Self-Replication of Oligonucleotides in Reverse Micelles

The coupling between the tri(deoxynucleotides) d[(MeO)C-G-Ap] ( 1 ) and d[(NH₂)T_d5′-C-G-] ( 2 ) to yield the phosphoramidate-linked (hexadeoxy-nucleotide) d[(MeO)C-G-Anh⁵′T_d5′-C-G] ( 3 ) was investigated both in aqueous solution and in reverse micelles constituted of CTAB (cetyl(trimethyl)ammonium bromide) in hexane/pentan-1-ol 9:1. No siginificant difference was found concerning the yield and the kinetics of the reaction in the two systems. The coupling between 1 and 2 was also carried out in the presence of the template d[(MeO)C-G-A-T-C-G] ( 4 ), an analogue of 3 , so as to reproduce the conditions of template-directed self replication. It was shown that the trinucleotide coupling in the presence of a template obeys the so-called square-root law both in H₂O and in reverse micelles. No significant difference of the time course of the reaction in H₂O and in reverse micelles was observed. This shows that self-replication of oligonucleotides occurs within geometrically bounded structures, which represents a step forward in the mimicking of minimal life processes.     

New approach based on fuzzy logic and principal component analysis for the classification of two-dimensional maps in health and disease. Application to lymphomas

Two-dimensional (2D) electrophoresis is the most wide spread technique for the separation of proteins in biological systems. This technique produces 2D maps of high complexity, which creates difficulties in the comparison of different samples. The method proposed in this paper for the comparison of different 2D maps can be summarised in four steps: (a) digitalisation of the image; (b) fuzzyfication of the digitalised map in order to consider the variability of the two-dimensional electrophoretic separation; (c) decoding by principal component analysis of the previously obtained fuzzy maps, in order to reduce the system dimensionality; (d) classification analysis (linear discriminant analysis), in order to separate the samples contained in the dataset according to the classes present in said dataset. This method was applied to a dataset constituted by eight samples: four belonging to healthy human lymph-nodes and four deriving from non-Hodgkin lymphomas. The amount of fuzzyfication of the original map is governed by the sigma parameter. The larger the value, the more fuzzy theresulting transformed map. The effect of the fuzzyfication parameter was investigated, the optimal results being obtained for sigma = 1.75 and 2.25. Principal component analysis and linear discriminant analysis allowed the separation of the two classes of samples without any misclassification.     

Gravitational instabilities in free diffusion boundaries

Gravitational instabilities and the conditions for the onset of convective motions in free diffusion boundaries are discussed for isothermal diffusion in ternary systems. It is shown that convective motion can grow even if the diffusion process does not promote density inversions inside the boundary.     

Condensed DNA in lipid microcompartments

DNA was studied in lipid reverse micelles with the aim of investigating the interactions of DNA with lipids in a restricted compartment with minimal water content. Circular dichroic (CD) spectra of DNA at low water content showed the characteristic polymer-salt-induced (psi) spectra of condensed DNA. Dynamic light scattering showed a peak around a radius of 400 nm (corresponding to DNA-containing micelles), and a peak around 2.5 nm (corresponding to "empty" micelles). Fourier Transform-IR (FT-IR) spectroscopy was carried out and analyzed in terms of three distinct states of water inside the micelle water pool, where the local concentration of DNA reached an estimated value of ca. 600 mg/mL, comparable to that found in restricted biological compartments.     

