Characterization of a single molecule DNA switch in free solution

We have studied a donor-acceptor fluorophore-labeled DNA switch where the acceptor is Alexa-647, a carbocyanine dye, in solution at the single molecule level to elucidate the fluorescence switching mechanism. The acceptor, which is in an initial high fluorescence trans state, undergoes a photoisomerization reaction resulting in two additional states during its sub-millisecond transit across the probe volume. These two states are assigned to a nonfluorescent triplet trans state that strongly quenches the donor emission and a singlet cis state that blocks the fluorescence resonance energy transfer (FRET) pathway and gives rise to donor-only fluorescence. The formation of these states is faster than the transit time, so that all three states are approximately equally populated under our experimental conditions. The acceptor dye can stick to the DNA in all these states, with the rate of unsticking determining the rate of isomerization into the other states. Measurement of the rate of change of the FRET signal therefore provides information about the fluorophore-DNA intramolecular dynamics. These results explain the large zero peak in the proximity ratio, often seen in single molecule FRET experiments, and suggest that photoinduced effects may be important in single molecule FRET experiments using carbocyanine dyes. They also suggest that for fast photoinduced switching the interactions of the acceptor dye with the DNA and other surfaces should be prevented.     

Reactivity of amino acids in nitrosation reactions and its relation to the alkylating potential of their products

Nitrosation reactions of amino acids with an -NH(2) group [namely, six alpha-amino acids (glycine, alanine, alpha-aminobutyric acid, alpha-aminoisobutyric acid, valine, and norvaline); two beta-amino acids (beta-alanine and beta-aminobutyric acid), and one gamma-amino acid (gamma-aminobutyric acid)] were studied. Nitrosation was carried out in aqueous acid media, mimicking the conditions of the stomach lumen. The rate equation was r = k(3)(exp)[amino acid][nitrite](2), with a maximum k(3)(exp) value in the 2.3-2.7 pH range. The existence of an isokinetic relationship supports the argument that all the reactions share a common mechanism. A nitrosation mechanism is proposed, and the following conclusions are drawn: (i) Nitrosation reactions of amino acids with a primary amino group in acid media occur with dinitrogen trioxide as the main nitrosating agent. The finding that the nitrosation rate is proportional to the square of the nitrite concentration suggests that the yield of nitrosation products in the stomach would increase sharply with higher nitrate/nitrite intakes. (ii) Stomach hypochlorhydria could be a potential enhancer of in vivo amino acid nitrosation. (iii) The reactivity (k(3)()(exp)) [alpha-amino acids > beta-amino acids > gamma-amino acids] is the same as that found in a previous work for the alkylating potential of lactones formed from nitrosation products of the same amino acids. This implies that the nitrosation reactions of the most common natural amino acids are the most efficient precursors of the most powerful alkylating agents. (iv) The order of magnitude (10(7)-10(8) M(-1) s(-1)) of the bimolecular rate constants of nitrosation shows that such reactions occur through an encounter process.     

Dendron rodcoils: synthesis of novel organic hybrid structures

Convergent and divergent syntheses of novel organic hybrid structures termed dendron rodcoils (DRC) containing dendritic, rodlike, and coillike segments are described. The aryl ester dendron masked with 32 trifluoromethyl groups is prepared via a convergent approach using 5-(tert-butyldimethylsiloxy)isophthalic acid as the monomer unit. The activation of the focal point of the dendron allows for successful coupling between the dendron and the diblock rodcoil molecules synthesized separately. In another example, the dendritic block is grown via divergent strategy from the terminus of rodcoil using 3,5-bis(tert-butyldimethylsiloxy)benzoic acid as an AB(2) monomer. A combination of catalyzed esterification reactions and silyl deprotection chemistry proved to be a very efficient method for construction of these nanosized structures with unusual molecular architecture. Both synthetic strategies allowed for the preparation of DRCs with nearly monodisperse dendritic blocks as demonstrated by NMR, MALDI-TOF, and GPC measurements.     

Toward fully synthetic carbohydrate-based HIV antigen design: on the critical role of bivalency

Synthetic gp120331-335 glycopeptide fragments carrying hybrid and high-mannose type N-linked glycans were evaluated for binding to broadly neutralizing antibody 2G12 using surface plasmon resonance technology. None of the hybrid-type constructs demonstrated binding to 2G12. In the high-mannose series, the "Cys dimer" construct, presenting two undecasaccharide glycans, showed significantly higher binding than the Cys-protected monomer. The binding of the dimeric structure was further investigated in competition with recombinant gp120. The data suggest that gp120 and its designed synthetic epitope construct bind to the same site on 2G12.     

