Thermochemistry of aqueous solutions of alkylated nucleic acid bases. VI. Enthalpies of hydration of 2-alkyl-9-methyladenines

Enthalpies of solution in water, delta H0sol, and vant'Hoff enthalpies of sublimation, delta H0subl, were determined experimentally for a number of crystalline 2-alkyl derivatives of 9-methyladenine: m2(2,9)Ade, e2m9Ade, pr2m9Ade and but2m9Ade. Standard enthalpies of hydration, delta H0hydr derived from these data were corrected for the calculated cavity terms, delta H0cav, to yield enthalpies of interaction, delta H0int, of the solutes with their hydration shells. The apparent residual contribution of alkyl groups, R, to the enthalpy of interaction delta delta H0int (R) was found to increase linearly with the number of CH2 groups added upon alkyl substitution, whereas this contribution calculated per unit area of the water-accessible molecular surface, SB, of alkyl residues delta delta H0int (R): delta SB(R) appeared constant over the whole series of the compounds investigated. This indicates that alkyl groups substituted at the C(2) carbon atom of the adenine contribute additively to the van der Waals' part of the enthalpy of interaction and do not affect the electrostatic part of the energy of interaction of the solutes with their hydration shells.     

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. III. Enthalpies of hydration of uracil, thymine and their derivatives

Enthalpies of sublimation DeltaH(0)(subl) crystalline uracil, thymine and their methylated derivatives as well as of N,N-diethylthymine were determinated by the quartz-resonator method and mass spectrometry. Enthalpies of solution at infinite dilution DeltaH(0)(sol) in water of aBcylated compounds were obtained calorimetrically. Hence the calculated enthalpies of hydration: DeltaH(0)(hydrsubal) = DeltaH(0)(sol) - DeltaH(0)(subl), were corrected for energies of cavity formation in pure liquid water to yield enthalpies of interaction DeltaH(0)(sint) of the solutes with their hydration shells. For uracil DeltaH(0)(int) = -59.8 kJ mole(-1) was obtained in this way. This value decreased linearly on N-methyl substitution with a mean increment of about 6.5 kJ mole CH2(-1). After C(5) or C(6) ring substitution it increased by about 3 kJ. These results are discussed in connection with heat of dilution data and theoretical schemes of hydration.     

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. II. Apparent molar relative enthalpies of dilution of solutions containing uracil and thymine derivatives

Apparent molar relative enthalpies of dilution φ_Lof aqueous solutions of a series of alkylated diketopyrimidines: m¹Ura, m^1,3₂Ura, m^1,3₂Thy, m^1,3,6₃Ura and e^1,3₂Thy were measured as a function of concentration of the solutes at three temperatures 298.15, 308.15 and 318.15 K. Dilution proved to be an endothermic process over the whole range of molalities m and temperatures studied for all compounds except the e^1,3₂Thy solution, the dilution of which, with the exception of the lowest concentrations (m > 0.2–0.3) was an exothermic process. Partial molar relative enthalpies of dilution -L₂(m) derived from φ_L(m) functions were analysed as if they were composed of two additive contributions: an endothermic one -L₂, (m₁) and an exothermic one 1.2, (m_as0), owing to the presence in the solutions of a free monomer m₁ or associated species m_as, respectively. Partial molar heat capacities of the solutes, evaluated by differentiation of -L₂(m) functions in respect to temperature, decreased with the rise of concentration in the order of the tendency of the solutes to stacking association. Changes in heat content and in heat capacity of solutions upon their dilution are interpreted in terms of involvement of hydrophobic hydration and association of the solutes.     

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. I. Apparent molar heat capacities of uracil, thymine and their derivatives

Apparent molar heat capacities phiC(p(1,3)) of uracil, thymine and a series of their alkylated derivatives: m(1)Ura,m(1,3)(2) Ura, m(1,3)(2)Thy, mi(1,3,6)(3)Ura, m(1,3)(2),e(5)Ura and e(1,3)(2)Thy in dilute aqueous solutions were measured in the temperature range of 293.15-388.15 K, using a differential adiabatic scanning microcalorimeter. They were found to lie (i) much higher than the estimated heat capacities C(p)(s) of solid compounds, (ii) comparable with the respective partial molar heat capacities at infinite dilution, C(o)(p2), and (iii) linearly related to the number nH of hydrogen atoms covalenuy bound to the solute molecules. The increment thus obtained DeltaC(o)(p2)=42.8 J mole(-1) K(-1)n(-1)(H) per each hydrogen atom at 298.15 K proved (i) to coincide closely with those found previously for homologous series of aliphatic amides and hydrocarbons, and (ii) to decrease with a rise of temperature. These findings imply the involvement of hydrophobic hydration of the solutes.     

Mass-spectrometric investigations on hydration of nucleic acid components in vacuum

Association reactions between water and alkylated uracils. occurring under field-ionization conditions in a mass spectrometer at the tungsten point emitter surface, were studied at several temperatures. The origin of peaks observed in the mass spectra at m/e ratios corresponding to M+H and M+H-H2O were attributed to M-H2O and M-(H2O)2 hydrates, respectively, hydrogen-bonded via carbonyl groups of the diketopyrimidines (M) investigated. The appearance of these ions is explained in terms of the field-ionization mechanism of the neutral hydrates involving intramolecular H+ transfer and concomitant release of the OH+ radical. Measurements of the relative peak intensities allowed the calculation of apparent equilibrium constants. K(ass). for the association reactions, and hence the respective van't Hoff enthalpies of hydrat'on. The latter are discussed in connection with the available quantum-mechanical hydration energies for specific groups of respective canonical nucleic acid bases and experimental enthalpies of hydration of alkylated uracils with water. Specific hydration is estimated to contribute about 15-20% to the total enthalpy of interaction of the solutes with their hydration shells.     

