Quantitative characterization of DNA films by X-ray photoelectron spectroscopy

We describe the use of self-assembled films of thiolated (dT)25 single-stranded DNA (ssDNA) on gold as a model system for quantitative characterization of DNA films by X-ray photoelectron spectroscopy (XPS). We evaluate the applicability of a uniform and homogeneous overlayer-substrate model for data analysis, examine model parameters used to describe DNA films (e.g., density and electron attenuation length), and validate the results. The model is used to obtain quantitative composition and coverage information as a function of immobilization time. We find that when the electron attenuation effects are properly included in the XPS data analysis, excellent agreement is obtained with Fourier transform infrared (FTIR) measurements for relative values of the DNA coverage, and the calculated absolute coverage is consistent with a previous radiolabeling study. Based on the effectiveness of the analysis procedure for model (dT)25 ssDNA films, it should be generally valid for direct quantitative comparison of DNA films prepared under widely varying conditions.     

Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA

The ratio of deoxyguanosine and thymidine can be determined in a complex mixture containing the major ribonucleosides and deoxynucleosides, the minor deoxynucleosides, and the nucleotide monophosphates by high-performance liquid chromatography. The isocratic procedure utilizes a C18 column and a solvent of methanol-triethylamine phosphate (pH 5.1). A single analysis requires 15 min. Within the range of 0.5-1.5 micrograms of total deoxynucleosides per sample, the determination is very precise and the relative standard deviation is about 0.1%. From the deoxyguanosine/thymidine ratio, a precise determination of the mole percentage guanine + cytosine of double-stranded DNA is calculated.     

Determination of Phase Stability of Elemental Boron

Boron is an important element, used in applications from superhard materials to superconductors. Boron exists in several forms (allotropes) and, surprisingly, it was not known which form (α or β) is stable at ambient conditions. Through experiment, we quantify the relative stability of α‐boron and β‐boron as a function of temperature. The ground‐state energies of α‐boron and β‐boron are nearly identical. For all temperatures up to 2000 K, the complicated β‐boron structure is more stable than the simpler α‐boron structure at ambient pressure. Below 1000 K, β‐boron is entropically stabilized with respect to α‐boron owing to its partially occupied sites, whereas at higher temperatures β‐boron is enthalpically stabilized with respect to α‐boron. We show that α‐boron only becomes stable on application of pressure.     

Pulse propagation of acoustic waves scattered in a three-dimensional channel

Abstract

In a previous paper (Whitman et al 1999 Waves Random Media 9 1–11) we discussed the scattering of acoustic waves by random sound-speed fluctuations in a two-dimensional channel and presented an asymptotic form for an acoustic pulse propagating in the channel. Here we include the three-dimensional effect of transverse scattering. We find an asymptotic solution in which initially the two-dimensional mode-transfer effect is more important than the transverse scattering effect. However, for large enough propagation distances the transverse scattering effect dominates the pulse spread. In this paper we shall show the form of the pulse shape in both propagation ranges as well as in the transition regime. We shall begin with a discussion of the physics of the problem and then present a mathematical discussion.     

MO-SCF calculations for B2O3

The results of ab-initio molecular self-consistent field calculations with atomic optimized Gaussian bases are reported for the B₂O₃ molecule. These distinguish between several plausible structures and yield a V-shaped structure as the minimum energy geometry.This work was supported by the National Science Foundation program of Research Participation for College Teachers, Grant No. GY-5404, and by the Air Force Office of Scientific Research, Grant No. AFOSR-68-1438.     

Novel use of doublet peaks in flow injection analysis : Simultaneous Spectrophotometric Determination of Nickel(II) and Iron(II)

A simple, non-separation method for the simultaneous, single-injection determination of nickel(II) and iron(II) is described. The method is based on doublet peaks in a single-line system, with multiple vertical (absorbance) measurements of the doublet peak profile. Doublet peaks occur when the center of the sample zone remains unmixed. Nickel(II), 0.17–0.24 M, in the presence of 2.7–5.4 mM iron(II) is determined by direct spectrophotometry of the nickel(II) ion at the center of the sample zone, Iron(II) is first oxidized on-line by peroxodisulfate to iron(III), which complexes with thiocyanate to form the intensely red complex; this is measured at the peak maximum corresponding to the trailing edge of the sample zone. Correction are made for absorbance of nickel and its reduction in the iron thiocyanate complex formation. The absorbance of nickel(II) ion and the iron thiocyanate complex are both measured at 395 nm from a single injected sample. The general utility of the doublet peak method is discussed.     

The hydratase activity of malonate semialdehyde decarboxylase: mechanistic and evolutionary implications

Malonate semialdehyde decarboxylase (MSAD) is a member of the tautomerase superfamily, a group of structurally homologous proteins that have a characteristic beta-alpha-beta-fold and a catalytic amino-terminal proline. In addition to its physiological decarboxylase activity, the conversion of malonate semialdehyde to acetaldehyde and carbon dioxide, the enzyme has now been found to display a promiscuous hydratase activity, converting 2-oxo-3-pentynoate to acetopyruvate, with a kcat/Km value of 6.0 x 102 M-1 s-1. Pro-1 and Arg-75 are critical for both activities, and the pKa of Pro-1 was determined to be approximately 9.2 by a direct 15N NMR titration. These observations implicate a decarboxylation mechanism in which Pro-1 polarizes the carbonyl oxygen of substrate by hydrogen bonding and/or an electrostatic interaction. Arg-75 may position the carboxylate group into a favorable orientation for decarboxylation. Both the hydratase activity and the pKa value of Pro-1 are shared with trans-3-chloroacrylic acid dehalogenase, another tautomerase superfamily member that precedes MSAD in a bacterial degradation pathway for trans-1,3-dichloropropene. Hence, MSAD and CaaD could have evolved by divergent evolution from a common ancestral protein, retaining the necessary catalytic components for the conjugate addition of water.