Hydration of nucleic bases in dilute aqueous solutions. Apparent molar adiabatic and isothermal compressibilities, apparent molar volumes and their temperature slopes at 25 degrees C

The volume changes of unfolding of dsDNA

High hydrostatic pressure can have profound effects on the stability of biomacromolecules. The magnitude and direction (stabilizing or destabilizing) of this effect is defined by the volume changes in the system, ΔV. Positive volume changes will stabilize the starting native state, whereas negative volume changes will lead to the stabilization of the final unfolded state. For the DNA double helix, experimental data suggested that when the thermostability of dsDNA is below 50°C, increase in hydrostatic pressure will lead to destabilization; i.e., helix-to-coil transition has negative ΔV. In contrast, the dsDNA sequences with the thermostability above 50°C showed positive ΔV values and were stabilized by hydrostatic pressure. In order to get insight into this switch in the response of dsDNA to hydrostatic pressure as a function of temperature, first we further validated this trend using experimental measurements of ΔV for 10 different dsDNA sequences using pressure perturbation calorimetry. We also developed a computational protocol to calculate the expected volume changes of dsDNA unfolding, which was benchmarked against the experimental set of 50 ΔV values that included, in addition to our data, the values from the literature. Computation predicts well the experimental values of ΔV. Such agreement between computation and experiment lends credibility to the computation protocol and provides molecular level rational for the observed temperature dependence of ΔV that can be traced to the hydration. Difference in the ΔV value for A/T versus G/C basepairs is also discussed.

Effects of combination treatments of lysozyme and high power ultrasound on the Salmonella typhimurium inactivation and quality of liquid whole egg

An investigation was conducted into the utilization of treatments combining ultrasound and lysozyme (US + Lys) to deactivate Salmonella typhimurium (S. typhimurium) in the liquid whole egg (LWE). Furthermore, US + Lys and heat treatment (HT) with a similar microbial inactivation effect were comparatively evaluated by examining their impact on the quality attributes of LWE. The LWE was treated with US at 35-45 °C and 605-968 W/cm² for 5-35 min, and with HT at 58-64 °C for 3-4 min. Lysozyme (Lys) alone achieved a minimal degree of inactivation in S. typhimurium, while it was enhanced with the application of US alone when the treatment temperature, time, and energy were increased. Furthermore, US and US + Lys caused a reduction of 3.31 and 4.26 log₁₀ cycles in S. typhimurium, respectively at 968 W/cm² and 35 °C for 20 min, indicating a synergistic relationship between US and Lys for the effective inactivation of S. typhimurium. Similarly, HT and HT + Lys achieved a reduction of 4.10 and 4.75 log₁₀ cycles at 64 °C/3 min, respectively. The L* and b* values of the LWE following US and US + Lys application were significantly higher than untreated and heat-treated LWE, indicating that US treated LWE had a brighter and yellower appearance. The protein solubility (PS) slightly decreased after all treatments, while the pH increased. Furthermore, the foaming capacity (FC) and foam stability (FS) were decreased, revealing that LWE had a lower FC and unstable foam after all treatments. Therefore, US and US + Lys could increase the viscosity and gelation temperature (Tg) of LWE, indicating that LWE exhibited higher heat resistance after US treatment. These results indicated that US + Lys might be a promising pasteurization technology in the processing of LWE.

DEAE-dextran hydrochloride behaviour in aqueous solution-The effect of ionic strength and concentration

DEAE-dextran hydrochloride is a positively charged biocompatible polyelectrolyte. Its behaviour in aqueous solutions - the changes in its colloidal characteristics and resulting conformation changes - were investigated using a combination of light scattering, densitometry and ultrasound spectrometry. The results indicated the formation of a voluminous, hydrated and coiled conformation of chains having average particle sizes in the range of units of microns at low ionic strength. This phenomenon was supported by an increase in DEAE-dextran hydrochloride concentration in the solution. The increase in ionic strength caused the shielding of DEAE-dextran hydrochloride charges on its chain, resulting in the destabilization of the conformation arrangement of the polyelectrolyte and the formation of denser, more compact and stiffer structures having smaller particle sizes. The proposed model of DEAE-dextran hydrochloride density in the studied environments (distilled water, NaCl solutions) showed the possibility of using a single equation model to calculate the overall density of the system.

