New aspects of the interaction of the antibiotic coralyne with RNA: coralyne induces triple helix formation in poly(rA)•poly(rU)

The interaction of coralyne with poly(A)•poly(U), poly(A)•2poly(U), poly(A) and poly(A)•poly(A) is analysed using spectrophotometric, spectrofluorometric, circular dichroism (CD), viscometric, stopped-flow and temperature-jump techniques. It is shown for the first time that coralyne induces disproportionation of poly(A)•poly(U) to triplex poly(A)•2poly(U) and single-stranded poly(A) under suitable values of the [dye]/[polymer] ratio (CD/CP). Kinetic, CD and spectrofluorometric experiments reveal that this process requires that coralyne (D) binds to duplex. The resulting complex (AUD) reacts with free duplex giving triplex (UAUD) and free poly(A); moreover, ligand exchange between duplex and triplex occurs. A reaction mechanism is proposed and the reaction parameters are evaluated. For CD/CP> 0.8 poly(A)•poly(U) does not disproportionate at 25°C and dye intercalation into AU to give AUD is the only observed process. Melting experiments as well show that coralyne induces the duplex disproportionation. Effects of temperature, ionic strength and ethanol content are investigated. One concludes that triplex formation requires coralyne be only partially intercalated into AUD. Under suitable concentration conditions, this feature favours the interaction of free AU with AUD to give the AUDAU intermediate which evolves into triplex UAUD and single-stranded poly(A). Duplex poly(A)•poly(A) undergoes aggregation as well, but only at much higher polymer concentrations compared to poly(A)•poly(U)

Mechanisms of the Interaction of Fluorescent Dyes with Nucleic Acids

In recent years, increased attention has been focused in the ways in which drugs interact with biological systems, with the goal of understanding the toxic as well as the chemotherapeutic effects of these small molecules. Dyes that non-covalently bind DNA have received considerable attention due to their potential use as antitumour-drugs and as tools to study and visualize DNA. Many efforts have been devoted to find fluorescent dyes which could provide a convenient alternative to the employment of classical ones (acridines, phenanthridines) and recent developments in biochemistry are often concerned with the study of new molecules that are able to bind and react with DNA and whose properties as drugs need to be tested. These new probes can provide a better understanding of the activity of many drugs and anticancer agents and be of help in developing new diagnostic tools. Many molecules containing planar aromatic ring systems can interact with nucleic acids, intercalating between base pairs or fitting into the polynucleotide grooves, these interactions being the basis of subsequent biological activity. The object of this PhD thesis is the study of the interactions of DNAs and RNAs with dyes, belonging to different chemical families, using a mechanistic approach. The interaction processes are investigated by UV-vis and fluorescence spectroscopy and by relaxation methods (T-Jump and/or stopped-flow), under different temperatures and ionic strength conditions. The dyes chosen in this work are small molecules that, although of different chemical constitution, all contain planar aromatic rings as a common feature. Among them an alkaloid, an acridine derivative and cyanines dyes

Gallium(III)/4-(2-Pyridylazo)resorcinol System in Water and SDS solution: Kinetics and Thermodynamics

The equilibria and kinetics of the complex formation and dissociation reaction between gallium(III) and PAR [4-(2-pyridylazo)resorcinol] have been investigated in water and in the presence of SDS micelles. The reactive form of Ga(III) is GaOH2+ in both cases. The addition of SDS results in an increase of both the binding affinity and velocity, the maximum accelerating effect being observed just above the cmc value of SDS that, under the conditions of the experiments, is 5.6 10-3 M. At pH ) 3.2, the maximum value of the equilibrium constant ratio Kapp(SDS)/Kapp(H2O) is 27.4, whereas that of the binding rate constants kf(SDS)/kf(H2O) is 16. The results are interpreted in terms of increased concentrations of the reactants on the micelle surface and on competition of PAR and SDS for GaOH2+

Development of new PLA-based biodegradable compounds for micro-irrigation applications

