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°.     

DNA conformation and thermostability of aqueous solutions of beta-alanine and gamma-aminobutyric acid

It has been shown that at low concentrations of rare amino acids (from 10(-3) M to 10(-1) M of the substance) stechiometric complexes amino acid -- DNA are formed, which bring about partial substitution of counterions screening phosphate groups and to a change of spatial structure of DNA water molecules. The DNA-solvent molecular interactions are changed, accompanied by an abrupt decrease of helix-coil enthalpy transition which leads to the unwinding of DNA double helix. In the region of amino acid high concentrations (greater than 1-1,5 M) a rise of thermostability and winding of DNA double helix is observed. It has been established that B----C-like conformational transition stimulated by the rise of DNA thermostability is a result of counterions dehydration and the increase of effective ionic strength of the solution which is due to the rise of amino acid-zwitterions content in it.     

An infrared study on the conformation of poly-L-proline in concentrated aqueous salt solutions

The infrared absorption of poly-L -proline in concentrated aqueous salt solutions was measured in the fundamental region. Of primary interest were the carbonyl absorption of the peptide linkage and the methylene C–H bending absorption of the pyrrolidine ring. These spectral regions each show an additional component in the concentrated salt solutions. Using the position of the absorptions of poly-L -proline I (cis) and II (trans) as models, we conclude that both cis–trans linkages are present in the peptide in salt solutions. Increasing the temperature shifts the equilibrium slightly in favor of cis.     

Effect of various physical factors on oscillations of light-dispersion in water and aqueous biopolymer solutions

Study of the dependence of light scattering fluctuation on temperature, mechanic perturbation and magnetic field in water and water hemoglobin and DNA solution has shown that an increase in temperature results in the decline of long-term fluctuation amplitude and in the increase of short-term fluctuation amplitude. Mechanical mixing removes long-term fluctuations and over 10 hours are spent for their recovery. Regular fluctuations appear when the constant magnetic field above 240 A/m is applied; the fluctuations are retained for many hours after the removal of the field (when the field is off). It was supposed that maintenance of long-range correlation of molecular rotation-translation fluctuation by the effect of long-range forces and external fields underlies the mechanism of long-term light scattering fluctuations.     

Effect of monovalent anions of various nature on conformation of DNA molecules in a water-salt solution

Methods of intrinsic viscosity [eta] and beam flow birefringence were used to study the effects of some single-charged ions (F-, Cl-, Br-, J-, NO2-, NO3-, ClO4-, SCN-, CH3COO-) on the size and thermodynamic rigidity of DNA molecule in aqueous solutions of sodium salts in a broad interval of ionic strength mu when temperature T is changed. It has been shown that the close interactions in a macromolecule and the resulting persistent length a of DNA are independent of the type of the salt anion over the whole interval of mu. On the contrary, specific volume of DNA molecule in solution, proportional to [eta] value, is quite sensitive to the anionic composition of a solvent which is due to the effect of anions and their hydration on the remote interactions in the macromolecule. The presence of polyatomic and halide anions is manifested differently in the [eta] value of DNA. Possible factors responsible for the observed effect and the role of structural alterations of water upon anion hydration are discussed.     

Effect of temperature on viscosity properties of some alpha-amino acids in aqueous urea solutions

Viscosities for solutions of glycine, DL-alpha-alanine, DL-alpha-amino-n-butyric acid, DL-valine, DL-leucine and L-serine in 5 mol kg(-1) aqueous urea have been determined at 278.15, 288.15, 298.15 and 308.15 K. The viscosity B-coefficients for the amino acids in the aqueous urea solution have been calculated at different temperatures. The effect of temperature on the B-coefficients is discussed on the basis of the Feakins equation. The contribution of solute to the activation parameters (delta mu0*2, deltaH0*2, deltaS0*2) for viscous flow of the solution have been calculated, together with the Gibbs energy, enthalpy and entropy of transfer for the amino acids from the ground-state solvent to the hypothetical viscous transition state solvent. The contributions of the charged end group (NH3+, COO-) and CH2 groups of the amino acids to B-coefficient and delta mu0*2 have been also estimated using the linear correlations between B-coefficient or delta mu0*2 and the number of carbon atoms in the alkyl chains of the amino acids. All the activation parameters are discussed in terms of the solute-solvent interactions in the ground and transition states.     

