Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4

The complex between distamycin A and the parallel DNA quadruplex [d(TGGGGT)]4 has been studied by 1H NMR spectroscopy and isothermal titration calorimetry (ITC). To unambiguously assert that distamycin A interacts with the grooves of the quadruplex [d(TGGGGT)]4, we have analyzed the NMR titration profile of a modified quadruplex, namely [d(TGGMeGGT)]4, and we have applied the recently developed differential frequency-saturation transfer difference (DF-STD) method, for assessing the ligand-DNA binding mode. The three-dimensional structure of the 4:1 distamycin A/[d(TGGGGT)]4 complex has been determined by an in-depth NMR study followed by dynamics and mechanics calculations. All results unequivocally indicate that distamycin molecules interact with [d(TGGGGT)]4 in a 4:1 binding mode, with two antiparallel distamycin dimers that bind simultaneously two opposite grooves of the quadruplex. The affinity between distamycin A and [d(TGGGGT)]4 enhances ( approximately 10-fold) when the ratio of distamycin A to the quadruplex is increased. In this paper we report the first three-dimensional structure of a groove-binder molecule complexed to a DNA quadruplex structure.     

Synthesis of uracil derivatives by oxidation of Fischer tungsten-carbene uracil complexes

A study on the oxidation of Fischer tungsten-carbene uracil complexes has been carried out. Several commonly used oxidants gave results strongly influenced by the presence of substituent on nitrogen atoms. In particular, usual oxidants failed in the oxidation of 3-alkyl uracil carbene complexes. Finally, we showed that t-butyl hydroperoxide is able to oxidize successfully also 3-alkyl uracil carbene complexes and can be used as a good alternative to the other methods.     

Numerical analysis of a shock-wave solution of the Enskog equation obtained via a Monte Carlo method

In this paper a planar stationary shock-wave-like solution of the Enskog equation obtained via a Monte Carlo technique is studied; both the algorithm used to obtain the solution and the qualitative behavior of the macroscopic quantities are discussed in comparison with the corresponding solution of the Boltzmann equation.     

A mixed algorithm for the calculation of rapidly varying fluid flows: The impulsively started circular cylinder

A mixed discrete Fourier transform-Finite difference algorithm is developed and used for the calculation of rapidly changing viscous fluid flows past a circular cylinder. The numerical approach has been designed to overcome certain difficulties arising for high Reynolds number simulations. The foremost advantage of the technique lies in its fast calculations of the convolution sums portraying the convective terms of the governing equations. Third-order spatial discretizations and fourth-order time marching are implemented. New schemes are proposed for the boundary conditions at the solid wall and at large distances. The techniques are tested on a case study with other schemes (summarized by Roache¹) in order to obtain an optimal choice. Definite indications on the stability and accuracy of boundary condition schemes are achieved. Support for the statement of dominant importance of boundary conditions is also given. A comparison of computational results with experimental data is presented for the case study of the flow past an impulsively started cylinder at Reynolds number 20. The time development of the symmetrical zone of recirculation, which is formed at an early stage of the flow, has been studied for 300 ≤ Re ≤ 9500 by means of the proposed algorithm. Computational results, comparisons with experimental data² and discussion of upper limits of validity of the procedure will be presented in a companion paper.     

Ab initio calculations including solvent effects of the structure of pyrazine, 4-nitropyridine and dicyanobenzenes ion pairs

The potential surfaces of pyrazine, 4-nitropyridine, 1,2-, 1,3-, 1,4- dicyanobenzene radical anions have been calculated within theab initio and electrostatic molecular potential formalism, including the effect of the solvent. These potential surfaces suggest models of ion pairs with alkali cations, which are in agreement with those deduced from related ESR spectra.     

Two-group kinetic theory of vehicular traffic

Summary We study a two-group model of vebicular traffic oli a highway which generalizes the Prigogine-Herman model. According to the two-group theory, drivers are divided into “slow” and “fast”. Correspondingly, we introduce a slow and a fast desired distribution representing the program that drivers of each of the two groups wish to follow. We first prove the existence and the uniqueness of a solution belonging to a suitable Banach space by using the theory of semigroups. Then, we indicate some sufficient conditions for the stability of an x and t independent solution.

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Sommario Si generalizza il modello di Prigogine-Herman del traffico automobilistico su un'autostrada, introducendo due gruppi di guidatori: i “lenti” ed i “veloci”. Ognuno dei due gruppi riene caratterizzato da un'opportuna funzione “desiderio”, che traduce i programmi che i guidatori intendono seguire nel corso del loro viaggio. Facendo poi uso della teoria dei semigruppi, si prova l'esistenza e l'unicità di una soluzione appartenente ad un opportuno spazio di Banach e si danno condizioni sufficienti per la stabilità.

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Work performed under the auspices of the National Research Council (C.N.R., Gruppo Nazionale per la Fisica Matematica).As the choice of the appropriate model for these problems is still a controversial matter, the Editorial Board welcomes any comment or discussion from the readers.     

Geometrical substituent parameters for benzene derivatives: inductive and resonance effects

A full set of geometrical parameters describing the effect of 21 substituents on the internal angles of the benzene ring has been derived by linear regression from many structural results. The parameters are shown to reflect the inductive and resonance effects of the substituents.     

Separation of human fibrinopeptides by capillary zone electrophoresis

We describe a method for the simultaneous determination of the five fibrinopeptide forms derived from the thrombin-promoted activation of human fibrinogen by capillary zone electrophoresis (CZE). The fibrinopeptide mixture was first desalted by a solid-phase extraction (SPE) step. The analysis was performed in reversed polarity in a highly cross-linked polyethylene glycol (PEG)-coated capillary with UV-light absorption detection at 200 nm. Several parameters including buffer concentration and pH, presence of an organic modifier, temperature, and applied voltage, have been tested. The best separations were obtained within 20 min, utilizing a 20 mM sodium phosphate buffer without organic modifier, in the narrow 6.1-6.2 pH range, at 25 degrees C, with an applied voltage of 20 kV. Quantitative analysis is made possible by the use of sheep fibrinopeptide A as an internal standard to correct for both extraction and injection errors.