Segregation effects on the properties of (AuAg)147.

AuAg nanoclusters are promising supported co-catalysts for photocatalytic hydrogen reduction. However, beyond the quantum regime (N > 100) little is known about how the electronic properties of these nanoparticles are affected by chemical ordering. We investigate the effects of chemical ordering on the properties of 147-atom cuboctahedral AuAg nanoclusters, using empirical potentials coupled with an atomic-swap basin-hopping search to optimise the elemental distribution, with the lowest energy arrangements then reminimised using Density Functional Theory (DFT). Force-field calculations show Au atoms preferentially occupy sub-surface positions in the bimetallic structures, which results in the formation of a pseudo-onion structure for Ag-rich compositions. At the DFT-level, however, an Ag core surrounded by an Au shell (Ag@Au) is energetically favoured, as electron density can be drawn more readily when Au atoms are positioned on the nanocluster surface, thus resulting in a partial negative charge. Core@shell configurations are analogous to structures that can be chemically synthesised, and further detailed electronic analysis is discussed in the context of nanocluster applications to co-catalysed photocatalysis.

Optical and electronic properties of mixed Ag-Au tetramer cations.

We present experimental and theoretical studies of the optical response of mixed Ag(n)Au(+)(4-n) (n=1-3) clusters in the photon energy range ℏω = 1.9-3.5 eV. Absorption spectra are recorded by a newly built longitudinal molecular beam depletion spectroscopy apparatus providing lower limits to absolute photodissociation cross sections. The experimental data are compared to optical response calculations in the framework of long-range corrected time-dependent density functional theory with initial cluster geometries obtained by the unbiased Birmingham Cluster Genetic Algorithm coupled with density functional theory. Experiments and excited state calculations shed light on the structural and electronic properties of the mixed Ag-Au tetramer cations.

Discrimination between mammalian RNases H-1 and H-2.

The two principal RNases H in mammalian cells, H-1 and H-2, differ in their responses to sale, divalent metal, and sulfhydryl inhibition. Specific reaction conditions that provide unambiguous discrimination between RNases H-1 and H-2 with only two assays are described. The assays were used for identification in a new purification procedure for RNases H-1 and H-2.

Discontinuous DNA synthesis by purified mammalian proteins.

Five proteins purified from mouse cells acting together efficiently convert a single-stranded circular DNA template to covalently closed duplex circle by a discontinuous mechanism. DNA polymerase alpha/primase with the assistance of alpha accessory factor covers the single-stranded circle with RNA-primed DNA fragments. Primers are removed by a combination of RNase H-1 and a 5'-exonuclease that was identified by its ability to complete this in vitro system. The 5'-exonuclease is required to remove residual one or two ribonucleotides at the primer/DNA junction that are resistant to RNase H-1. Gap filling is by the DNA polymerase alpha/primase, and DNA ligase I converts the DNA fragments to continuous strand. The concerted action of the five proteins emulates synthesis of the staging strand at the replication fork.

The mechanism of action of an accessory protein for DNA polymerase alpha/primase.

A previous paper reported the purification (from mouse cell extracts) and some of the properties of a protein, alpha accessory factor (AAF), that specifically stimulates DNA polymerase alpha/primase (1). We describe here studies on the mechanism of action of AAF. In the presence of AAF and a large excess of single-stranded circular DNA template, a molecule of DNA polymerase alpha/primase interacts with a single template DNA molecule priming and synthesizing multiple short DNA fragments covering thousands of nucleotides without detaching from the template, and, by many-fold repetition of the process, accomplishes serial replication of the population of DNA molecules. In contrast, without AAF the reaction involves the whole population of DNA molecules in parallel and with a very large number of binding events between DNA polymerase alpha/primase and DNA [corrected] template. The profound [corrected] increase in affinity of DNA polymerase alpha/primase for the DNA template that characterizes the mechanism suggests a functional identification of AAF as a template affinity protein. The resulting greater efficiency accounts for the ability of AAF to stimulate both the primase and polymerase activities of DNA polymerase alpha/primase. AAF also increases the processivity of DNA polymerase alpha/primase from approximately 15 to approximately 115 nucleotides, a size similar to that of mammalian Okazaki fragments, and it appears to allow DNA polymerase alpha/primase to traverse double-stranded regions of a DNA template. These features of the mechanism of AAF suggest that it may have a role in assisting DNA polymerase alpha/primase in synthesis of the lagging strand of a replication fork.

