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.     

Conformation of xanthan dissolved in aqueous urea and sodium chloride solutions

Quasielastic light-scattering and other physical-chemical techniques have been used to compare the conformation and intermolecular interactions of xanthan in water, aqueous sodium chloride, and urea solutions. The results showed that xanthan dissolved in 4m urea has a disordered conformation after the solution has been maintained for 3 h at 95° and then cooled to room temperature. This conformation is similar to that previously observed only in solutions having low ionic strength at higher temperatures, following disruption of the ordered, low-temperature form. “Anomalous” behavior is seen for xanthan as a function of ionic strength, in that the hydrodynamic radius increases with increase in ionic strength, whereas a decrease is typical for polyelectrolytes. These observations suggest that aggregation of rod-like chains, similar to that seen for other stiff-chain polymers, occurs for xanthan in salt solutions, where the charged groups of the polyelectrolyte are screened by the salt ions. This aggregation may explain some of the high values reported in the literature for the molecular weight.     

Long-range order of nucleic acids in aqueous solutions

The structural order of short nucleic acid fragments (having a mean length of 170 nm) in aqueous solution in the presence of high magnetic fields (up to 18.5 tesla) has been investigated by small-angle neutron scattering, light diffraction and by precision measurements of the magnetic birefringence. Our data give clear evidence that, above a critical concentration, the semi-rigid electrically charged fragments arrange themselves into a periodic lattice having an interparticle spacing of ～6 nm. Neighbouring rods show a nearly parallel orientation, but a slight twist seems to exist, leading to a well defined pitch of the order of 1000 nm, which gives rise to a strong diffraction of visible light. The unexpectedly low saturation of the birefringence in the high magnetic field, however, indicates that the order is not of the simple cholesteric type. The forces which are responsible for inducing the twist across the large interparticle distance are mainly anisotropic Van der Waals forces.     

Nanoconstructions based on double-stranded nucleic acids

We describe the formation and properties of nanoconstruction that consists of the double-stranded DNA molecules located at distance of 35-50 A in the spatial structure of particles of their cholesteric liquid-crystalline dispersions and cross-linked by artificial nanobridges. The resulting nanostructures possess the peculiar spatial and optical properties.     

Intercalation conformations in single- and double-stranded nucleic acids

Two regions in the crystal structure of yeast phenylalanine tRNA, where single-stranded loops interact by intercalation, have been examined in detail. There are four examples of a nucleotide base from one loop intercalating between two sequential bases of another loop in these two regions. These four dinucleoside phosphate conformations serve as models for intercalation in single-stranded nucleic acids. Double-stranded DNA and RNA polymers were constructed by computer model building methods, which incorporated the dinucleoside phosphate conformations found in these single-stranded, intercalation regions in otherwise standard double-helices. The results suggest that it is unlikely that there is a unique intercalation geometry for either single- or double-stranded nucleic acids, but that nucleic acids may assume one of a variety of intercalation geometries which will best accommodate a particular intercalating agent for a particular base sequence.     

Conformation of poly-S-carboxyethyl-L-cysteine in aqueous solutions

Poly-S-carboxyethyl-L -cysteine, a higher side-chain homolog of poly-S-carboxymethyl-L -cysteine, has been prepared from poly-S-carbobenzoxyethyl-L -cysteine with hydrogen bromide in chloroform or acetic acid. The polymer is found to be in the β-conformation of an antiparallel arrangement of polypeptide chains in solid films, both in acid and salt forms, when examined by infrared spectra. Aqueous solutions of t he polymer have been investigated by measurements of rotatory dispersion and circular dichroism as well as by infrared spectra in D₂O. These properties show sharp changes around pH 5.5, as the pH of solution is varied. At higher ionization the polymer is randomly coiled, but at lower ionization it is in the β-conformation. Dependence of the rotatory properties upon polymer concentration as well as on ionic strength has been observed even at the lowest degree of ionization attained, and this has been attributed to the formation of intermolecular β-conformation in solutions. The β-structure is characterized by a negative circular dichroic band at 223 mμ and a positive dichroic band at a wavelength lower than 200 mμ, and furt her by a negative b_o value, ?140°. The pH-induced coil-β transition of the polymer is compared with that of poly-S-carboxymethl-L -cysteine.     