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.

Factors influencing structural heat-induced structural relaxation of dissolved organic matter

Physical and chemical structure affect properties of dissolved organic matter (DOM). Recent observations revealed that heating and cooling cycles at higher temperature amplitude lead to a change in DOM physical conformation assumingly followed by a slow structural relaxation. In this study, changes at lower temperature amplitudes and their relation to DOM composition were investigated using simultaneous measurements of density and ultrasonic velocity in order to evaluate the adiabatic compressibility, which is sensitive indicator of DOM structural microelasticity. Six fulvic acids (FAs) having various origins were analyzed at concentrations of 0.12, 0.6 and 1.2 g L^-1 and at different temperature amplitudes. First, we validated that the used technique is sensitive to distinguish conclusively the structural changes upon heating and cooling of DOM with heating/cooling amplitude of ± 3 °C and higher. This amplitude was then applied to observe the relationship between change in adiabatic compressibility and chemical composition of FA. No correlation was observed with elemental composition and aromatic structures. Positive correlations were observed with content of alkyl moieties, carboxylic and carbonyl carbons and biological activity. Based on literature data, it was concluded that alkyl moieties undergo (re)crystalization during thermal fluctuation and their structural relaxation back is very slow (if occurs). The polar moieties form a flexible hydrogel responding to thermal fluctuation by moderate dissolution and re-aggregation. Negative correlation was observed in relation to the amount of peptide and O-alkyl systems, which can be attributed to very fast structural relaxation of proteinaceous materials, i.e. their larger content leads to lower difference between original and heat-induced compressibility. Last, the increase of the heating/cooling amplitude from ± 3 to ± 15 °C resulted in an increase of the change of the adiabatic compressibility and in the extension of the relaxation time needed for DOM structure to return to the equilibrium. We conclude that this increase is caused by the increase in inner energy, and DOM conformation can reach a cascade of energy minima, which may influence DOM reactivity and biodegradability.

High-resolution ultrasonic spectroscopy study of interactions between hyaluronan and cationic surfactants

Interactions in a cationic surfactant-hyaluronan system in water and in sodium chloride solution were investigated by high-resolution ultrasonic spectroscopy at 25 °C. Two alkyltrimethylammonium bromide surfactants of different chain lengths (tetradecyl and hexadecyl) were used; hyaluronan molecular weight ranged from 10 to 1750 kDa. Two main parameters-ultrasonic velocity and attenuation-were measured in the titration regime. Up to six different regions could be identified in the velocity titration profiles in water in a narrow interval of surfactant concentration. These regions differed primarily in the compressibility of structures formed in the system. The number of detected transitions was higher for the tetradecyl surfactant; therefore, the increased length of the hydrophobic chain simplified the details of the structure-forming behavior. The measurement of attenuation was much less sensitive and detected only the formation of microheterogeneous structures or visible phase separates. The richness of the titration profiles was depressed in salt solution, where essentially only two principal regions were observed. On the other hand, the effect of hyaluronan molecular weight on the positions of boundaries between regions was more significant in the presence of salt. Besides electrostatic interactions, hydrophobic interactions are also relevant for determining the behavior of hyaluronan-surfactant systems and the properties of formed complexes (aggregates).

