CAAC–Aminoborylene Adduct: A Hetero‐Allene or an Organoboron Isoelectronic with Singlet Carbenes

A one‐electron reduction of a cyclic (alkyl)(amino)carbene (CAAC)–bis(trimethylsilyl)aminodichloroborane adduct leads to a stable aminoboryl radical. A second one‐electron reduction gives rise to a CAAC–aminoborylene adduct, which features an allenic structure. However, in manner similar to that of stable electrophilic singlet carbenes, this compound activates small molecules, such as CO and H₂.     

UV and thermally stable polystyrene‐MWCNT superhydrophobic coatings

A facile method for ultraviolet (UV) and thermally stable polystyrene‐multiwalled carbon nanotubes (PS‐MWCNT) superhydrophobic coatings was demonstrated by a simple spray coating method. The superhydrophobicity was understood by an increase in micro/nano roughness with the addition of MWCNTs. Surface morphology of the coatings showed protrusion like structure. The wetting behavior of the coatings was studied as a function of temperature, and it is observed that the coatings were superhydrophobically stable up to 250 °C. A transformation of superhydrophobic to superhydrophilic state is achieved at 300 °C. The coatings remained superhydrophobically stable when it was subjected to UV‐irradiation and water immersion of 50 h. Thermogravimetric analysis showed a small shift (10°) towards higher temperature region with an addition of MWCNTs, suggesting the presence of weak interactions between PS and MWCNT, which is also supported by Fourier transform infrared spectroscopy, Raman and X‐ray photoelectron spectroscopy studies. Both hydrophilic and superhydrophobic coatings find potential applications in our daily life. Copyright © 2016 John Wiley & Sons, Ltd.     

Novel structures of a smectic C* phase with high spontaneous polarization in free-standing films

New stable structures of the liquid crystalline smectic C* phase are observed in free standing films of a material with high spontaneous polarization. A stable configuration of thick films is a stripe of state with an in-plane rotation of the director. In ultra-thin films an anisotropic state was observed. The director fields of the observed structures are modelled and compared with theoretical predictions.     

Pb12 2-: plumbaspherene

Although Si or Ge is not known to form empty cage clusters such as the fullerenes, we recently found a unique 12-atom icosahedral tin cluster, Sn12 2- (stannaspherene). Here we report photoelectron spectroscopy and theoretical evidence that Pb12 2- is also a highly stable icosahedral cage cluster and bonded by four delocalized radial pi bonds and nine delocalized on-sphere sigma bonds from the 6p orbitals of the Pb atoms. Following Sn12 2-, we coin a name, plumbaspherene, for the highly stable and nearly spherical Pb12 2- cluster, which is expected to be stable in solution and the solid state. Plumbaspherene has a diameter of approximately 6.3 A with an empty interior volume large enough to host most transition metal atoms, affording a new class of endohedral clusters.     

Hydrogen-bonded PTCDA-melamine networks and mixed phases

A stable hydrogen-bonding junction is formed between 3,4,9,10-perylene-3,4,9,10-tetracarboxylic-dianhydride (PTCDA) and 1,3,5-triazine-2,4,6-triamine (melamine). This bimolecular system was studied on the Ag-Si(111) square root 3 x square root R 30 degrees surface at sub-monolayer coverage, and two distinct phases are observed. A hexagonal lattice is formed that is stabilized by hydrogen bonding between PTCDA and melamine. This phase, in which melamine acts as a 3-fold vertex, is a close analogue to the 3,4,9,10-perylene-3,4,9,10-tetracarboxylic-diimide-melamine network reported recently. To our knowledge this hydrogen-bonding junction has not been previously observed and might not be expected due to lone pair repulsion. However we confirm that this combination is stable using ab initio methods. In the second intermixed phase parallel rows of PTCDA molecules coexist with an array of melamine molecules, and we propose a model for this structure.     

Quantitative prediction of biodegradability,metabolite distribution and toxicity of stable metabolites

An evaluation of the capability of organic chemicals to mineralize is an important factor to consider when assessing their fate in the environment. Microbial degradation can convert a toxic chemical into an innocuous one, and vice versa, or alter the toxicity of a chemical. Moreover, primary biodegradation can convert chemicals into stable products that can be difficult to mineralize. In this paper, we present some new results obtained on the basis of a recently developed probabilistic approach to modeling biodegradation based on microbial transformation pathways. The metabolic transformations and their hierarchy were calibrated by making use of the ready biodegradability data from the MITI-I test and expert knowledge for the most probable transformation pathways. A model was developed and integrated into an expert software system named CATABOL that is able to predict the probability of biodegradation of organic chemicals directly from their structure. CATABOL simulates the effects of microbial enzyme systems, generates the most plausible transformation pathways, and quantitatively predicts the persistence and toxicity of the biodegradation products. A subset of 300 organic chemicals were selected from Canada's Domestic Substances List and subjected to CATABOL to compare predicted properties of the parent chemicals with their respective first stable metabolite. The results show that most of the stable metabolites have a lower acute toxicity to fish and a lower bioaccumulation potential compared to the parent chemicals. In contrast, the metabolites appear to be generally more estrogenic than the parent chemicals.