New biodegradable compounds having high renewable resources starting materials content were developed and formulated at Lab, pilot and industrial level. Pipes were prepared using the here developed compounds, and perfectly mimic the mechanical behavior as well as the chemical resistance of the currently used polyethylene based materials. This work is currently developed within the EC founded HYDRUS project

Influence of cyanine dye structure on self-aggregation and interaction with nucleic acids: A kinetic approach to TO and BO binding

Kinetics and equilibria of cyanine dyes thiazole orange (TO) and benzothiazole orange (BO) self-aggregation and binding to CTDNA are investigated in aqueous solution at 25 C and pH 7. Absorbance spectra and T-jump experiments reveal that BO forms J-aggregates while TO forms more stable H-aggregates. Fluorescence and absorbance titrations show that TO binds to DNA more tightly than BO. TO stacks externally to DNA for low polymer-to-dye concentration ratios (C-P/C-D) while dye intercalation occurs for high values of CP/CD. T-jump and stopped-flow experiments performed at high CP/CD agree with reaction scheme D+S reversible arrow D,S reversible arrow: DSI reversible arrow DSII where the precursor complex D,S evolves to a partially intercalated complex DS, which converts to the more stable intercalate DSII. Non-electrostatic forces play a major role in D,S stabilization. Last step is similar for both dyes suggesting accommodation of the common benzothiazole residue between base pairs. Experiments using poly(dA-dT)-poly(dA-dT) and poly(dG-dC)-poly(dG-dC) confirm base pair preference for TO. (c) 2007 Elsevier Inc. All rights reserved

Cover Picture: Macromol. Mater. Eng. 2/2015

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Evidences of Transesterification, Chain Branching and Cross-Linking in a Biopolyester Commercial Blend upon Reaction with Dicumyl Peroxide in the Melt

Aiming at the tuning of thermo-mechanical features by chemical cross-linking, a biopolyester commercial blend based on poly(lactic acid) (PLA) with poly(butylene adipate-co-terephthalate)(PBAT) (ecovio (R) T2280, BASF) was processed in Brabender in the presence of dicumyl peroxide (DCP, 0-0.2 wt.-\%). The effect of DCP addition was investigated and rationalized by means of solubility tests and gel content evaluation, as well as rheological, mechanical, and molecular weight analysis of the prepared compounds. Moreover, detailed DSC and TMDSC investigations provided a deep insight into the structural modifications occurred at the macromolecular level. We found that chain branching as well as cross-linking occurred in the samples processed in the presence of DCP, thus returning compounds having increased toughness and modulated crystalline content and thermal behavior. Noteworthy, the presence of specific, undisclosed additives, triggers the occurrence of peculiar behaviors in the ecovio (R) commercial blend, not previously observed in model PLA/PBAT blends of similar composition. Despite only partially soluble in chloroform, the new ecovio (R) DCP-modified compounds still remained workable in the melt, thus providing a suitable, simple and economically affordable strategy to finely modulate the thermo-mechanical properties starting from a commercially available, compostable compound

Solvent Effects on the Thermodynamics and Kinetics of Coralyne Self-Aggregation

The role of solvent effects on the thermodynamics and kinetics of the coralyne self-aggregation process has been investigated in ethanol-water mixtures of different compositions. The changes in the UV/visible spectra of coralyne and FAB/LSIMS mass spectrometry agreed well with the formation of a dimer species. ID and 2D (1)H experiments have allowed one to look into the features of the self-aggregation process and to determine the equilibrium constant and the Delta H degrees and Delta S degrees values for the aggregate formation in 0-50% ethanol-water mixtures. The kinetics of self-aggregation has been investigated by the T-jump chemical relaxation method, and the results have been interpreted in terms of dimer formation. The dependence of the relative viscosity of coralyne solutions on the dye concentration was studied in different ethanol-water mixtures. Finally, it was found that coralyne behaves as a solvatochromic indicator which is preferentially solvated according to the sequence ethanol > ethanol-water > water. All of the results concur in elucidating the relevant role of the hydrophobic interaction process of coralyne stack formation