Origin of heat-induced structural changes in dissolved organic matter

Humic substances play an important role in many environmental processes such as sequestration and transport of hydrophobic compounds. The supramolecular character of humic substances imparts high flexibility of the aggregates associated with their variable reactivity under different conditions. In this study, heat-induced transitions and character of the hydration shell of sodium salts of humic and fulvic acids originating from various sources were investigated using ultrasonic velocimetry in the temperature interval from 5 to 90 °C. Results clearly showed differences in stability and characteristics of the hydrated states at concentrations above and below 1 g L(-1) with the exception of Pahokee peat fulvic acids. It has been concluded that predominantly the relaxation part of the adiabatic compressibility plays an important role below 1 g L(-1) in contrast to both relaxation and intrinsic parts of the compressibility being important at higher concentrations. Dilution brought several temperature induced transitions which were investigated with respect to composition of all investigated humic substances. Correlation analysis revealed that the transition around 17 °C is associated with disruption of H-interactions whereas the transition around 42 °C depends on the aromaticity. Comparison of cooling and heating records revealed hysteresis in the structural relaxation resembling the behavior of physically stabilized hydrogels. Results indicated a difference in the conformation and therefore reactivity of dissolved humic substances in the dependence on temperature and thermal history. It has been hypothesized that this may play an important role in the transport and sequestration of hydrophobic pollutants by dissolved organic matter.

β-Casein aids in the formation of a sodium caprate-induced β-lactoglobulin B gel

The effects of sodium caprate on the gelation of β-lactoglobulin B and a β-lactoglobulin B/β-casein mixture at ambient temperature were investigated using ultrasonic spectroscopy and rheology. A 12% β-lactoglobulin B solution gelled in the presence of 3.6% sodium caprate. Conversely, sodium caprate did not induce the formation of a gel when β-casein was in isolation, regardless of the protein concentration. Although a 6% β-lactoglobulin B/1.8% sodium caprate solution did not form a gel, a gel was formed when 6% β-casein was added to a mixture containing 6% β-lactoglobulin B and 3.6% sodium caprate. This gel showed comparable rheological properties to that of a gel containing 12% β-lactoglobulin B. The results clearly indicated that β-casein aids in the gelation of a β-lactoglobulin B/sodium caprate mixture, when the concentration of β-lactoglobulin B is insufficient to allow for gelation. It appears that β-casein self-aggregation is also inhibited. Therefore, it could be concluded that β-casein can be used as a texture modifier for β-lactoglobulin gelation induced by sodium caprate.

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.

Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs

The thermodynamics of base pairing is of fundamental importance. Fluorinated base analogs are valuable tools for investigating pairing interactions. To understand the influence of direct base-base interactions in relation to the role of water, pairing free energies between natural nucleobases and fluorinated analogs are estimated by potential of mean force calculations. Compared to pairing of AU and GC, pairing involving fluorinated analogs is unfavorable by 0.5-1.0 kcal mol(-1). Decomposing the pairing free energies into enthalpic and entropic contributions reveals fundamental differences for Watson-Crick pairs compared to pairs involving fluorinated analogs. These differences originate from direct base-base interactions and contributions of water. Pairing free energies of fluorinated base analogs with natural bases are less unfavorable by 0.5-1.0 kcal mol(-1) compared to non-fluorinated analogs. This is attributed to stabilizing C-F(...)H-N dipolar interactions and stronger N(...)H-C hydrogen bonds, demonstrating direct and indirect influences of fluorine. 7-methyl-7H-purine and its 9-deaza analog (Z) have been suggested as members of a new class of non-fluorinated base analogs. Z is found to be the least destabilizing universal base in the context of RNA known to date. This is the first experimental evidence for nitrogen-containing heterocylces as bioisosteres of aromatic rings bearing fluorine atoms.

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.

