DNA conformation and thermostability in urea aqueous solutions

It is suggested from the character of the change of circular dichroism spectra that in the presence of urea winding of DNA double helix takes place within the bounds of B-family of forms. It is shown that the realized conformation of DNA differs from the experimentally known forms of DNA belonging to B-family. Urea destabilizes the DNA molecules without connection with helical and melt pairs of DNA nitrous bases. Urea affects the conformational state of DNA by water destruction around DNA, which is accompanied by dehydration of DNA and basic metal ions.     

Molecular conformation of poly-S-carboxymethyl-L-cysteine in aqueous solutions

Poly-S-carboxymethyl-L -cysteine has been prepared by debenzylation of poly-S-carbobenzoxymethyl-L -cysteine with hydrogen bromide in acetic acid. By the infrared spectroscopic method the polymer is found to be in the extended β-conformation with an antiparallel arrangement of polypeptide chains in solid film, if it has been regenerated from dimethyl sulfoxide solution. Aqueous solutions of the polymer have been investigated by measurements of optical rotatory dispersion and viscosity. Various properties sharply change around pH 5 at different ionic strengths. By combining these with infrared studies in D₂O solutions, it has been shown that the polymer exists in the random coil conformation at higher ionization but associates into the intermolecular β-conformation at lower ionization. At the lowest pH attainable in solution, the β-form is partly converted into the random coil as the temperature is raised. The rotatory dispersion of the polymer is described by the Moffitt equation. While the random coil form has a large negative a₀ value and a zero b₀ value, the β-form is characterized by a positive a₀ value and a negative b₀ value, ?130°.     

Conformation and thermostability of double-stranded nucleic acids in aqueous urea solutions

The conformation and thermostability of DNA and double-helical synthetic RNA in aqueous solutions with 0-10 M urea have been investigated. A weak dependence of DNA conformation, realized in the presence of urea, on the GC-content has been found. The increase of urea concentration leads to destabilization of DNA and synthetic RNA. The character of changes in the spectra of RNA circular dichroism at the increase of urea concentration testifies that a conformational transition (different from A----A' transition) takes place. Urea stimulates the B----Z transition in poly(dG-dC).poly(dG-dC) molecules upon NaCl addition.     

Effect of temperature on the conformation of native DNA in aqueous solutions of various electrolytes

Effect of the temperature on the conformation of the native DNA molecule in solution of different electrolytes (LiCl, NaCl, KCl, CsCl, Gu-HCl) at ionic strengths mu = 5; 0.1; 0.01; 0.005 and temperatures ranging from 10 to 40 degrees C were studied by the methods of flow birefringence and viscometry. The experiments showed that the value of intrinsic viscosity [eta] of DNA increases at increase of temperatures in solutions of all the chlorides studied, excluding guanidine. The effect of temperature on the value of [eta] doesn't depend on the type of the cation at a fixed value of mu and is elevated when mu decreases. The observed alterations of the value of [eta] for DNA in water-salt solutions at different temperatures can be explained by an increase in the hydration of the alkaline ions at temperature increase. The experiments showed the specificity of the effect of different ions on the dimensions of the DNA molecule in solution. The data on optical anisotropy of the DNA molecule testify, that the thermodynamic rigidity of the latter doesn't depend on the temperature of solutions of different electrolytes in the temperature range studied.     

In vivo effects of gamma-aminobutyric acid and beta-alanine on thyrotrophin secretion in the normal and hypothyroid rat

The effect of pharmacological doses of two amino acids neurotransmitters, gamma-aminobutyric acid (GABA) and beta-alanine (beta-Ala), on thyrotrophin (TSH) secretion was studied in normal and hypothyroid (PTU-treated) male rats. Inhibition of TSH secretion was observed in normal rats treated with the drugs, 30 min after their administration. Hypothyroid animals responded only to GABA administration, decreasing their serum TSH at 30 min. Response to thyrotrophin-releasing hormone (TRH) after 15 min of drug administration was blunted in GABA injected animals, as compared to saline-injected controls. When TRH was injected at the same time as GABA and beta-Ala, the response was significantly lower than in controls. It is suggested that beta-Ala and GABA act at the pituitary by impairing the TSH response to TRH. The possibility that beta-Ala actions may be due to decreased GABA catabolism is considered, since beta-Ala administration increased GABA synaptosomal levels.     