Apparent molar volumes of some amino acids and peptides in aqueous urea solutions

Densities of solutions of several α-amino acids and peptides in 3 and 6m aqueous urea solvents have been determined at 298.15 K. These data have been used to evaluate the infinite-dilution apparent molar volumes of the solutes and the volume changes due to transfer (V ) of the α-amino acids and peptides at infinite dilution from water to aqueous urea solutions. The sign and magnitude of the V values have been rationalized in the framework of Friedman's cosphere-overlap model. The V values for the glycyl group (? CH₂CONH? ) and alkyl side chains have been estimated.     

Conformation of carboxymethyl amylose in aqueous solutions

Intrinsic viscosity and specific optical rotation measurements have been carried out for Carboxymethyl amylose (CMA) solutions in 0.15M sodium chloride at various pH values. Potentiometric titrations of CMA have been performed at various polymer concentrations as well as in presence of different divalent cations. The amount of divalent cation (Ni⁺²) bound to CMA has been determined by using a new method af analysis based on polyelectrolyte theory. Finally from the results it is shown that CMA may exist as a random coil in solution.     

Prediction of hybridization and melting for double-stranded nucleic acids

This article presents a general statistical mechanical approach to describe self-folding together with the hybridization between a pair of finite length DNA or RNA molecules. The model takes into account the entire ensemble of single- and double-stranded species in solution and their mole fractions at different temperatures. The folding and hybridization models deal with matched pairs, mismatches, symmetric and asymmetric interior loops, bulges, and single-base stacking that might exist at duplex ends or at the ends of helices. All possible conformations of the single- and double-stranded species are explored. Only intermolecular basepairs are considered in duplexes at this stage.In particular we focus on the role of stacking between neighboring nucleotide residues of single unfolded strands as an important source of enthalpy change on helix formation which has not been modeled computationally thus far. Changes in the states of the single strands with temperature are shown to lead to a larger heat effect at higher temperature. An important consequence of this is that predictions of enthalpies, which are based on databases of nearest-neighbor energy parameters determined for molecules or duplexes with lower melting temperatures compared with the melting temperatures of the oligos for which they are used as a predictive tool, will be underestimated.     

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.     

The differential precipition of nucleic acids and proteins from aqueous solutions by ethanol.

The addition of an appropriate mixture of ethanol, water and sodium perchlorate to crude extracts of some biological material results in the selective precipitation of nucleic acids. Detergent extracts of tissue-cultured plant cells treated with this reagent yielded as much as 95–100% of the nucleic acid while a similar percentage of the total protein remained in solution.     

Recognition of double-stranded RNA by guanidine-modified peptide nucleic acids

Double-helical RNA has become an attractive target for molecular recognition because many noncoding RNAs play important roles in the control of gene expression. Recently, we discovered that short peptide nucleic acids (PNA) bind strongly and sequence selectively to a homopurine tract of double-helical RNA via formation of a triple helix. Herein, we tested if the molecular recognition of RNA could be enhanced by α-guanidine modification of PNA. Our study was motivated by the discovery of Ly and co-workers that the guanidine modification greatly enhances the cellular delivery of PNA. Isothermal titration calorimetry showed that the guanidine-modified PNA (GPNA) had reduced affinity and sequence selectivity for triple-helical recognition of RNA. The data suggested that in contrast to unmodified PNA, which formed a 1:1 PNA-RNA triple helix, GPNA preferred a 2:1 GPNA-RNA triplex invasion complex. Nevertheless, promising results were obtained for recognition of biologically relevant double-helical RNA. Consistent with enhanced strand invasion ability, GPNA derived from d-arginine recognized the transactivation response element of HIV-1 with high affinity and sequence selectivity, presumably via Watson-Crick duplex formation. On the other hand, strong and sequence selective triple helices were formed by unmodified and nucelobase-modified PNA and the purine-rich strand of the bacterial A-site. These results suggest that appropriate chemical modifications of PNA may enhance molecular recognition of complex noncoding RNAs.     

Preferential interactions in aqueous solutions of urea and KCl

A quantitative characterization of the thermodynamic effects due to interactions of salt ions and urea in aqueous solution is needed for rigorous analyses of the effects of changing urea concentration on biopolymer processes in solutions that also contain salt. Therefore, we investigate preferential interactions in aqueous solutions containing KCl and urea by using vapor pressure osmometry (VPO) to measure osmolality as a function of the molality of urea (component 3) over the range 0.09相似文献