ALBERT

Notes: The rate constants of the natural degradation processes of low density polyethylene and polypropylene films have been calculated on the basis of the molecular weights of weathered samples. Moreover, the optical densities, obtained by means of IR spectroscopy, indicate that the formations of carbonyl and vinyl groups are zero-order reactions.

Notes: CD spectra and melting curves were collected for a 28 base-pair DNA fragment in the form of a DNA dumbbell (linked on both ends by T4 single-strand loops) and the same DNA sequence in the linear form (without end loops). The central 16 base pairs (bp) of the 28-bp duplex region is the poly(pu) sequence: 5′-AGGAAGGAGGAAAGAG-3′. Mixtures of the dumbbell and linear DNAs with the 16-base single-strand sequence 5′-TCCTTCCTCCTTTCTC-3′ were also prepared and studied. At 22°C, CD measurements of the mixtures in 950 mM NaCl, 10 mM sodium acetate, 1 mM EDTA, pH 5.5, at a duplex concentration of 1.8 μM, provided evidence for triplex formation. Spectroscopic features of the triplexes formed with either a dumbbell or linear substrate were quite similar. Melting curves of the duplex molecules alone and in mixtures with the third strand were collected as a function of duplex concentration from 0.16 to 2.15 μM. Melting curves of the dumbbell alone and mixtures with the third strand were entirely independent of DNA concentration. In contrast, melting curves of the linear duplex alone or mixed with the third strand were concentration dependent. At identical duplex concentrations, the dumbbell alone melts ∼20°C higher than the linear duplex. The curve of the linear duplex displayed a significant pretransition probably due to end fraying.On melting curves of mixtures of the dumbbell or linear duplex with the third strand, a low temperature transition with much lower relative hyperchromicity change (∼ 5%) was observed. This transition was attributed to the melting of a new molecular species, e.g., the triplex formed between the duplex and single-strand DNA molecules. In the case of the dumbbell/single-strand mixture, these melting transitions of the triplex and the dumbbell were entirely resolvable. In contrast, the melting transitions of the linear duplex and the triplex overlapped, thereby preventing their clear distinction. To analyze the data, a three-state equilibrium model is presented. The analysis utilizes differences in relative absorbance vs temperature curves of dumbbells (or linear molecules) alone and in mixtures with the third strand. From the model analysis a straightforward derivation of fT(T), the fraction of triplex as a function of temperature, was obtained. Analysis of fT vs temperature curves, in effect melting curves of the triplexes, provided evaluation of thermodynamic parameters of the melting transition. For the triplex formed with the dumbbell substrate, the total transition enthalpy is ΔHT = 118.4 ± 12.8 kcal/mol (7.4 ± 0.8 kcal/mol per triplet unit) and the total transition entropy is ΔST = 344 ± 36.8 cal/K · mol (eu) (21.5 ± 2.3 eu per triple unit). The transition curves of the triplex formed with the linear duplex substrate displayed two distinct regions. A broad pretransition region from fT = 0 to 0.55 and a higher, sharper transition above fT = 0.55. The transition parameters derived from the lower temperature region of the curve are ΔH′T = 44.8 ± 9.6 kcal/mol and ΔS′T = 112 ± 33.6 eu (or ΔH′ = 2.8 ± 0.6 kcal/mol and ΔS′ = 7.0 ± 2.1 eu per triplet). These values are probably too small to correspond to actual melting of the triplex but instead likely reveal effects of end fraying of the duplex substrate on triplex stability. Transition parameters of the upper transition are ΔH′T = 128.0 ± 2.3 kcal/mol and ΔS′T = 379.2 ± 6.4 eu (ΔH′ = 8.0 ± 0.2 kcal/mol and ΔS′ = 23.7 ± 0.4 eu per triplet) in good agreement (within experimental error) with the transition parameters of the triplex formed with the dumbbell substrate. Supposing this upper transition reflects actual dissociation of the third strand from the linear duplex substrate this triplex is comparable in thermodynamic stability to the triplex formed with a dumbbell substrate. Even so, the biphasic melting character of the linear triplex obscures the whole analysis, casting doubt on its absolute reliability. Apparently triplexes formed with a dumbbell substrate offer technical advantages over triplexes formed from linear or hairpin duplex substrates for studies of DNA triplex stability. © 1993 John Wiley & Sons, Inc.

