Hydration of nucleosides in dilute aqueous solutions. Ultrasonic velocity and density measurements

State of Oxygen Molecules in Aqueous Supersaturated Solutions

The state of oxygen in aqueous supersaturated solutions prepared by different methods was studied using high-resolution ultrasonic spectroscopy in combination with other techniques. This allowed for nondestructive evaluation of the properties of oxygen solute particles, composed of oxygen molecules and surrounding (coordinating) molecules of water, at equilibrium, supersaturated conditions, and different temperatures and concentrations of O₂. The results were compared with the behaviors of other types of solutes in water, including H₂O₂, which has similar molecular size and mass to O₂ but is characterized by a significantly different type of interaction with water molecules. Additionally, theoretical modeling was performed to assess the ultrasonic characteristics of dispersions of oxygen nanobubbles stabilized by a surface electrical charge. The obtained data indicate a clathrate-like organization of water in the coordination shells of single molecules of O₂. We did not find any signs of formation of clusters of oxygen molecules in supersaturated solutions. No quantifiable presence of oxygen nanobubbles in the solutions was detected. The state of O₂ molecules was not affected by supersaturation within the analyzed concentration range of oxygen. The results also demonstrated the potential of the ultrasonic technique in precision real-time nondestructive monitoring of oxygen solubilization and outgassing processes.

Ultrasonic analysis of kinetic mechanism of hydrolysis of cellobiose by β-glucosidase

High-resolution ultrasonic spectroscopy (HR-US) was applied for real-time analysis of enzymatic hydrolysis of cellobiose by a β-glucosidase from Aspergillus niger (Novozyme 188) at 50°C and pH 4.9. This technique is noninvasive, it does not require optical transparency and is suitable to continuously monitor the time dependence of the reaction progress in a broad range of experimental conditions. The time profiles of the amount of glucose released and the reaction rate were obtained from the time profile of ultrasonic velocity. The results are in good agreement with a discontinuous glucose assay (hexokinase method). The kinetic parameters of the reaction were estimated by fitting the ultrasonic time profiles of the reaction rates to several inhibition models. In addition, the equilibrium constant for the reaction of hydrolysis of cellobiose and the molar Gibbs free energy of hydrolysis were determined from the ultrasonic time profiles of concentration of glucose in the reverse reaction (glucose condensation). The results suggest the existence of more complex mechanisms regulating the activity of cellobiase than the combination of simple inhibitions. An extended kinetic model based on two sites for the competitive inhibitor (glucose) is proposed.

Dielectric properties of fully hydrated nucleotides in the terahertz frequency range

We use terahertz time domain spectroscopy (THz-TDS) to determine the complex frequency-dependent dielectric response of all four nucleotides at different dilute concentrations. In addition, the suspension model's ability to extract the dielectric response of just the nucleotide with the hydration shell epsilon(b) excluding the dielectric information relating to the bulk will be verified. The suspension model enables us to make the determination that the nucleotides have influences on the water molecules out to the fourth hydration shell. We use a two Debye relaxation fit model for water, all concentrations and all epsilon(b) values. We observed how the nucleotides affect the relaxation parameters in relation to that of pure bulk water. With this information, we notice a transition between purines and pyrimidines, where one is a hydrogen-bond network structure building type material with a low concentration increment and the other is a structure breaking type material with a low concentration decrement. Due to conductivity measurements, we determine that kinetic depolarization is a negligible affect compared to that of dielectric saturation, which we find to dominate where a decrement is found.

Analysis of the phase diagram and microstructural transitions in phospholipid microemulsion systems using high-resolution ultrasonic spectroscopy

In the present work, high-resolution ultrasonic spectroscopy was applied to analyze a pseudoternary phase diagram for mixtures consisting of water/isopropyl myristate/Epikuron 200 and a cosurfactant (n-propanol). Changes in the ultrasonic velocity and attenuation in the megahertz frequency range were measured in the course of titration of the oil/surfactant/cosurfactant mixture with water at 25 degrees C. The ultrasonic titration profiles showed several phase transitions in the samples, which allowed the construction of an "ultrasonic" phase diagram. Quantitative analysis of the ultrasonic parameters enabled the characterization of various phases (swollen micelles, microemulsion, coarse emulsion, and pseudo-bicontinuous) as well as the evaluation of the state of the water and the particle size. The particle size obtained for the microemulsion region ranged from 5 to 14 nm over the measured concentrations of water/isopropyl myristate/Epikuron 200 and n-propanol, which agreed well with the previous literature data.

