SEDIMENTATION ANALYSIS OF DNA PHOTOOXIDIZED IN THE PRESENCE OF THIOPYRONINE

Abstract. Illumination of single-stranded φ×174 phage DNA with visible lightλ > 500 nm) in the presence of the sensitizer thiopyronine results in both chain scissions detectable by velocity sedimentation in neutral medium and in alkali-labile bonds which yield secondary strand breaks after alkaline treatment. Compared with the generation of primary strand breaks, the formation of alkali-labile sites seems to be the predominant reaction.
Photodynamic treatment of homogeneous double-stranded Ta, phage DNA leads to changes in the overall conformation of DNA as revealed by an initial increase of the sedimentation coefficient. The simultaneous occurrence of different effects (decrease of molecular weight, increase of effective DNA flexibility) is particularly evident from changes in the sedimentation coefficient distribution. The fact that both processes influence the sedimentation behaviour questions the common procedure of calculating double-strand break numbers from sedimentation coefficient distributions on the basis of s#-M relations which are valid for intact DNA only.
Photooxidized double-stranded DNA exhibits an increased sensitivity against shear forces.     

Low-temperature vibrational spectra of cis-dichloro-(meso-2,3-diaminobutane)palladium(II) and platinum(II)

IR and Raman spectra of MCl₂(meso-2,3-diaminobutane), (M = Pd, Pt), have been recorded down to liquid nitrogen temperature or lower. It is shown that correlation coupling occurs between closely spaced hydrogen-bonded pairs of molecules, which form a “super molecule,” but not between all eight molecules in the unit cell. The lattice mode region is also understood in outline on the basis of motions of the “super molecules” Methyl torsional modes appear to be near 140 cm^?1.     

Fast, generic gradient high performance liquid chromatography coupled to fourier transform ion cyclotron resonance mass spectrometry for the accurate mass analysis of mixtures

Fast gradient high performance liquid chromatography (HPLC) has been combined with a commercially available Fourier transform ion cyclotron resonance (FTICR) mass spectrometer for the routine and high performance analysis of mixtures. With this combination we were able to separate and detect, under high mass accuracy conditions, a six-component drug mixture in less than 5 minutes. The fast gradients described are now possible due to the development of mechanically robust, ultra pure silica packing materials, which allow relatively high flow rates (ca. 1 mL/min for a 2 mm diameter column). For the six compounds present in the model mixture, relative mass errors of less than 1 ppm were obtained (based on an external calibration) providing sufficient mass accuracy to make unequivocal assignments of empirical formulae. Preliminary results of fast gradient HPLC/FTICR-MS/MS are also shown for the same six-component mixture. Copyright 2000 John Wiley & Sons, Ltd.     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.     

Gear effect—10 : Conformational aspects of the positive or negative buttressing effects of methyl groups: polymethylpyridines

The effect of the shape of a methyl group on reactivity, which cannot be accounted for by considering a methyl group as a spherical substituent with the appropriate van der Waals radius, was considered in kinetics of alkylalion of substituted pyridines and barriers to rotation and ground state conformations of an isopropyl group attached to a planar framework. The perturbation of a methyl group by an o-methyl group is accounted for by a unique conformational explanation which involves the polyhedral shape of the methyl group.     

Plutonium(IV) mononitrate and dinitrate complex formation in acid solutions as a function of ionic strength

Titrations of Pu(IV) with HNO₃ in a series of aqueous HClO₄ solutions ranging in ionic strength from 2 to 19 molal were followed using visible and near-infrared absorption spectrophotometry. The Pu 5f-5f spectra in the visible and near IR range change with complex formation. At each ionic strength, a series of spectra were obtained by varying nitrate concentration. Each series was deconvoluted into spectra of Pu⁴⁺ (aq), Pu(NO₃)³⁻ and Pu(NO₃)₂ ²⁺ complexes, and simultaneously their formation constants were determined. When corrected for the incomplete dissociation of nitric acid, the ionic strength dependence of each formation constant can be described by two parameters, β⁰ and Δε using the formulae of specific ion interaction theory.     

Relevance of electrokinetic theory for "soft" particles to bacterial cells: implications for bacterial adhesion

Bacterial cells and other biological particles carry charged macromolecules on their surface that form a "soft" ion-permeable layer. In this paper, we test the applicability of an electrokinetic theory for soft particles to characterize the electrophoretic mobility (EPM) and adhesion kinetics of bacterial cells. The theory allows the calculation of two parameters--the electrophoretic softness and the fixed charged density--that define the characteristics of the polyelectrolyte layer at the soft particle surface. The theory also allows the calculation of an outer-surface potential that may better predict the electrostatic interaction of soft particles with solid surfaces. To verify its relevance for bacterial cells, the theory was applied to EPM measurements of two well-characterized Escherichia coli K12 mutants having lipopolysaccharide (LPS) layers of different lengths and molecular compositions. Results showed that the obtained softness and fixed charge density were not directly related to the known characteristics of the LPS of the selected strains. Interaction energy profiles calculated from Derjaguin-Landau-Verwey-Overbeek (DLVO) theory were used to interpret bacterial deposition (adhesion) rates on a pure quartz surface. The outer surface potential failed to predict the low attachment efficiencies of the two bacterial strains. The lack of success in the application of the theory for soft particles to bacterial cells is attributed to chemical and physical heterogeneities of the polyelectrolyte layer at the cell surface.     

Aggregate restructuring by polymer solvency effects

This study investigates the aggregation in cyclohexane of silica particles initially stabilized by grafted polystyrene and destabilized by temperature reduction. It complements an earlier study by Zhu and Napper (P.W. Zhu, D.H. Napper, Phys. Rev. E 50 (1994) 1360) in which the aggregation of polystyrene latex particles with tethered poly(N-isopropyl acrylamide) (PNIPAM) in water was investigated. Their dynamic light scattering results showed that both the rate of aggregation and the aggregate fractal dimension increased with a sufficient decrease in the PNIPAM adlayer solvency, achieved by means of either salt (NaNO3) addition or temperature rise. This result stands in contrast to those obtained when an electrostatically stabilized colloid is destabilized, i.e., that the more rapidly aggregates are formed, the lower the resulting fractal dimension. The authors explained their results in terms of the effects of both salt effects and increased temperature on the extent of the hydrophobic interactions between the adlayer-covered surfaces in the water. The present study examines a sterically-stabilized colloid in a nonaqueous solvent, where neither salt effects nor hydrophobic effects play a role. Temperature is decreased to bring the system from better-than-theta-conditions to worse-than-theta-conditions. Power-law aggregation kinetics are observed at 15.7 degrees C by dynamic light scattering. The particles first undergo reduced rate aggregation, producing low-fractal-dimension aggregates, which after some time, restructure into more compact aged clusters. The fractal dimension of these aged clusters increases with increasing initial aggregation rate, consistent with results seen by Zhu and Napper, but without the presence of hydrophobic effects. The ability of the polymer-grafted particles to rearrange suggests aggregation into a secondary minimum, with the ability to slide over one another to achieve a more energetically favorable, denser configuration. The reversible nature of the aggregation is verified by additional experiments gradually bringing the system from worse-than-theta-conditions back to better-than-theta-conditions, with an attendant decrease in aggregate fractal dimension, and ultimately full redispersion.