Notes: The conformational behavior in solution of a cyclic peptide with sequence cyclo-(Pro1-Pro2-Dab3 (cHexA)ψ[N7HCO]-Leu4ψ[NHCO]-Suc5-Gly6-) has been throughly investigated with the combined use of nmr and molecular dynamic techniques. The compound, which has been modeled to mimic the FK506 macrolide bound to the FK506 binding protein structure, can be considered as a peptidic analogue of the FK506 system.The synthesis was carried out on a phenylacetoamidomethyl resin using an appropriate protocol for the peptide chain elongation. The conformational properties of the cyclic hexapeptide were studied in DMSO and water. The nmr data in DMSO and restrained molecular dynamics simulations show the presence of two contiguous cis peptide bonds involving the -Gly-Pro-Pro- segment. This segment in water exhibits conformational heterogeneity presenting at least two distinct conformational families, characterized the first by cis-cis and the second by a trans-cis Gly-Pro-Pro configuration; the trans-cis isomer was fully characterized. © 1997 John Wiley & Sons, Inc. Biopoly 42: 349-361, 1997

Notes: Many important applications of DNA sequence-dependent hybridization reactions have recently emerged. This has sparked a renewed interest in analytical calculations of sequence-dependent melting stability of duplex DNA. In particular, for many applications it is often desirable to accurately predict the transition temperature, or tm, of short duplex DNA oligomers (∼ 20 base pairs or less) from their sequence and concentration. The thermodynamic analytical method underlying these predictive calculations is based on the nearest-neighbor model. At least 11 sets of nearest-neighbor sequence-dependent thermodynamic parameters for DNA have been published. These sets are compared. Use of the nearest-neighbor sets in predicting tm from the DNA sequence is demonstrated, and the ability of the nearest-neighbor parameters to provide accurate predictions of experimental tm's of short duplex DNA oligomers is assessed. © 1998 John Wiley & Sons, Inc. Biopoly 44: 217-239, 1997

Notes: Seventeen DNA dumbbells were constructed that have duplex sequences ranging in length from 14 to 18 base pairs linked on the ends by T4 single-strand loops. Fifteen of the molecules have the core duplexes with the sequences 5′G-T-A-T-C-C-(W-X-Y-Z)-G-G-A-T-A-C3′, where (W-X-Y-Z) represents a unique combination of A · T, T · A, G · C, and C · G base pairs. The remaining two molecules have the central sequences (W-X-Y-Z) = A-C and A-C-A-C-A-C. These duplex sequences were designed such that the central sequences include different combinations of the 10 possible nearest-neighbor (n-n) stacks in DNA. In this sense the set of molecules is complete and serves as a model system for evaluating sequence-dependent local stability of DNA. Optical melting curves of the samples were collected in 25, 55, 85, and 115 mM [Na +], and showed, regardless of solvent ionic strength, that the transition temperatures of the dumbbells vary by as much as 14° for different molecules of the set.Results of melting experiments analyzed in terms of a n-n sequence-dependent model allowed evaluation of nine independent linear combinations of the n-n stacking interactions in DNA as a function of solvent ionic strength. Although there are in principle 10 possible different n-n interactions in DNA, these 10 are not linearly independent and therefore can not be uniquely determined. For molecules with ends, there are 9 linearly independent combinations, as opposed to circular or semiinfinite repeating copolymers where only 8 linear combinations of the 10 possible n-n interactions are linearly independent. The n-n interactions are presented as combinations of the deviations from average stacking for the 5′-3′ base-pair doublets, δGi, and reveal several interesting features: (1) Titratable changes in the values of δGi, with changing salt environment are observed. In all salts the most stable unique combination is δG4 = (δGGpC + δGCpG,)/2, and the least stable is the GpG/CpC stack, δG2 = δGGpG/CpC. (2) The χ2 values of the fits of the evaluated δGi's to experimental data increased with decreasing [Na +], suggesting that significant interactions beyond nearest neighbors become more pronounced, particularly at 25 mM Na +. (3) In 85 and 115 mM Na +, where the n-n approximation seems to be most valid, the absolute value of δGi for any n-n stack or average of two n-n stacks is not more than ∼ 220 cal/mole, indicating that deviations from average stacking due to n-n interactions represent about 15% of the total stability of a base pair. The overall thermodynamic stability of DNA is predominantly determined by the sequence content (%G · C). Even though the contribution of n-n interactions to overall stability are intrinsically small, reliable predictions of DNA transition temperatures de novo from sequence can be significantly compromised by cumulative errors in the δGi's. (4) Comparisons of our set of n-n linear combinations evaluated in 115 mM Na+ with various published sets evaluated from melting experiments of long restriction fragments, synthetic polymers, and short oligomers, and those obtained from a reanalysis of published melting data of synthetic polymers, are presented. The analysis reveals a major consensus agreement between n-n free energies evaluated from melting data of restriction fragments and long synthetic repeating copolymers. In contrast, only a minor consensus agreement is obtained between our n-n set and these values or those obtained from melting analysis of a combination of short oligomers and long polymers or those theoretically calculated. Results of these comparisons suggest the values of n-n interactions evaluated from DNA melting curves depend on the length of the melted duplex regions of the DNA molecules that comprise the sample set.