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.     

Low-temperature heat capacity of DNA in various conformation states

Experimental results are presented on temperature--dependent DNA heat capacity in three different states: a) intact--native DNA in the conformation of double helix, b) disordered conformation of polynucleotide chains in the state of statistical coils, c) completely "degenerated" polynucleotide chains--mechanical mixture of nucleotides. Data on heat capacity (4-400 K) at different water content in the specimens allow a definition of relative changes in the pattern of the entropy temperature dependence for these conformational states with the account for the structural effect of water.     

Effect of pH on the conformation of gellan chains in aqueous systems

The optical rotation and fluorescence anisotropy for gellan aqueous systems were measured at pH 4, 7, and 10 to elucidate the effect of pH on the conformation of gellan chains. The optical rotation study suggests that pH affects the conformation of helical gellan chains and their aggregation behavior but the coil-helix transition temperature. By comparing the chain mobility estimated from the fluorescence anisotropy between different pH conditions, it has been revealed that the degree of expansion of random-coiled gellan chains varies with pH. These results indicate that the effect of pH is explained by the change in the anionic nature of gellan chains rather than in the shielding effect of hydrogen ions surrounding gellan chains as a cation species.     

Protein-protein and protein-salt interactions in aqueous protein solutions containing concentrated electrolytes

Protein-protein and protein-salt interactions have been obtained for ovalbumin in solutions of ammonium sulfate and for lysozyme in solutions of ammonium sulfate, sodium chloride, potassium isothiocyanate, and potassium chloride. The two-body interactions between ovalbumin molecules in concentrated ammonium-sulfate solutions can be described by the DLVO potentials plus a potential that accounts for the decrease in free volume available to the protein due to the presence of the salt ions. The interaction between ovalbumin and ammonium sulfate is unfavorable, reflecting the kosmotropic nature of sulfate anions. Lysozyme-lysozyme interactions cannot be described by the above potentials because anion binding to lysozyme alters these interactions. Lysozyme-isothiocyanate complexes are strongly attractive due to electrostatic interactions resulting from bridging by the isothiocyanate ion. Lysozyme-lysozyme interactions in sulfate solutions are more repulsive than expected, possibly resulting from a larger excluded volume of a lysozyme-sulfate bound complex or perhaps, hydration forces between the lysozyme-sulfate complexes.     

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.     

Effect of the pH of the medium on DNA conformation

The hydrodynamical and optical properties of DNA were investigated in the wide-range of pH by the methods of streaming birefringence, viscometry and spectrophotometry for the different ionic strengths of environment. The measurements of the intrinsic viscosity as a function of pH allow us to determine the compactization of protonated DNA without the destruction of double-helical conformation. This transition is accompanied by a decrease in the optical anisotropy of DNA and the coefficient of molar extinction E260 (P). The increase of volume and persistence length of DNA was observed in the alkaline range of pH. Analyses of experimental data lead to an assumption that the predominant cause of these effects is the change of flexibility of DNA as a result of ionization of its bases. The data obtained were compared with those for polycationic molecules.     

Sol-gel transition temperature of PLGA-g-PEG aqueous solutions

Aqueous solutions of poly(DL-lactic acid-co-glycolic acid)-g-poly(ethylene glycol) copolymers exhibited sol-to-gel transition with increasing temperature. Further increase in temperature makes the system flow and form a sol phase again. Subcutaneous injection of a copolymer aqueous solution (0.5 mL) resulted in a formation of a hydrogel depot by temperature-sensitive sol-to-gel transition in a rat model. The reliable determination and control of sol-to-gel transition temperatures are the most important issues for this kind of sol-gel reversible hydrogel. The sol-to-gel transition temperature determined by the test tube inverting method, falling ball method, and dynamic mechanical analysis coincided within 1-2 degrees C. Fine tuning of the sol-to-gel transition temperature was achieved by varying the ionic strength of the polymer solutions and by mixing two polymer aqueous solutions with different sol-to-gel transition temperatures. The sol-to-gel transition temperature of polymer mixture aqueous solutions was well described by an empirical equation of miscible blends, indicating miscibility of the two polymer systems in water on the molecular level.     

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.