Detection of DNA hybridization on a liposome surface using ultrasound velocimetry and turbidimetry methods

19-mer oligonucleotides with oleylamine tethered at 3' and 5' terminal, respectively, were incorporated into unilamellar liposomes of dioleoylphosphatidylcholine (DOPC). Addition of complementary nucleotide resulted in hybridization with oligonucleotides located on different liposomes and caused liposome aggregation. Significant changes of sound velocimetry and turbidity were readily observed at 10 nM concentration of the complementary chain.

Binding of Mg2+ to single-stranded polynucleotides: hydration and optical studies

The binding of Mg(2+) to single-stranded ribo- and deoxy-polynucleotides, poly(rA), poly(rU), poly(dA) and poly(dT), has been investigated in dilute aqueous solutions at pH 7.5 and 20 degrees C. A combination of ultrasound velocimetry, density, UV and CD spectroscopy have been employed to study hydration and spectral effects of Mg(2+) binding to the polynucleotides. Volume and compressibility effects of Mg(2+) binding to random-coiled poly(rU) and poly(dT) correspond to two coordination bonds probably between the adjacent phosphate groups. The same parameters for poly(rA)+Mg(2+) correspond to an inner-sphere complex with three-four direct contacts. However, almost no hydration effects are arising in binding to its deoxy analog, poly(dA), indicating mostly a delocalized binding mode. In agreement with hydration studies, optical investigations revealed almost no influence of Mg(2+) on poly(dA) properties, while it stabilizes and aggregates poly(rA) single-helix. The evidence presented here indicates that Mg(2+) are able to bind specifically to single-stranded polynucleotides, and recognize their composition and backbone conformation.

Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration

It has been shown that the DNA aptamer d(G(2)T(2)G(2)TGTG(2)T(2)G(2)) adopts an intramolecular G-quadruplex structure in the presence of K+. Its affinity for trombin has been associated with the inhibition of thrombin-catalyzed fibrin clot formation. In this work, we used a combination of spectroscopy, calorimetry, density, and ultrasound techniques to determine the spectral characteristics, thermodynamics, and hydration effects for the formation of G-quadruplexes with a variety of monovalent and divalent metal ions. The formation of cation-aptamer complexes is relatively fast and highly reproducible. The comparison of their CD spectra and melting profiles as a function of strand concentration shows that K+, Rb+, NH(4)+, Sr(2+), and Ba(2+) form intramolecular cation-aptamer complexes with transition temperatures above 25 degrees C. However, the cations Li+, Na+, Cs+, Mg(2+), and Ca(2+) form weaker complexes at very low temperatures. This is consistent with the observation that metal ions with ionic radii in the range 1.3-1.5 A fit well within the two G-quartets of the complex, while the other cations cannot. The comparison of thermodynamic unfolding profiles of the Sr(2+)-aptamer and K+ -aptamer complexes shows that the Sr(2+)-aptamer complex is more stable, by approximately 18 degrees C, and unfolds with a lower endothermic heat of 8.3 kcal/mol. This is in excellent agreement with the exothermic heats of -16.8 kcal/mol and -25.7 kcal/mol for the binding of Sr(2+) and K+ to the aptamer, respectively. Furthermore, volume and compressibility parameters of cation binding show hydration effects resulting mainly from two contributions: the dehydration of both cation and guanine atomic groups and water uptake upon the folding of a single-strand into a G- quadruplex structure.

Volumetric characterization of the hydration properties of heterocyclic bases and nucleosides

We have determined the partial molar volumes, expansibilities, and adiabatic compressibilities of six heterocyclic nucleic acid bases, five ribonucleosides, and six 2'-deoxyribonucleosides within the temperature range 18-55 degrees C. We interpret the resulting data in terms of the hydration of the component hydrophobic and polar atomic groups. From our temperature-dependent volumetric studies, we found that the total contraction of water caused by polar groups of each individual heterocyclic base and nucleoside depends on the proximity and chemical nature of other functional groups of the solute. In addition, the compressibility contributions of polar groups vary greatly in sign and magnitude depending on the surrounding functional groups. In agreement with previous studies, our results are suggestive of little or no interaction between the sugar and base moieties of a nucleoside. In general, our data shed light into the hydration properties of individual heterocyclic bases and nucleosides, which may have significant implications for the sequence-dependent hydration of nucleic acids. We discuss the potential importance of our results for developing an understanding of the role that solvent plays in the stabilization/destabilization of nucleic acid structures.

