Ion atmosphere relaxation and percolative electron transfer in Co bipyridine DNA molten salts

Polypyridyl complexes of Co decorated with 350-Da polyether chains (Co(350)(2+)) form molten phases of nucleic acids when paired with DNA counterions (Co(350)DNA) or 25-mer oligonucleotides. Analysis of voltammetry and chronoamperometry of mixtures of these phases with complexes having ClO(4)(-) counterions (Co(350)(ClO(4))(2)) and no other diluent provides charge transport rates from the oxidation and reduction currents for the complexes. As the mole fraction of the Co(350)(ClO(4))(2) complex in the mixture is varied from ca. 0.25 to 1, the physical diffusion constants derived from the Co(III/II) wave increase from 1 x 10(-11) cm(2)/s to 5 x 10(-10) cm(2)/s, and apparent diffusion constants dominated by the Co(II/I) electron self-exchange increase from 1 x 10(-10) cm(2)/s to 2 x 10(-8) cm(2)/s. Pure Co(350)DNA melts, containing no Co(350)(ClO(4))(2) complex, do not exhibit recognizable voltammetric waves; DNA suppresses the Co(II/I) electron transfer reactions of Co complexes for which it is the counterion. There are therefore two microscopically distinct kinds of Co(350) complexes, those with DNA and those with ClO(4)(-) counterions, with respect to their Co(II/I) electron-transfer dynamics, leading to percolative behavior in their mixtures. The electron-transfer rates of the Co(II/I) couple are controlled by the diffusive relaxation of the ionic atmosphere around the reaction pair, and the inactivity of the bound Co complexes can be attributed to the very low mobility of the anionic phosphate groups in the DNA counterion. Substitution of sulfonated polystyrene for DNA produced similar results, suggesting that this phenomenon is general to other polymer counterions of low mobility. We conclude that the measured Co(II/I) charge transport and electron-transfer rate constants reflect more the diffusive mobility of the perchlorate counterion than the intrinsic Co(II/I) electron hopping rate.     

Synthesis of PbTiO3 ceramics using mechanical alloying and solid state sintering

The pressure-less sintering behavior of PbTiO₃ powders synthesized by mechanical alloying TiO₂ and PbO was investigated using dilatometry and Rietveld refinements of X-ray diffraction patterns. As-synthesized, the powders are nanocrystalline with a mean particle size of 20 nm. Pressure-less sintering in the range 500-1050°C gives single phase ceramics with densities of 85-90% and crystallite sizes in the range 80-400 nm. Cracking due to the paraelectric-ferroelectric phase transition was not observed in samples sintered below 700°C due to the small crystallite size whereas macroscopic cracks formed in samples sintered above 700°C. Rietveld analysis indicates the formation of Pb vacancies in samples sintered and held for 24 h at intermediate temperatures (600-1000°C) which gives some insight into the mechanism of Pb loss and second phase formation in this system.     

Phosphorus-based SAHA analogues as histone deacetylase inhibitors

[structure: see text] Three analogues of suberoyl anilide hydroxamic acid (SAHA) with phosphorus metal-chelating functionalities were synthesized as inhibitors of histone deacetylases (HDACs). The compounds showed weak activity for HeLa nuclear extracts (IC(50) = 0.57-6.1 mM), HDAC8 (IC(50) = 0.28-0.41 mM), and histone-deacetylase-like protein (HDLP, IC(50) = 0.33-1.9 mM), suggesting that the transition state of HDAC is not analogous to zinc proteases. Antiproliferative activity against A2780 cancer cells (IC(50) = 0.11-0.12 mM), comparable to SAHA (0.15 mM), was observed.     