The structural characteristics of organozinc complexes incorporating N,N'-bidentate ligands

Dimethylzinc reacts with an excess of N-2-pyridylaniline 6 to give the homoleptic species, Zn[PhN(2-C(5)H(4)N)](2) 8. Single crystal X-ray diffraction reveals a solid-state dimer based on an 8-membered (NCNZn)(2) core motif. Zn[CyN(2-C(5)H(4)N)]Me (Cy =c-C(6)H(11)) 10, prepared by the combination of ZnMe(2) with the corresponding cyclohexyl-substituted pyridylamine, is also dimeric in the solid state but reveals a central (ZnN)(2) metallacycle. Employment of (p-Tol)NH(2-C(5)H(4)N)(p-Tol = 4-MeC(6)H(4)) 11 yielded the tris(zinc) adduct Zn(3)[(p-Tol)N(2-C(5)H(4)N)](4)Me(2) 12, which incorporates a central chiral molecule of 'Zn[(p-Tol)N(2-C(5)H(4)N)](2)' 12a, that bridges two 'Zn[(p-Tol)N(2-C(5)H(4)N)]Me' 12b units. A similar trimetallic structure is noted when the pyridylaniline substrate 11 is replaced with the bicyclic guanidine 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine (hppH), affording Zn(3)(hpp)(4)Me(2) 13. Spectroscopic studies point to retention of the solid-state structure of in hydrocarbon solution. Reaction of 13 with dimesityl borinic acid, Mes(2)BOH (Mes = mesityl), affords Zn(3)(hpp)(4)(OBMes(2))(2) 14 in which the trimetallic core is retained. This reactivity is in contrast to the closely related reaction of dimeric Zn[Me(2)NC[N(i)Pr](2)]Me 15 with Mes(2)BOH, which yielded Zn[Me(2)NC[N(i)Pr](2)][OBMes(2)].Me(2)NC[N(i)Pr][NH(i)Pr] 16 as a result of protonation at the guanidine ligand in addition to the Zn-Me bond.     

MODs vs. NPs: Vying for the Future of Printed Electronics

This Minireview compares two distinct ink types, namely metal-organic decomposition (MOD) and nanoparticle (NP) formulations, for use in the printing of some of the most conductive elements: silver, copper and aluminium. Printing of highly conductive features has found purpose across a broad array of electronics and as processing times and temperatures reduce, the avenues of application expand to low-cost flexible substrates, materials for wearable devices and beyond. Printing techniques such as screen, aerosol jet and inkjet printing are scalable, solution-based processes that historically have employed NP formulations to achieve low resistivity coatings printed at high resolution. Since the turn of the century, the rise in MOD inks has vastly extended the range of potentially applicable compounds that can be printed, whilst simultaneously addressing shelf life and sintering issues. A brief introduction to the field and requirements of an ink will be presented followed by a detailed discussion of a wide array of synthetic routes to both MOD and NP inks. Unindustrialized materials will be discussed, with the challenges and outlook considered for the market leaders: silver and copper, in comparison with the emerging field of aluminium inks.     

Pressure‐Tuneable Visible‐Range Band Gap in the Ionic Spinel Tin Nitride

The application of pressure allows systematic tuning of the charge density of a material cleanly, that is, without changes to the chemical composition via dopants, and exploratory high‐pressure experiments can inform the design of bulk syntheses of materials that benefit from their properties under compression. The electronic and structural response of semiconducting tin nitride Sn₃N₄ under compression is now reported. A continuous opening of the optical band gap was observed from 1.3 eV to 3.0 eV over a range of 100 GPa, a 540 nm blue‐shift spanning the entire visible spectrum. The pressure‐mediated band gap opening is general to this material across numerous high‐density polymorphs, implicating the predominant ionic bonding in the material as the cause. The rate of decompression to ambient conditions permits access to recoverable metastable states with varying band gaps energies, opening the possibility of pressure‐tuneable electronic properties for future applications.     

Towards a Sustainable Synthesis of Oxymethylene Dimethyl Ether by Homogeneous Catalysis and Uptake of Molecular Formaldehyde

Oxymethylene dimethyl ethers (OME_n; CH₃(‐OCH₂‐)_nO‐CH₃, n=3–5) are a novel class of sustainable synthetic fuels, which are of increasing interest due to their soot‐free combustion. Herein a novel anhydrous OME_n synthesis route is presented. Catalyzed by trimethyloxonium salts, dimethoxymethane takes up monomeric gaseous formaldehyde instantaneously and forms high purity OME_n at temperatures of 25–30 °C. This new anhydrous approach using molecular formaldehyde and catalytic amounts of highly active trimethyloxonium salts represents a promising new step towards a sustainable formation of OME_n emanating from CO₂ and H₂.     

Influence of pH and microwave calcination on the morphology of KGd(WO<Subscript>4</Subscript>)<Subscript>2</Subscript> particles derived by Pechini Sol–Gel method

KGd(WO₄)₂ (KGW) particles were synthesized at 3.5, 5.5 and 7.5 pH values by Pechini polymeric complex sol–gel method using potassium nitrate, gadolinium nitrate, ammonium paratungstate, citric acid and ethylene glycol as starting materials. Deionized water was used as solvent. Polymeric precursor gel was formed with citric acid as complexing agent and ethylene glycol as binder. Synthesized gel was analyzed by FT-IR spectroscopy. Prepared precursor gels were further annealed using resistive and microwave processes at 550 and 700 °C, respectively. The properties of heat treated samples were characterized by powder XRD, FT-IR, Raman and SEM analysis to understand the crystallinity, organic liberation, tungstate ribbon formation and surface morphology, respectively. The phase formation and different phases of intermediate oxides in pre-fired samples were investigated by powder XRD. Organic liberation in the samples in relation to temperature, and the carbon content in the pre-fired powder was analyzed using FT-IR spectrum. Raman spectrum reveals the formation of tungsten ribbons as well as the quality of the samples. The morphological changes at different synthesis conditions were observed with SEM micrographs.