The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques

Using high precision densimetric and ultrasonic measurements, we have determined, at 25 degrees C, the apparent molar volumes PhiV and the apparent molar compressibilities PhiK(S) of four nucleic acid duplexes-namely, the DNA duplex, poly(dIdC)poly(dIdC); the RNA duplex, poly(rA)poly(rU); and the two DNA/RNA hybrid duplexes, poly(rA)poly(dT) and poly(dA)poly(rU). Using available fiber diffraction data on these duplexes, we have calculated the molecular volumes as well as the solvent-accessible surface areas of the constituent charged, polar, and nonpolar atomic groups. We found that the hydration properties of these nucleic acid duplexes do not correlate with the extent and the chemical nature of the solvent-exposed surfaces, thereby suggesting a more specific set of duplex-water interactions beyond general solvation effects. A comparative analysis of our volumetric data on the four duplexes, in conjunction with available structural information, suggests the following features of duplex hydration: (a) The four duplexes exhibit different degrees of hydration, in the order poly(dIdC)poly(dIdC) > poly(dGdC)poly(dGdC) > poly(dAdT)poly(dAdT) approximately poly(dA)poly(dT). (b) Repetitive AT and IC sequences within a duplex are solvated beyond general effects by a spine of hydration in the minor groove, with this sequence-specific water network involving about 8 additional water molecules from the second and, perhaps, even the third hydration layers. (c) Repetitive GC and IC sequences within a duplex are solvated beyond general effects by a "patch of hydration" in the major groove, with this water network involving about 13 additional water molecules from the second and, perhaps, even the third hydration layers. (d) Random sequence, polymeric DNA duplexes, which statistically lack extended regions of repetitive AT, GC, or IC sequences, do not experience such specific enhancements of hydration. Consequently, consistent with our previous observations (T. V. Chalikian, A. P. Sarvazyan, G. E. Plum, and K. J. Breslauer, Biochemistry, 1994, Vol. 33, pp. 2394-2401), duplexes with approximately 50% AT content exhibit the weakest hydration, while an increase or decrease from this AT content causes enhancement of hydration, either due to stronger hydration of the minor groove (an increase in AT content) or due to stronger hydration of the major groove (an increase in GC content). (e) In dilute aqueous solutions, a B-DNA duplex is more hydrated than an A-DNA duplex, a volumetric-based conclusion that is in agreement with previous results obtained on crystals, fibers, and DNA solutions in organic solvent-water mixtures. (f) the A-like, RNA duplex poly(rA)poly(rU) and the structurally similar A-like, hybrid duplex poly(rA)poly(dT), exhibit similar hydration properties, while the structurally distinct A-like, hybrid duplex poly(rA)poly(dT) and non-A-like, hybrid duplex poly(dA)poly(rU) exhibit differential hydration properties, consistent with structural features dictating hydration characteristics. We discuss how volumetric characterizations, in conjunction with structural studies, can be used to describe, define, and resolve the general and sequence/conformation-specific hydration properties of nucleic acid duplexes.

Hydration and partial compressibility of biological compounds

We review the results of compressibility studies on proteins, nucleic acids, and systematically altered low molecular weight compounds that model the constituents of these biopolymers. The model compound data allow one to define the compressibility properties of water surrounding charged, polar, and nonpolar groups. These results, in conjunction with compressibility data on proteins and nucleic acids, were used to define the properties of water that is perturbed by the presence of these biopolymers in aqueous solutions. Throughout this review, we emphasize the importance of compressibility data for characterizing the hydration properties of solutes (particularly, proteins, nucleic acids, and their constituents), while describing how such data can be interpreted to gain insight into role that hydration can play in modulating the stability of and recognition between biologically important compounds.