Specific volume and compressibility of human serum albumin–polyanion complexes

The ultrasound velocimetry, densitometry, and differential scanning calorimetry have been used to study the formation of the complexes between human serum albumin (HSA) and polyanions heparin (HEP) and/or dextran sulfate (DS). The values of the ultrasound velocity and specific volume allowed us to determine the specific adiabatic compressibility, phi(K)/beta(0), which reflects the degree of volume compressibility of the complexes. We showed that in the presence of HEP and DS the adiabatic compressibility of HSA decreases with increasing concentration of polyanions. HEP more strongly interacts with HSA than DS. pH of electrolyte in the range 4.7-8.5 weakly affects the adiabatic compressibility. Changes of compressibility of HSA can be caused by increase of the hydration due to the formation of the HSA-polyanion complexes and due to partial unfolding of HSA. The HSA-polyanion interaction resulted in decrease of phase transition temperature of the protein. This evidences about protein destabilization in the presence of polyanions.

Heat-induced changes in the ultrasonic properties of whey proteins

The physical aggregation of commercial whey protein isolate (WPI) and purified beta-lactoglobulin was studied by ultrasound spectroscopy. Protein samples were dialyzed to achieve constant ionic strength backgrounds of 0.01 and 0.1 NaCl, and gelation was induced in situ at constant temperatures (from 50 to 75 degrees C) or with a temperature ramp from 20 to 85 degrees C. Changes in the ultrasonic properties were shown in the early stages of heating, at temperatures below those reported for protein denaturation. During heating, the relative ultrasound velocity (defined as the difference between sample velocity and reference velocity) decreased continuously with temperature, indicating a rearrangement of the hydration layer of the protein and an increase in compressibility of the protein shell. At temperatures <50 degrees C the ultrasonic attenuation decreased, and <65 degrees C both velocity and attenuation differentials showed increasing values. A sharp decrease in the relative velocity and an increase in the attenuation at 70 degrees C were indications of "classical" protein denaturation and the formation of a gel network. Values of attenuation were significantly different between samples prepared with 0.01 and 0.1 M NaCl, although no difference was shown in the overall ultrasonic behavior. WPI and beta-lactoglobulin showed similar ultrasonic properties during heating, but some differences were noted in the values of attenuation of WPI solutions, which may relate to a less homogeneous distribution of aggregates caused by the presence of alpha-lactalbumin and other minor proteins in WPI.

DNA oligonucleotide duplexes containing intramolecular platinated cross-links: energetics, hydration, sequence, and ionic effects

The anticancer activity of cisplatin arises from its ability to bind covalently to DNA, forming primarily intrastrand cross-links to adjacent purine residues; the most common adducts involve d(GpG) (65%) and d(ApG) (25%) intrastrand cross-links. The incorporation of these platinum adducts in a B-DNA helix induces local distortions, causing bending and unwinding of the DNA. In this work, we used temperature-dependent UV spectroscopy to investigate the unfolding thermodynamics, and associated ionic effects, of two sets of DNA decamer duplexes containing either cis-[Pt(NH(3))(2)[d(GpG]] or cis-[Pt(NH(3))(2) [d(ApG]] cross-links, and their corresponding unmodified duplexes. The platinated duplexes are less stable and unfold with lower T(M)s (and Delta G degrees s) in enthalpy-driven reactions, which indicates a loss of favorable base-pair stacking interactions. The folding thermodynamics and hydration effects for the first set of decamers containing the d(GpG) cross-link was investigated by a combination of titration calorimetry, density, and ultrasound techniques. The hydration parameters showed an uptake of structural water by the platinated duplex and a release of electrostricted water by the control duplex. Relative to the unmodified duplex, the folding of the platinated duplex at 20 degrees C yielded a positive Delta Delta G degrees term [and positive Delta Delta H-Delta(T Delta S) compensation] and a negative differential volume change. The opposite signs of the Delta Delta G degrees and Delta Delta V terms confirmed its uptake of structural water. Further, solvent-accessible surface areas calculations for a similar pair of dodecamer duplexes indicated that the modified duplex has a 503 oeA(2) higher polar and nonpolar surface area that is exposed to the solvent. Therefore, the incorporation of a platinum adduct in duplex DNA disrupts favorable base-pair stacking interactions, yielding a greater exposure of aromatic bases to the solvent, which in turn immobilizes structural water. The overall results correlate nicely with the results reported in the available structural data of nuclear magnetic resonance solution studies.

