FUROCOUMARIN-PHOTOSENSITIZEDHYDROXYLATION OF GUANOSINE IN RNA AND DNA

Abstract— Guanosine hydroxylation was used as a marker for assessing photooxidation of DNA and RNA sensitized by monofunctional and bifunctional furocoumarins. DNA or RNA, treated with sensitizer and UVA light, was enzymatically hydrolyzed, dephosphorylated and then analyzed by reversed-phase HPLC with electrochemical detection. Hydroxylated guanosine, i.e. 8-hydroxy-2'-deoxyguanosine (8-OHdG) or 8-hydroxyguanosine (8-OHG), was quantitated. 3-Carbethoxypsoralen (3-CP) was found to be an efficient photosensitizer for oxidation of guanosine in DNA, resulting in conversion of up to 0.4% of guanosine residues to 8-OHdG. In contrast, dramatically lower levels of guanosine hydroxylation were observed in 3-CP-photosensitized RNA. Psoralen was found to be a more efficient photosensitizer than angelicin in both DNA and RNA. Additional studies of oxidation of 3-CP-photosensitized DNA indicated that double-stranded DNA is 10 times more susceptible to photooxidation than single-stranded DNA, implicating 3-CP binding to DNA as an important mechanistic step in photooxidation of guanosine. The effects of D₂O and degassing with argon on photooxidation of guanosine in DNA sensitized by 3-CP were inconsistent with a mechanism involving ¹O₂. In addition, chelation of adventitious metal ions present in preparations of DNA photosensitized by 3-CP had no effect on hydroxylation of guanosine.     

De novo synthesis of aceric acid and an aceric acid building block

The de novo synthesis of an aceric acid thioglycoside building block and the total synthesis of the plant carbohydrate aceric acid are described via a highly convergent strategy. Aldol reaction of acetaldehyde and a protected tartaric acid derivative provided the open chain carbohydrate. Subsequent acid treatment yielded the aceric acid thioglycoside in 35% total yield over five steps. Oxidative cleavage of the thioketal in the open chain carbohydrate and basic hydrolysis of the methyl ester furnished fully deprotected aceric acid in 31% yield over six steps.     

A stochastic method for global optimization

A stochastic method for global optimization is described and evaluated. The method involves a combination of sampling, clustering and local search, and terminates with a range of confidence intervals on the value of the global optimum. Computational results on standard test functions are included as well.     

Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional,Distant Electrostatic Binding Site

Electrostatic interactions can strongly increase the efficiency of protein complex formation. The charge distribution in redox proteins is often optimized to steer a redox partner to the electron transfer active binding site. To test whether the optimized distribution is more important than the strength of the electrostatic interactions, an additional negative patch was introduced on the surface of cytochrome c peroxidase, away from the stereospecific binding site, and its effect on the encounter complex as well as the rate of complex formation was determined. Monte Carlo simulations and paramagnetic relaxation enhancement NMR experiments indicate that the partner, cytochrome c, interacts with the new patch. Unexpectedly, the rate of the active complex formation was not reduced, but rather slightly increased. The findings support the idea that for efficient protein complex formation the strength of the electrostatic interaction is more critical than an optimized charge distribution.     

Linear Transformation of Products: Games and Economies

In this paper, we introduce situations involving the linear transformation of products (LTP). LTP situations are production situations where each producer has a single linear transformation technique. First, we approach LTP situations from a (cooperative) game theoretical point of view. We show that the corresponding LTP games are totally balanced. By extending an LTP situation to one where a producer may have more than one linear transformation technique, we derive a new characterization of (nonnegative) totally balanced games: each totally balanced game with nonnegative values is a game corresponding to such an extended LTP situation. The second approach to LTP situations is based on a more economic point of view. We relate (standard) LTP situations to economies in two ways and we prove that the economies are standard exchange economies (with production). Relations between the equilibria of these economies and the cores of cooperative LTP games are investigated.     

A duopoly model with heterogeneous congestion-sensitive customers

This paper analyzes a model with two firms (providers), and two classes of customers. These customers classes are characterized by their attitude towards ‘congestion’ (caused by other customers using the same resources); a firm is selected on the basis of both the prices charged by the firms, and the ‘congestion levels’. The model can be represented by a two-stage game: in the first providers set their prices, whereas in the second the customers choose the provider (or to not use any service at all) for given prices. We explicitly allow the providers to split their resources, in order to serve more than just one market segment. This enables us to further analyze the Paris metro pricing (Pmp) proposal for service differentiation in the Internet.     

Linear and nonlinear time series analysis of the black hole candidate cygnus X-1

We analyze the variability in the x-ray lightcurves of the black hole candidate Cygnus X-1 by linear and nonlinear time series analysis methods. While a linear model describes the overall second order properties of the observed data well, surrogate data analysis reveals a significant deviation from linearity. We discuss the relation between shot noise models usually applied to analyze these data and linear stochastic autoregressive models. We debate statistical and interpretational issues of surrogate data testing for the present context. Finally, we suggest a combination of tools from linear and nonlinear time series analysis methods as a procedure to test the predictions of astrophysical models on observed data.