An inhibitor of DNA polymerases alpha and delta in calf thymus DNA.

Most, although not all, samples of commercial calf thymus DNA were strongly inhibitory to DNA polymerase alpha; the inhibition made the DNA useless as a template for this enzyme. In a pre-assembled DNA polymerase assay mixture (minus enzyme but including activated DNA) the inhibition tended to diminish with time but at a rate that was not predictable, and some inhibition usually persisted. It was concluded that the inhibition was the result of contamination of the DNA by a heparin-like material on the basis of the following: 1) the inhibition could be reversed by treatment of the DNA with heparinase; 2) both the endogenous inhibitory effect of calf thymus DNA as well as the inhibitory effect of heparin on DNA polymerase alpha are reversed by protamine (which is known to prevent the antithrombin activity of heparin); 3) both the endogenous inhibition and inhibition by heparin are also reversed by ampholyte (which also prevents the antithrombin activity of heparin); and 4) both the endogenous and the heparin-induced inhibitory effects display the same spectrum of activity against mammalian DNA polymerases, i.e. both DNA polymerases alpha and delta are extremely sensitive whereas, DNA polymerases beta and gamma are resistant. The last result also suggests the use of heparin as a specific inhibitor of purified mammalian DNA polymerases alpha and delta, similar to the use of aphidicolin.

Purification and properties of an accessory protein for DNA polymerase alpha/primase.

A protein that stimulates DNA polymerase alpha/primase many-fold on unprimed poly(dT) was purified to homogeneity from extracts of cultured mouse cells. The protein contains polypeptides of approximately 132 and 44 kDa, and the total molecular mass of 150 kDa calculated from Stokes radius (54 A) and sedimentation coefficient (6.7 S) indicates that it contains one each of the two subunits. The purified "alpha accessory factor" (AAF) also stimulates DNA polymerase alpha/primase in the self-primed reaction with unprimed single-stranded DNA. In addition to these effects on the coordinate activities of DNA polymerase alpha and DNA primase, stimulatory effects were also demonstrated separately on both the polymerase and primase activities of the enzyme complex. However, there was no stimulation with DNase-treated ("activated") DNA under normal conditions for assay of DNA polymerase alpha. The stimulatory activity of mouse AAF is highly specific for DNA polymerase alpha/primase; no effect was observed with mouse DNA polymerases beta, gamma, or delta, nor with retroviral, bacteriophage, or bacterial DNA polymerases. Mouse AAF stimulated human DNA polymerase alpha/primase with several different templates, similar to results with the mouse enzyme. However, it had very little effect on the DNA polymerase/primase from either Drosophila embryo or from yeast.

Intact DNA polymerase alpha/primase from mouse cells. Purification and structure.

A procedure is described for purification of DNA polymerase alpha/primase from cultured mouse lymphoblasts. Approximately 0.5 mg of enzyme, free of detectable contaminants, was obtained from 40 g of cells using seven conventional purification steps. The mouse enzyme contains subunits of 180, 70, 56, and 47 kDa, almost completely intact and similar to the subunit sizes reported for DNA polymerase alpha/primase from Drosophila embryos (Kaguni, L. S., Rossignol, J-M., Conaway, R. C., and Lehman, I. R. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2221-2225) and Saccharomyces (Plevani, P., Foiani, M., Valsasnini, P., Badaracco, G., Cheriathundam, E., and Chang, L.M.S. (1985) J. Biol. Chem. 260, 7102-7107). A similar structure has also been inferred for mammalian DNA polymerase alpha/primase; however, previous descriptions of the highly purified mammalian enzyme complex have included substantial evidence of proteolysis and/or partial loss of subunits. In particular, the intact 180-kDa subunit has ordinarily been a minor component, and the molecular mass of the complex and total number of subunits have not been established. Results reported here indicate that the native DNA polymerase alpha/primase consists of one each of the four subunit sizes for a total of 353 kDa, based on estimates from denaturing gels, or 344 kDa when sizes deduced from available nucleic acid sequence data are substituted for three of the four subunits. A figure of 313 kDa was calculated from the sedimentation coefficient (8.9 S) and Stokes radius (81.1 A), the values for which also indicate a frictional ratio of 1.80, corresponding to an axial ratio of approximately 16 and suggesting a highly extended structure.