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.

Hexamminecobalt(III)-induced condensation of calf thymus DNA: circular dichroism and hydration measurements

The interaction of hexamminecobalt(III), Co(NH(3))(6)(3+), with 160 and 3000-8000 bp length calf thymus DNA has been investigated by circular dichroism, acoustic and densimetric techniques. The acoustic titration curves of 160 bp DNA revealed three stages of interaction: (i) Co(NH(3))(6)(3+) binding up to the molar ratio [Co(NH(3))(6)(3+)]/[P] = 0.25, prior to DNA condensation; (ii) a condensation process between [Co(NH(3))(6)(3+)]/[P] = 0.25 and 0.30; and (iii) precipitation after [Co(NH(3))(6)(3+)]/[P] = 0.3. In the case of 3000-8000 bp DNA only two processes were observed: (i) binding up to [Co(NH(3))(6)(3+)]/[P] = 0.3; and (ii) precipitation after this point. In agreement with earlier observations, long DNA aggregates without changes in its B-form circular dichroism spectrum, while short DNA demonstrates a positive B-->Psi transition after [Co(NH(3))(6)(3+)]/[P] = 0.25. From ultrasonic and densimetric measurements the effects of Co(NH(3))(6)(3+) binding on volume and compressibility have been obtained. The binding of Co(NH(3))(6)(3+) to both short and long DNA is characterized by similar changes in volume and compressibility calculated per mole Co(NH(3))(6)(3+): DeltaV = 9 cm(3) mol(-1) and Deltakappa = 33 x 10(-4) cm(3) mol(-1) bar(-1). The positive sign of the parameters indicates dehydration, i.e. water release from Co(NH(3))(6)(3+) and the atomic groups of DNA. This extent of water displacement would be consistent with the formation of two direct, hydrogen bonded contacts between the cation and the phosphates of DNA.

Ultrasonic shear wave rheology of weak particle gels

Weak particle gels have attracted increasing attention in the last decade. These gels have a very short region of deformation over which their viscoelastic parameters are constant. They can be broken easily in response to external forces. Therefore the rheological measurements in these systems must be performed at very small deformations, which may frequently be below the accuracy limits of conventional rheological instruments. In the present paper we discuss the application of the thickness shear mode resonator technique for the measurement of viscoelastic parameters of weak particle gels in the MHz frequency range. The technique provides information on the viscoelasticity of weak gels in the time scale 10(-7)-10(-9) s. The length scale of the measurements, determined by the depth of penetration and the wavelength of the shear wave, falls in the submicron and micron range. The displacements in the shear deformations generated in this technique are extremely small, in the order of Angstroms, and the shear strain, approximately 10(-3), corresponds to the low limits in the classical dynamic rheology measurements. Only small volumes, down to 0.1 ml, of sample are required and this is another advantage of this technique. The measurements of the storage, G', and the loss, G'', moduli can be carried out non-invasively and continuously at various frequencies in the same sample during the whole length of the process of gelation. General and specific aspects of the measurements and interpretation of experimental results are discussed in the present paper.

Interaction of alkaline-earth metal ions with calf thymus DNA. Volume and compressibility effects in diluted aqueous solutions

The binding of Mg2+, Ca2+, Sr2+ and Ba2+ ions to calf thymus DNA in solutions has been investigated by ultrasonic and densimetric techniques. The obtained parameters, the apparent molar volume, phiV, and the apparent molar adiabatic compressibility, phiK(S), are very sensitive to hydration of investigated molecules. The interaction between the cations and DNA is accompanied by overlapping their hydration shells and consequently releasing the water molecules from hydration shells to bulk state. The change in the hydration is reflected in the measured parameters, phiV and phiK(S). The magnitude of these hydration changes is determined by the position of the cation relative to DNA atomic groups involved in the binding, and thus can characterize the structure of cation-DNA complexes. The values of the dehydration effects of the binding, deltaphiV and deltaphiK(S), correspond to two direct or higher number of indirect contacts between calf thymus DNA and the cations.

