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 study of 16, 17, 18, 19, 28, 29-hexahydrorifamycin S by 1H-NMR. spectroscopy using INDOR at 100 MHz and homodecoupling at 270 MHz has shown that the conformation of the ansa fragment C(20)-C(27) and the position of this fragment relative to the naphthoquinone chromophore are practically the same as those of rifamycin S. This finding rules out the hypothesis that the lower activity of the hydrogenated rifamycins could be due to a different conformation.

Notes: The synthesis of new photolabeling analogues of luteinizing hormone releasing hormone is described. Peptides were prepared by the solid-phase method, and the photolabeling moiety was introduced as the 4′-nitrophenyl-alanine precursor. This amino acid, either of the L or D configuration, was placed at different positions and was modified afterwards to 4′-azidophenylalanine. Structures with agonistic or antagonistic character were prepared, together with a peptide containing simultaneously the photolabeling moiety and a biotin substituent for future receptor isolations. Binding studies on placental and pituitary membranes indicate that these compounds represent promising candidates for receptor labeling studies.

Notes: The amount of ATP produced during n-alkane, fatty acid, or acetate metabolism in Candida tropicalis has been established from the P/O ratios measured on isolated mitochondria, yield on substrate andcarbon balance. For these three kinds of substrates, YATP value has been found to be close to 4, although Ysub on acetate is very different from those found with n-alkanes or fatty acids.

Notes: By employing a two-stage continuous-culture system, some of the more important physiological parameters involved in cellulose biosynthesis have been evaluated with an ultimate objective of designing an optimally controlled cellulose process. The two-stage continuous-culture system was run for a period of 1350 hr with Trichoderma reesei strain MCG-77. The temperature and pH were controlled at 32°C and pH 4.5 for the first stage (growth) and 28°C and pH 3.5 for the second stage (enzyme production). Lactose was the only carbon source for the both stages. The ratio of specific uptake rate of carbon to that of nitrogen, Q(C)/Q(N), that supported good cell growth ranged from 11 to 15, and the ratio for maximum specific enzyme productivity ranged from 5 to 13. The maintenance coefficients determined for oxygen, MO, and for carbon source, MC, are 0.85 mmol O2/g biomass/hr and 0.14 mmol hexose/g biomass/hr, respectively. The yield constants determined are: YX/O = 32.3 g biomass/mol O2, YX/C = 1.1 g biomass/g C or YX/C = 0.44 g biomass/g hexose, YX/N = 12.5 g biomass/g nitrogen for the cell growth stage, and YX/N = 16.6 g biomass/g nitrogen for the enzyme production stage. Enzyme was produced only in the second stage. Volumetric and specific enzyme productivities obtained were 90 IU/liter/hr and 8 IU/g biomass/hr, respectively. The maximum specific enzyme productivity observed was 14.8 IU/g biomass/hr. The optimal dilution rate in the second stage that corresponded to the maximum enzyme productivity was 0.026 ∼ 0.028 hr-1, and the specific growth rate in the second stage that supported maximum specific enzyme productivity was equal to or slightly less than zero.

Notes: The controlled ionization of the linear [Cl-Ti-O-Ti-Cl] skeleton allowed the generation of the [Cl-Ti-O-Ti]+ dimer, which is nonsymmetrical as a consequence of extended Cl-Ti-O π interactions. The [Ti=O] unit thus formed is a building block for a variety of titanoxane structures. This chemistry has been investigated from a theoretical point of view by ab initio MO analysis of the [Cl-Ti-O-Ti-Cl] and [Cl-Ti-O=Ti]+ fragments. These calculations lead to the conclusion that single ionization generates the [Ti=O] unit, whereas double ionization does not affect the μ-oxo bonding mode in [Ti-O-Ti]2+ or [S-Ti-O-Ti-S]2+ (where S is a pure σ-donor ligand or solvent). This observation has been confirmed experimentally by ionizing the following model complexes: [(Cl)(acacen)-Ti-O-Ti(acacen)(Cl)] (3) (acacen = N,N'-ethylenebisacetylacetoneiminato dianion) and [(Cl)(salen)Ti-O-Ti(salen)-(Cl)] (4) (salen = N,N'-ethylenebissalicylideneiminato dianion), where the linear Cl-Ti-O-Ti-Cl unit is assured by the square-planar bonding mode of the tetradentate Schiff base ligand. The double ionization of 3 with AgNO3 gave the conventional μ-oxo derivative [(acacen)(η1-ONO2)Ti-O-Ti(acacen)(η1-ONO2)] (5). In contrast, the stepwise ionization of 3 and 4 with NaBPh4 in THF led to the nonsymmetrical [Cl-Ti-O=Ti]+ intermediates, which are the parent compounds for a variety of linear titanoxanes. The following species containing a Ti=O unit have been isolated from the NaBPh4-assisted ionization of 3: [(acacen)Ti=O-BPh3] (6) and [(L)(acacen)Ti=O-Ti(acacen)-O-(acacen)Ti-O=Ti(acacen)(L)]2+2 BPh-4 (L = THF, 7; L = none, 8). The same reaction carried out on 4 led to [(THF)-(salen)Ti=O - Ti (salen) - O - (salen)Ti-(THF)]2+2 BPh-4 (9) and [(L)(salen)-Ti=O-Ti(salen) - O - (salen)Ti-O=Ti-(salen)(L)]2+ 2BPh-4 (L = THF, 10; L = Py, 11; L = none, 12, polymeric form). A scheme is proposed to explain the formation of the species derived from the single ionization of 3 and 4, where the origin and the binding properties of the [Ti=O] unit play a major role.

Notes: GE2270A is a novel antibiotic active against Gram-positive bacteria and anaerobes. Its structure originates from a peptidic backbone, the amino acids of which have been modified to produce a macrocycle and a side-chain. It contains a heterocyclic chrornophonc system, a number of thiazoleamino acids and three unmodified natural amino acids. The structure [relative molecular mass (RMM) 1289] was determined using various spectroscopic techniques, of which fast atom bombardment mess spectrometry, gas chromatography/mass spectrometry, desorption chemical ionization mass spectrometry and fast atom bombardment tandem mass spectrometry played an important role. The mass spectrometric approach was applied to the intact molecule and to the various hydrolysis products, including the chromophoric part (RMM 634).

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