Analytical characterization of poly(pyrrole-3-carboxylic acid) films electrosynthesised on Pt, Ti and Ti/Al/V substrates

With the aim of developing a polymeric multilayer film for application in advanced biomaterials, as a first step poly(pyrrole-3-carboxylic acid) films (abbreviated as PPy-3-carbox) were electropolymerised from pyrrole-3-carboxylic acid solutions by cyclic voltammetry and chronoamperometry on platinum, titanium and Ti90Al6V4 substrates and characterised both electrochemically (cyclic voltammetry) and spectroscopically (X-Ray Photoelectron Spectroscopy, XPS). Electrochemical experiments showed that the potential range adopted for electropolymerization affects the polymer electroactivity, by analogy with unsubstituted polypyrrole. The combination of conventional and chemical derivation-XPS provided information on PPy-3-carbox surface structure, showing no significant difference between films grown on different substrates and an increase of the COOH groups amount (one group over three pyrrole rings, as an average) with respect to unsubstituted polypyrrole (PPy), as expected. Finally, a preliminary Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) investigation was performed in order to get further information on the polymer structure and electroactivity.     

Potential binding of borate ions to mono- and oligonucleotides: a capillary electrophoresis investigation

The potential binding of borate to oligonucleotides and DNA fragments is here investigated. In case of free nucleotides, such as AMP, there appears to be a weak binding, although no free versus complexed species could ever be separated under any experimental condition. The binding was suggested by the strong peak asymmetry and by the fact that, at progressively lower borate molarities in the background electrolyte, the peak shape suddenly switched from fronting to tailing. This indicated, as also confirmed by theoretical simulations, that the AMP-borate complex was the slow, not the fast moving species. On the contrary, in the case of free adenosine, strong binding ensued, since in Tris-acetate buffer this compound was only eluted with the electroendoosmotic flux, being neutral, whereas in Tris-borate it had a much higher mobility, comparable to, although lower than, that of AMP. When running oligonucleotides, at standard borate molarities (ca. 45 mM), and under strict iso-ionic strength conditions, no binding to borate could be demonstrated, since the free mobility of a 24-mer DNA was identical in TA and TB buffers. However, at very high borate molarities (200 mM) and high pH values (pH 8.92), some binding to oligonucleotides could occur, since in these latter conditions the mobility of a 24-mer was seen to be ca. 20% lower than at pH 7.69, a pH value that should discourage any complex formation.     

A novel synthesis of diaminomethanes

Diaminomethanes have been synthesized by reaction of 1,3-benzodioxole and 1,3-benzoxathiole with a double amount of sodium dialkyl and alkyl aryl amides.     

Oxygen electrodes in fused salts: Investigation and mechanistic remarks on the system (Ni)O2, H2O/OH− in the (Na,K)NO3 eutectic melt

A potentiometric investigation on the system (Ni)O₂, H₂O/OH^? was carried out within the temperature range 513?T?636 K in the (Na, K)NO₃ equimolar mixture containing OH^? ions in the concentration range 5×10^?6<[OH^?]<10^?1m and flushed with a mixture of O₂ and H₂O at variable partial pressures. The system has been found to behave reversibly in all hydroxide concentration and temperature intervals studied with respect to all the species involved in the over-all electrode reaction ½ O₂+H₂O+2e^?=2OH^? so that the following nernstian relationship could be written E=E_O2,H₂O/OH^?+RT/Fln{[O₂]^1/4[H₂O]^1/2/[OH^?]} This potentiometric behaviour was tentatively interpreted on the basis of mechanistic models involving, in some steps, solid nickel oxides formed on the electrode surface by contact with the melt. The actual formation and existence of these compounds on the electrode surface under the given experimental conditions was proved by a proper XPS investigation.     

Thermal decomposition of the tert-butyl perester of thymidine-5′-carboxylic acid. Formation and fate of the pseudo-C4′ radical

Thermal decomposition of the tert-butyl perester of thymidine-5′-carboxylic acid 1 carried out at 85 °C in different solvents affords the tert-butylacetal 4a, deriving from in cage decomposition, and pseudo C4′ radicals 2. Radicals 2 can be reduced to 5 by hydrogen atom abstraction from thiol (thiophenol or glutathione) or THF, or can be oxidized to cations 8 by dioxygen or perester 1 itself. Cations 8 are stereoselectively trapped by the nucleophilic solvent (tert-butanol, methanol, water) to give acetals 4a-c.