On the effect of covalently appended quinolones on termini of DNA duplexes

Quinolones are gyrase inhibitors that are widely used as antibiotics in the clinic. When covalently attached to oligonucleotides as 5'-acylamido substituents, quinolones were found to stabilize duplexes of oligonucleotides against thermal denaturation. For short duplexes, such as qu-T*GCGCA, where qu is a quinolone residue and T is a 5'-amino-5'-deoxythymidine residue, an increase in the UV melting point of up to 27.8 degrees C was measured. The stabilizing effect was demonstrated for all quinolones tested, namely nalidixic acid, oxolinic acid, pipemidic acid, cinoxacin, norfloxacin, and ofloxacin. The three-dimensional structure of (oa-T*GCGCA)2, where oa is an oxolinic acid residue, was solved by two-dimensional NMR spectroscopy and restrained molecular dynamics. In this complex, the oxolinic acid residues disrupt the terminal T1:A6 base pairs and stack on the G2:C5 base pairs. The displaced adenosine residues bind in the minor groove of the core duplex, while the thymidine residues pack against the oxolinic acid residues. The "molecular cap" thus formed fits tightly on the G:C base pairs, resulting in increased base-pairing fidelity, as demonstrated in UV melting experiments with the sequence oa-T*GGTTGAC and target strands containing a mismatched nucleobase. The structure of the "molecular cap" with its disrupted terminal base pair may also be helpful for modeling how quinolones block re-ligation of DNA strands in the active site of gyrases.     

Tertiary contact formation in alpha-synuclein probed by electron transfer

To explore tertiary contact formation in alpha-synuclein, a natively unfolded protein implicated in Parkinson's disease, we have measured the rates of reaction between a powerful electron donor, the tryptophan (W) triplet excited state, and an acceptor, 3-nitro-tyrosine (Y(NO2)) in six different variants, probing loop sizes between 15 and 132 residues. Electron transfer rates decrease with loop size with the fastest contact time of 140 ns for the N-terminal pair and the slowest of 1.2 mus for the N- to C-terminal pair. Diffusion coefficients ranging from approximately 2 x 10-6 to approximately 10-5 cm2 s-1 were extracted from simultaneous fits of the W to Y(NO2) electron (triplet excited state) and energy transfer (singlet excited state) kinetics.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

The interaction of water and dibromine in the gas phase: an investigation of the complex H(2)O...Br(2) by rotational spectroscopy and ab initio calculations

The ground-state rotational spectra of eight isotopomers of a complex formed by water and dibromine in the gas phase were observed by pulsed-jet, Fourier transform microwave spectroscopy. The spectroscopic constants B(0), C(0), delta(J), delta(JK), chi(aa)(Br(x)) (x=i for inner, o for outer), [chi(bb)(Br(x))-chi(cc)(Br(x))] and M(bb)(Br(x)) were determined for H(2)O...(79)Br(79)Br, H(2)O...(81)Br(79)Br, H(2)O...(79)Br(81)Br, H(2)O...(81)Br(81)Br, D(2)O...(79)Br(81)Br and D(2)O...(81)Br(81)Br. For the isotopomers HDO...(79)Br(81)Br and HDO...(81)Br(81)Br, only (B(0) + C(0))/2, delta(J), the chi(aa)(Br(x)) and M(bb)(Br(x)) were determinable. The spectroscopic constants were interpreted on the basis of several models of the complex to give information about its geometry, binding strength and the extent of electronic rearrangement on complex formation. The molecule H(2)O...Br(2) has C(s) symmetry with a pyramidal configuration at O. The zero-point effective quantities r(O...Br(i))=2.8506(1) A and phi(0)=46.8(1), where phi is the angle between the C(2) axis of H(2)O and the O...Br-Br internuclear axis, were obtained under the assumption of monomer geometries unchanged by complexation. Ab initio calculations, carried out at the aug-cc-pVDZ/MP2 level of theory, gave the equilibrium values r(e)(O...Br(i))=2.7908 A and phi(e)=45.7 degrees and confirmed the collinearity of the O...Br-Br nuclei. The potential energy function V(phi), also determined ab initio, showed that the wavenumber required for inversion of the configuration at O in the zero-point state is only 9 cm(-1). By interpreting the Br nuclear quadrupole coupling constants, the fractions delta(O-->Br(i))=0.004(5) and delta (Br(i)-->Br(o))=0.050(2) of an electron were determined to be transferred from O to Br(i) and Br(i) to Br(o), respectively, when the complex is formed. The complex is relatively weak, as indicated by the small value k(sigma)=9.8(2) N m(-1) of the intermolecular stretching force constant obtained from delta(J). A comparison of the properties, similarly determined, of H(2)O...F(2), H(2)O...Cl(2), H(2)O...Br(2), H(2)O...BrCl, H(2)O...ClF and H(2)O...ICl is presented.     