Theoretical research on structures of gamma-aminobutyric acid and glutamic acid in aqueous conditions

Even though glutamic acid contains only one more carboxyl group than gamma-aminobutyric acid (GABA), these neurotransmitters are recognized by their own specific receptors. To understand the ligand-recognition mechanism of the receptors, we must determine the geometric and electronic structures of GABA and glutamic acid in aqueous conditions using the ab initio calculation. The results of the present study showed that the stable structure of GABA was the extended form, and it attracted both cations and anions. Glutamic acid only attracted cations and was stabilized in four forms in aqueous conditions: Type 1 (an extended form), Type 2 (a rounded form), and Types 3 and 4 (twisted forms of Type 1). The former two types had low energy and the energy barrier between them was estimated to be small. These results showed that most free glutamic acid is present as Type 1, Type 2, and transient forms. The present results therefore suggest that the flexibility of the geometric structures of ligands should be taken into account when we attempt to elucidate the mechanism of recognition between ligands and receptors, in addition to the physicochemical characteristics of ligands and receptors.     

Proton relaxation in aqueous DNA solutions

By use of D₂O we found that the shortening of the longitudinal proton relaxation time which occurs in the investigated aqueous yeast DNA solutions (≦ 2.4% with 2% protein) was not based on a hydration effect, but was caused by magnetic impurities only. An estimate shows that the mobility of the hydrated water molecules is reduced by less than two orders of magnitude in comparison with the free water molecules.     

Change in conformation of proteins in aqueous solutions of heterofunctional nonelectrolytes]

In narrow ranges of concentrations of heterofunctional nonelectrolytes in aqueous solutions, structural transitions occur, which manifest themselves in the self-association of nonelectrolytes molecules and are accompanied by the screening of their hydrophobic groups from the contact with the solvent. In the same nonelectrolytes concentration ranges, conformational changes of protein molecules in solutions take place. The compatibility of the concentration ranges of these two processes is due to the fact that when nonelectrolytes molecules are extruded from the network of hydrogen bonds during the structural transition, both the self-association of nonelectrolytes molecules and their incorporation into the hydrate shell of the protein occur. The dehydration of the protein results in the disturbance of the balance of intra- and intermolecular interactions maintaining the native protein structure, which leads to the rearrangement of the macromolecule conformation.     

Decomposition of gibberellic acid in aqueous solutions

Исследовалось влияние рН и температуры на гидролитическое разложение гибберелевой кислоты в бу?ерных водных растворах. Отдельные продукты гидролиха определяли с помощью хроматогра?ии на бумаге при одновременной спектро?отометриче ской оцерке концентрации образующейся гиббереленовой кислоты. Было установлено, что разложение гибберелевой кислоты в кислой, нейтральной и щелочной среде начинается с образования 1-карбокси-2,3,7-тригидрок си-1-метил-8-метиленгиб б-4-ен 1–3лактон 10 карбоно войкислоты. Это вещес твоприсутствует так же в?ерментационных средах и на различных этапах выделения гибберелевой кислоты. Дальнейшее разложение в растворах с рН 2–8 проходит потом через гиббереленовую кислоту до аллогибберовой кислоты. Следующее превращение аллогибберовой кислоты в гибберовую наблюдалось только в растворе с рН 2 иосле 24-часового прогревания при при 100° С. В растворе с рН 9 процесс разложения приводие к образованию 2,3,7-тригидрокси-1-метил-8-м етиленгибб-4-ен 1,10 дикарбоновой кислоты, которая возникает как главный окончательный продукт гидролиза, наряду с небольшим количеством гиббереленовой кислоты, при данном рН также уже не подвергающейся дальнейшим изменениям. Наибольшей устойчивостью гиььерелевая кислота отличается в растворах с рН 3–4. В нейтральной, а в особенности в слабо щелочной среде ее устойчивость резко понижается. Разложение гибберелевой кислоты в водных растворах значительно ускозяется также при повышении температуры.     

Increased gamma-aminobutyric acid (GABA), homocarnosine and beta-alanine in cerebrospinal fluid of patients treated with gamma-vinyl GABA (4-amino-hex-5-enoic acid)

γ-Vinyl GABA, an enzyme-activated irreversible inhibitor of GABA transaminase (GABA-T), was administered orally to 15 patients with various neurological conditions at daily doses of 0.5, 1, 2 or 6 g/day for 3 days. CSF samples were obtained by lumbar puncture before treatment and within 24 hours after the last dose and the CSF concentrations of free GABA, total GABA, homocarnosine, β-alanine and γ-vinyl GABA determined by ion-exchange chromatography with fluorometric detection. γ-Vinyl GABA treatment produced dose-dependent increases in free GABA, conjugated GABA (defined as total minus free GABA), homocarnosine and β-alanine. The concentrations of CSF γ-vinyl GABA also depended on the dose administered. These results indicate that γ-vinyl GABA enters the CNS after oral administration and alters GABA metabolism by inhibition of GABA-T and suggest that such treatment may achieve therapeutic benefit in conditions where such neurochemical alterations are desirable.     

