Spectrophotometric determination of fusicoccin

Fusicoccin incubated for 17 h in 6 M HCl at 37°C gives rise to a chromophoric system having an absorption maximum at 555 nm. A colorimetric method for the determination of pure fusicoccin and of fusicoccin in fermentation liquors and infected plant tissues is described. The method is useful for 50–800 μg of fusicoccin.     

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.     

Laboratory tests addressed to realize customized restoration procedures of underwater archaeological ceramic finds

The present contribution is part of a biennial research project funded by the Italian Ministry of Education, Universities and Research (MIUR). This study, currently in progress, deals with innovative experimental approaches applied to the chemical, mineralogical and physical transformations occurring during the prolonged permanence of archaeological ceramic finds in seawater environments as well as to restoration and conservation issues of the same underwater artifacts. The experimental approach used in this research consisted in the manufacture of ceramic test-pieces (briquettes) and their successive placing in underwater environment. This work aims at assessing how textural and compositional parameters along with firing temperatures of a ceramic paste could affect total porosity, pore size distribution and kinetics of capillary water absorption. A further purpose is concerned with the study of the potential modification of porosity and pore size distribution in the same ceramic bodies after immersion in seawater (3 and 6 months). The study was carried out using a multi-technique approach including investigations through polarized light microscopy (PLM), capillary water absorption test, mercury intrusion porosimetry (MIP) analyses and theoretical calculation of salt crystallization pressures. The obtained results show a different behavior of the six experimental pastes as a function of their compositional and textural features as well as pore size distribution and firing temperatures. These parameters, in various extents, have been found significantly influencing the kinetics of water absorption and the susceptibility of ceramic artifacts to salt crystallization processes, with important implications on conservation procedures needed before the musealization.     

A Comparison of Optimal Methods for Local Access Uncapacitated Network Design

We compare some optimal methods addressed to a problem of local access network design. We see this problem arising in telecommunication as a flow extension of the Steiner problem in directed graphs, thus including as particular cases some alternative approaches based on the spanning tree problem. We work with two equivalent flow formulations for the problem, the first referring to a single commodity and the second being a multicommodity flow model. The objective in both cases is the cost minimization of the sum of the fixed (structural) and variable (operational) costs of all the arcs composing an arborescence that links the origin node (switching center) to every demand node. The weak single commodity flow formulation is solved by a branch-and-bound strategy that applies Lagrangian relaxation for computing the bounds. The strong multicommodity flow model is solved by a branch-and-cut algorithm and by Benders decomposition. The use of a linear programming solver to address both the single commodity and the multicommodity models has also been investigated. Our experience suggests that a certain number of these modeling and solution strategies can be applied to the frequently occurring problems where basic optimal solutions to the linear program are automatically integral, so it also solves the combinatorial optimization problem right away. On the other hand, our main conclusion is that a well tailored Benders partitioning approach emerges as a robust method to cope with that fabricated cases where the linear programming relaxation exhibits a gap between the continuous and the integral optimal values.     

A general method to obtain Sturmian functions for continuum and bound state problems with Coulomb interactions

In this article, we investigate discretization schemes to represent Sturmian functions for both positive and negative energies in the presence of a long range Coulomb potential. We explore two methods to obtain Sturmian functions for positive energy. The first one involves the expansion of the radial wave function in a L² finite basis set, whereas the second one introduces the discretization of the radial coordinate domain of the Hamiltonian or, alternatively, the Green function. We apply them to find the bound states and scattering phase shift for ‐electron atoms close to the critical charge. Both methods are able to describe bound states near threshold, as well as continuum states with very good convergence properties. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Effects of an 8-bromodeoxyguanosine incorporation on the parallel quadruplex structure [d(TGGGT)]4

NMR, molecular dynamics and mechanics calculations, and CD spectroscopy were used to characterise three tetramolecular quadruplex complexes: [d(TG(Br)GGT)](4), [d(TGG(Br)GT)](4) and [d(TGGG(Br)T)](4), where G(Br) indicates an 8-bromoguanine residue. All three quadruplexes are characterised by a 4-fold symmetry with all strands parallel to each other and, differently to what has been observed for other parallel quadruplex structures, with a tetrad (formed by 8-Br-dGs) in a syn conformation. The whole of the data demonstrates that the replacement in turn of different dG residues with 8-Br-dG in the sequence 5[prime or minute]-TGGGT-3[prime or minute] affects the resulting structures in different ways, leading to different CD profiles and thermal stabilities. Particularly, [d(TG(Br)GGT)](4) and [d(TGG(Br)GT)](4) are more stable than the unmodified sequence, whereas [d(TGGG(Br)T)](4) is much less stable than the natural counterpart. The conformational features found in the three quadruplexes might, in principle, amplify the range of applicability of synthetic oligonucleotides as aptamers or catalysts, by providing novel structural motifs with different molecular recognition capabilities from those of native DNA sequences.     

Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR study

A comparative study of the competitive cation exchange between the alkali metal ions K⁺, Rb⁺, and Cs⁺ and the Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂ was performed in aqueous solution by a combined use of the ²³Na and ¹H NMR spectroscopy. The titration data confirm the different binding affinities of these ions for the G‐quadruplex and, in particular, major differences in the behavior of Cs⁺ as compared to the other ions were found. Accordingly, Cs⁺ competes with Na⁺ only for the binding sites at the quadruplex surface (primarily phosphate groups), while K⁺ and Rb⁺ are also able to replace sodium ions located inside the quadruplex. Furthermore, the ¹H NMR results relative to the CsCl titration evidence a close approach of Cs⁺ ions to the phosphate groups in the narrow groove of [d(G₄T₄G₄)]₂. Based on a three‐site exchange model, the ²³Na NMR relaxation data lead to an estimate of the relative binding affinity of Cs⁺ versus Na⁺ for the quadruplex surface of 0.5 at 298 K. Comparing this value to those reported in the literature for the surface of the G‐quadruplex formed by 5′‐guanosinemonophosphate and for the surface of double‐helical DNA suggests that topology factors may have an important influence on the cation affinity for the phosphate groups on DNA. Copyright © 2009 John Wiley & Sons, Ltd.