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.

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

The values of the concentration increments of the ultrasound velocity and their temperature slopes, apparent molar volumes, apparent molar expansibilities, apparent molar adiabatic compressibilities and their temperature gradients for 12 nucleosides and their analogs, as well as for ribose and deoxyribose, have been obtained using precision measurements of ultrasound velocity and density. The following hydration parameters for the atomic groups of the nucleosides, reflecting the state of water in the hydration shells of these groups, have been analyzed: (1) the contribution of ribose to the values of the concentration increment of ultrasound velocity A, the apparent molar volumes phi v and apparent molar adiabatic compressibilities phi ks of nucleosides; (2) contributions of the CH3, NH2 and O = ... -H groups of nucleic bases to the A, phi v and phi ks values of nucleosides and free nucleic bases; (3) contributions of the 2'-OH group of ribose to the values of A, phi v and phi ks nucleosides; (4) changes in the A values of nucleosides and free nucleic bases upon their protonation and deprotonation. Data have been obtained on the mutual influence of the atomic groups of nucleosides on their hydration. It is shown that the GC pairs of free deoxynucleosides undergo hydration more vigorously than the AT pairs, which contrasts with the relation of the degree of hydration of the GC and AT pairs of the double helix.

Measurement of anomalously high hydration of (dA)n.(dT)n double helices in dilute solution

Different DNA sequences have different physical properties, which seem to be important for their biological function. In particular, (dA)n.(dT)n has many unusual features, which include resistance to conformational changes in a variable chemical environment, an unusual thermodynamics of interaction with ligands, and the inability to reassociate into nucleosomes. Short A.T base-pair runs also play a critical role in DNA bending. It is believed that hydration of DNA is an important factor in determining the physical chemical and biological properties of different regions of DNA. Until now, however, it has not been possible to study the details of the hydration of DNA in dilute solution with sufficient sensitivity and precision. Moreover, it was not known if different base sequences differ in the extent of their hydration. Indirect evidence that (dA)n.(dT)n can be hydrated to a greater extent than other DNA sequences may be inferred from a recent study of the binding of drugs to polynucleotides. Here we used a novel high-precision technique measuring ultrasonic velocity to obtain direct estimates of the extent of hydration of various oligo- and polynucleotides in dilute solution. We report that different DNA sequences differ in their hydration, and that (dA)n.(dT)n in particular has an anomalously high level of hydration.

Acoustical investigation of poly(dA).poly(dT), poly[d(A-T)], poly(A).poly(U) and DNA hydration in dilute aqueous solutions

Apparent molar adiabatic compressibilities and apparent molar volumes of poly[d(A-T)].poly[d(A-T)], poly(dA).poly(dT), DNA and poly(A).poly(U) in aqueous solutions were determined at 1 degree C. The change of concentration increment of the ultrasonic velocity upon replacing counter ion Cs+ by the Mg2+ ion was also determined for these polymers. The following conclusions have been made: (1) the hydration of the double helix of poly(dA).poly(dT) is remarkably larger than that of other polynucleotides; (2) the hydration of the AT pair in the B-form DNA is larger than that of the GC pair; (3) the substitution of Cs+ for Mg2+ ions as counter ions results in a decrease of hydration of the system polynucleotide plus Mg2+, and (4) the magnitude of this dehydration depends on the nucleotide sequence; the following rule is true: the lesser is a polynucleotide hydration, the larger dehydration upon changing Cs+ for Mg2+ ions in the ionic atmosphere of polynucleotide.