Dielectric relaxation of DNA in aqueous solutions.

Using a four-electrode cell and a new electronic system for direct detection of the frequency differences specturm of solution impedance, the complex dielectric constant of calf thymus DNA (M_r = 4 × 10⁶) in aqueous NaCl at 10°C is measured at frequencies ranging from 0.2 Hz to 30 kHz. The DNA concentrations are C_p = 0.01% and 0.05%, and the NaCl concentrations are varied from C_s = 10^?4 M to 10^?3 M. A single relaxation regions is found in this frequency range, the relaxation frequency being 10 Hz at C_p = 0.01% and C_s = 10^?3 M. At C_p = 0.05% it is evidenced that the DNA chains have appreciable intermolecular interactions. The dielectric relaxaton time τ_d at C_p = 0.01% agrees well with the rotational relaxation time estimated from the reduced visocisty on the assumption that the DNA is not representable as a rigid rod but a coiled chain. It is concluded that the dielectric relaxiatioinis ascribed to the rotation of the molecule. Observed values of dielectric increment and other experimental findings are reasonably explained by assuming that the dipole moment of DNA results from the slow counterion fluctuation which has a longer relaxation time than τ_d.     

Studies of the conformation of apomyoglobin in aqueous solutions and denaturing organic solvents.

The properties of apomyoglobin were examined in aqueous solutions and various helix- and random-coil-forming solvents by solvent perturbation, optical rotation, circular dichroism, and viscosity measurements. The solvent perturbation data obtained in neutral aqueous solutions suggest 25–40% exposure of the two tryptophyl residues and 50–60% exposure of the three tyrosyls. The estimates of burial of these groups are in the ranges expected for myoglobin based on its X-ray structure. In the helicogenic alcohols, methanol, ethanol, 2-chloroethanol, trifluoroethanol, and 1-propyl alcohol, as well as in acidic solutions, 8 M urea and 6M guanidine hydrochloride, essentially all the tryptophyl and tyrosyl residues are found to be exposed to solvent based on this method. Analysis of the ORD and CD data indicates that in the alcohols the α-helix content of apomyoglobin has in most cases changed from 58–59% to about 80–95%. Analysis of the intrinsic viscosity data based on the equations of Simha and Kirkwood and Auer indicates that the polypeptide chain in these solvents has the dimensions of fully extended α-helical rods, with lengths of 221–251 Å and mean diameters of 12.8–13.6 Å. It is concluded that apomyoglobin in the various alcohols must have an extended but somewhat irregular rodlike structure, having a few bend or irregular sequences between the α-helical segments due largely to the presence of the four proline residues, 37, 88, 100, and 120 in the amino acid sequence.     

DNA conformation in N,N-dimethyl formamide-H2O solutions

Optical density, viscosity, and light scattering measurements for calf thymus DNA in water–N,N dimethyl formamide (DMF) solutions are presented. DMF content varied between 0 and 60% (v/v) and DNA molecular weight varied between 15 × 10⁶ and 0.5 × 10⁶. Complementary measurements of the solubility of adenine, thymine, guanine, and cytosine in H₂O–DMF mixtures are presented. The denaturation temperature of DNA, manifested by about a 35% increase of optical density, is gradually depressed by increasing DMF content. However, a significant increase of OD occurs even before (and even after) the denaturation point, when DMF content is increased isothermally. The intrinsic viscosity also exhibits a large decrease when DMF content is increased both before and after the denaturation point. Light scattering data for high-molecular-weight DNA in the predenaturation range indicate a decrease of the mean-square radius and a constant molecular weight on increasing DMF content. The results, interpreted in terms of the wormlike chain of Kratky and Porod, indicate a large decrease of the persistence length of DNA. For low-molecular-weight DNA, radius and molecular weight increase with DMF content, indicating intermolecular aggregation. The formation of compact structures of native DNA is discussed in terms of an increased solubility of uncharged bases, and a decreased solubility of phosphate and deoxyribose groups, when a less polar environment is provided by the addition of DMF.