PNA/dsDNA complexes: site specific binding and dsDNA biosensor applications

The ability of peptide nucleic acids (PNA) to form specific higher-order (i.e., three- and four-stranded) complexes with DNA makes it an ideal structural probe for designing strand-specific dsDNA biosensors. Higher-order complexes are formed between a dye-labeled charge-neutral PNA probe and complementary dsDNA. Addition of a light-harvesting cationic conjugated polymer (CCP) yields supramolecular structures held together by electrostatic forces that incorporate the CCP and the dye-labeled PNA/DNA complexes. Optimization of optical properties allows for excitation of the CCP and subsequent fluorescence resonance energy transfer (FRET) to the PNA-bound dye. In the case of noncomplementary dsDNA, complexation between the probe and target does not occur, and dye emission is weak. The binding between PNA and noncomplementary and complementary dsDNA was examined by several methods. Gel electrophoresis confirms specificity of binding and the formation of higher-order complexes. Nano-electrospray mass spectrometry gives insight into the stoichiometric composition, including PNA/DNA, PNA(2)/DNA, PNA/DNA(2), and PNA(2)/DNA(2) complexes. Finally, structural characteristics and binding-site specificity were examined using ion mobility mass spectrometry in conjunction with molecular dynamics. These results give possible conformations for each of the higher-order complexes formed and show exclusive binding of PNA to the complementary stretch of DNA for all PNA/DNA complexes. Overall, the capability and specificity of binding indicates that the CCP/PNA assay is a feasible detection method for dsDNA and eliminates the need for thermal denaturing steps typically required for DNA hybridization probe assays.     

Optimization of the molecular orbital energies of conjugated polymers for optical amplification of fluorescent sensors

Cationic water-soluble poly(fluorene-co-phenylene)s with electron withdrawing or donating substituents on the conjugated backbone were designed and synthesized. Fluorescence resonance energy transfer (FRET) experiments between these conjugated polymers and dye-labeled single-stranded DNA (ssDNA-C*) reveal the importance of matching donor and acceptor orbital energy levels to improve the sensitization of C* emission. Quenching of polymer fluorescence with ssDNA-C* and differences in C* emission suggest involvement of photoinduced charge transfer (PCT) as an energy wasting mechanism. The HOMO and LUMO energy levels of the conjugated polymers and C serve as a preliminary basis to understand the competition between FRET and PCT. Dilution of C in polymer/ssDNA-C complexes by addition of ssDNA yields insight into C*...C self-quenching. Under optimized conditions, where there is no probe self-quenching and minimum PCT, efficient signal amplification is demonstrated despite poor spectral overlap between polymer and C.     

Working group report: Heavy-ion physics and quark-gluon plasma

This is the report of Heavy Ion Physics and Quark-Gluon Plasma at WHEPP-09 which was part of Working Group-4. Discussion and work on some aspects of quark-gluon plasma believed to have created in heavy-ion collisions and in early Universe are reported.     

Fullerene-carbene Lewis acid-base adducts

The reaction between a bulky N-heterocylic carbene (NHC) and C(60) leads to the formation of a thermally stable zwitterionic Lewis acid-base adduct that is connected via a C-C single bond. Low-energy absorption bands with weak oscillator strengths similar to those of n-doped fullerenes were observed for the product, consistent with a net transfer of electron density to the C(60) core. Corroborating information was obtained using UV photoelectron spectroscopy, which revealed that the adduct has an ionization potential ～1.5 eV lower than that of C(60). Density functional theory calculations showed that the C-C bond is polarized, with a total charge of +0.84e located on the NHC framework and -0.84e delocalized on the C(60) cage. The combination of reactivity, characterization, and theoretical studies demonstrates that fullerenes can behave as Lewis acids that react with C-based Lewis bases and that the overall process describes n-doping via C-C bond formation.     

Adsorption equilibria of O<Subscript>2</Subscript>, Ar,Kr and Xe on activated carbon and zeolites: single component and mixture data

This work provides a set of experimental data on the adsorption of pure component, binary and ternary mixtures on activated carbon sample and two different zeolites at 303 K and moderate pressures (up to 10 bar for mixtures). Pure component data were measured by gravimetry and mixture data by volumetry coupled with chromatography. Results encourage more research on new materials and enhancement of adsorption-based separation processes with the proposed target.     

Pseudo-tetrablock copolymers with ethylene and a functionalized comonomer

Pseudo-tetrablock copolymers comprised of ethylene and 5-norbomen-2-yl acetate (1), were synthesized using the initiator system (L(i)Pr2)Ni(eta1-CH2Ph)(PMe3)(2)[(L(i)Pr2) = N-(2,6-diisopropylphenyl)-2-(2,6-diisopropylphenylimino)propanamide] and 2.5 equivalents of Ni(COD)2 [bis(1,5-cyclooctadiene) nickel.