Pseudooctahedral complexes of vanadium(III): electronic structure investigation by magnetic and electronic spectroscopy

A variety of physical methods has been used to probe the non-Kramers, S = 1, V(III) ion in two types of pseudooctahedral complexes: V(acac)(3), where acac = anion of 2,4-pentanedione, and VX(3)(thf)(3), where thf = tetrahydrofuran and X = Cl and Br. These methods include tunable frequency and high-field electron paramagnetic resonance (HFEPR) spectroscopy (using frequencies of approximately 95-700 GHz and fields up to 25 T) in conjunction with electronic absorption, magnetic circular dichroism (MCD), and variable-temperature variable-field MCD (VTVH-MCD) spectroscopies. Variable-temperature magnetic susceptibility and field-dependent magnetization measurements were also performed. All measurements were conducted on complexes in the solid state (powder or mull samples). The field versus sub-THz wave quantum energy dependence of observed HFEPR resonances yielded the following spin Hamiltonian parameters for V(acac)(3): D = +7.470(1) cm(-1); E = +1.916(1) cm(-1); g(x) = 1.833(4); g(y) = 1.72(2); g(z) = 2.03(2). For VCl(3)(thf)(3), HFEPR detected a single zero-field transition at 15.8 cm(-1) (474 GHz), which was insufficient to determine the complete set of spin Hamiltonian parameters. For VBr(3)(thf)(3), however, a particularly rich data set was obtained using tunable-frequency HFEPR, and analysis of this data set gave the folowing: D = -16.162(6) cm(-1); E = -3.694(4) cm(-1); g(x) = 1.86(1); g(y) = 1.90(1); g(z) = 1.710(4). Analysis of the VTVH-MCD data gave spin Hamiltonian parameters in good agreement with those determined by HFEPR for both V(acac)(3) and VBr(3)(thf)(3) and in rough agreement with the estimate for VCl(3)(thf)(3) (D approximately 10 cm(-1), |E/D| approximately 0.18), together with the finding that the value of D is negative for both thf complexes. The electronic structures of these V(III) complexes are discussed in terms of their molecular structures and the electronic transitions observed by electronic absorption and MCD spectroscopies.     

Superexcited state reconstruction of HCl using photoelectron and photoion imaging

The velocity-map imaging technique was used to record photoelectron and photofragment ion images of HCl following two-photon excitation of the E Sigma(+)(0+), V 1Sigma(+)(0+) (nu=9,10,11) states and subsequent ionization. The images allowed us to determine the branching ratios between autoionization and dissociation channels for the different intermediate states. These branching ratios can be explained on the basis of intermediate state electron configurations, since the configuration largely prohibits direct ionization in a one-electron process, and competition between autoionization and dissociation into H* (n=2)+Cl and H+Cl*(4s,4p,3d) is observed. From a fit to the vibrationally resolved photoelectron spectrum of HCl+ it is apparent that a single superexcited state acts as a gateway to autoionization and dissociation into H+Cl*(4s). Potential reconstruction of the superexcited state to autoionization was undertaken and from a comparison of different autoionization models it appears most likely that the gateway state is a purely repulsive and low-n Rydberg state with a (4Pi) ion core.