Notes: Cyclophilin A, a peptidyl-prolyl cis-trans isomerase that catalyzes the otherwise slow isomerization of Xaa-Pro imidic bond, specifically binds the immunosuppressant cyclosporin A. Herein we reportevidence on binding of cyclolinopeptide A and its synthetic analogue, [Aib5,6-D-Ala8] cyclolinopeptide, to bovine cyclophilin A. Binding experiments were monitored by fluorescence. CD, and second-derivative spectroscopies, evidencing no remarkable rearrangement of protein structure organization. The possibility that cyclolinopeptide A could act as a substitute of cyclosporin A in the immunosuppression modulation is also briefly discussed. © 1995 John Wiley & Sons, Inc.

Notes: Toluene Sulfonamide Formaldehyde Resins (TSFR), having elemental analysis close to (C8H9NSO2)n, are shown by GPC to exist as a mixture of a few (5 to 6) oligomers, having masses between 400 and 1900 g. A complete scheme of all the possible intermediates involved in their preparation is derived from the results of synthesis and from mechanistic steps; this allows one to propose the structure of oligomers having end groups OH and NH. IR, 1H NMR, and 13C NMR data on oligomers, compared to those of authentic samples specially designed and prepared, agree with the structures proposed. These results are helpful in designing modified or new resins to be used in nail lacquers. © 1993 John Wiley & Sons, Inc.

Notes: Delivery of drugs to brain tumors is difficult due to the impermeability, and variable nature of the blood/tumor barrier. Of the various strategies designed to improve drug uptake-intracellularly and into the brain, cationic carriers seem to offer an advantage. In the current investigation cationic polysaccharide-methotrexate conjugates were examined in the rat. Conjugates were prepared from N,O-carboxymethyl chitosan (NOCC) and 3H-methotrexate (MTX) by two different synthetic schemes, resulting in NOCCMTX-1 and NOCCMTX-2. NOCCMTX-1 appeared to have a higher degree of cross-polymerization than NOCCMTX-2. Each conjugate and free MTX were administered intra-arterially in a retrograde manner in the external carotid artery at a MTX dose of 1 mg/kg as a constant rate infusion over 30 min. Animals were sacrificed at various times after administration, and blood and tissue samples collected, processed in a sample oxidizer, and then measured for radioactivity. Brain MTX concentrations were 18- and 12-fold greater at 15 min and 3 hr, respectively, following NOCCMTX-1 administration compared to free MTX treatment. However, NOCCMTX-1 resulted in animal death at about 12 hr after administration. NOCMTX-2 was found to be non-toxic, yet did not increase brain MTX concentrations compared to free drug administrations after correction for MTX in residual blood. Further investigations are planned to combine the positive drug targeting effect of NOCCMTX-1 with the safety of NOCCMTX-2.

Notes: Polyurethanes (PUs) were synthesized from toluenediisocyanates (TDIs) and a polymeric diol having polydimethylsiloxane and polyoxyethylene blocks of the ABA type, ended with OH groups. Prepolymers, prepared in toluene solution using ratios [NCO]/[OH] ≥ 2, were crosslinked with triisopropanolamine (TIPA) (ratio [OH]/[NCO] = 1.1) (two-step process). PUs were also obtained with a one-step process using, contemporaneously, TDI, block copolymer, and, as crosslinking agent, TIPA or the glyceride of ε-hydroxyhexanoic acid. Polydimethylsiloxane (PDMSO) was prepared as a reference material. The course of the reaction between block copolymer and TDI was studied by differential scanning calorimetry in the absence and presence of benzoyl chloride (BzCl). Without BzCl, with ratios [NCO]/[OH] 〉 2, uncontrolled crosslinking side reactions occur. The properties of the PU films obtained with the two methods were studied both for the density of crosslinking and for gas transport properties. The two-step polymers are less crosslinked than the others and are characterized by higher diffusion coefficients and by higher permeability to gases. The permeability order is 10-9 (N cm3 cm-1 cm-1 cm Hg-1 s-1) for CH4, O2, CO, and N2 and is 10 times higher for CO2. The selectivity for the couple O2/N2 is higher than that obtained with PDMSO films. Considerable selectivities are shown for the couples CO2/N2 and CO2/CO. © 1995 John Wiley & Sons, Inc.

Notes: A natural polymer in a commercially available form (chitosan) has been tested using a factorial design of experiments for its application to cobalt recovery either in hydrometallurgy and in analytical separations. A simple mechanically stirred system has been used, evaluating the influence of the contact time, iron(II), cobalt (II), chitosan concentration, salinity, and pH in the separation. The pH value has a dramatic influence on the metal recovery from a negligible amount of metals at pH = 1.0 to a quantitative sorption at pH = 3.0. Linear relationships between sorbed metal and the variables have been determined at constant pH value and a quantitative evaluation of the metal recovery at different pH values can be performed using the maximum sorption capacity of the chitosan (a0) and the selectivity for both metals. The obtained results allow the evaluation of the recovery of metals using chitosan as solid phase.