Mass-spectrometric investigations on hydration of nucleic acid components in vacuum. II. N-methylated adenines

Association reactions between water and N-methylated adenines (M), occurring under field-ionization conditions in a mass spectrometer at the tungsten point emitter surface, were studied at a number of temperatures. The origin of the peaks observed in the mass spectra at m/e ratios corresponding to MH+ was assigned to M X H2O monohydrates , of those corresponding to (MH X H2O)+ and (MH2)2+ to double hydrates M(H2O)3. Measurements of the relative peak intensities allowed calculation of apparent equilibrium constants, Kass, for successive hydration steps, and hence the respective van't Hoff enthalpies of hydration. Both the equilibrium and the energy parameters obtained support the available quantum-mechanical single-layer hydration schemes of adenine and of its N-methylated derivatives.     

A hydrophobic similarity analysis of solvation effects on nucleic acid bases

We investigate the changes in the solvation properties of the natural nucleic acid bases due to the formation of the canonical Watson–Crick hydrogen-bonded complexes. To this end, the changes in the free energy of solvation of the bases induced upon hydrogen-bonded dimerization are analyzed by means of the hydrophobic similarity index, which relies on the atomic contributions to the free energy of solvation determined by the partitioning method implemented in the framework of the MST continuum model. Such an index is also used to examine the hydrophobic similarity between the canonical nucleic acid bases and a series of highly apolar analogues, which have been designed as potential candidates to expand the genetic alphabet. The ability of these analogues to be incorporated into modified DNA duplexes can be related to the large reduction in the hydrophilicity of the natural bases upon formation of the canonical hydrogen-bonded dimers. The results illustrate the suitability of the hydrophobic similarity index to rationalize the role played by solvation in molecular recognition. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

Contributions from hydration of carboxylate groups to the spectrum of water-polypeptide proton-proton Overhauser effects in aqueous solution

Summary Nuclear Overhauser effects (NOE) were measured between water protons and protons of the glutamic acid side chain of the bicyclic decapeptide in aqueous solution. Positive NOEs were observed between the CH₂ group of Glu and the water resonance, with similar NOE intensities at pH 2.0 and pH 6.3 in both the laboratory frame and the rotating frame of reference. These results indicate that the residence times of the hydration water molecules near the side-chain methylene protons are shorter than 500 ps for both the charged form and the uncharged form of Glu, and hence comparable to the water residence times near uncharged amino acid side chains. Furthermore, this study shows that the acidic proton in protonated carboxylic acid groups is not likely to interfere with the observation of polypeptide-hydration water NOEs, which is in contrast to the hydroxyl protons of the side chains of serine, threonine and tyrosine.Abbreviations NOE nuclear Overhauser effect - NOESY NOE spectroscopy in the laboratory frame - ROESY NOE spectroscopy in the rotating frame - ID one-dimensional - 2D two-dimensional - HPLC high-pressure liquid chromatography     

X-ray and neutron scattering studies of the hydration structure of alkali ions in concentrated aqueous solutions

The presence of ions in water provides a rich and varied environment in which many natural processes occur with important consequences in biology, geology and chemistry. This article will focus on the structural properties of ions in water and it will be shown how the 'difference' methods of neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction (AXD) can be used to obtain direct information regarding the radial pair distribution functions of many cations and anions in solution. This information can subsequently be used to calculate coordination numbers and to determine ion-water conformation in great detail. As well as enabling comparisons to be made amongst ions in particular groups in the periodic table, such information can also be contrasted with results provided by molecular dynamics (MD) simulation techniques. To illustrate the power of these 'difference' methods, reference will be made to the alkali group of ions, all of which have been successfully investigated by the above methods, with the exception of the radioactive element francium. Additional comments will be made on how NDIS measurements are currently being combined with MD simulations to determine the structure around complex ions and molecules, many of which are common in biological systems.     

Chlorination studies. IV. The reaction of aqueous hypochlorous acid with pyrimidine and purine bases

The labile intermediates and stable end products formed by the reaction of aqueous HOCl with thymine, uracil, 5-Br-uracil, N,N-dimethyluracil and 6-methyluracil have been identified. The purine ring system of guanine, adenine and xanthine was more resistant to attack by aqueous HOCl and reaction times of one week resulted in the formation of parabanic acid. Caffeine and theophylline under similar reaction conditions yielded N,N-dimethylparabanic acid.     

Free radical generation by ultrasound in aqueous solutions of nucleic acid bases and nucleosides: an ESR and spin-trapping study

Direct evidence for the detection of intermediate radicals of nucleic acid constituents induced by ultrasound in argon-saturated aqueous solution is presented. The method of spin trapping with 3,5-dibromo-4-nitrosobenzene sulphonate, which is a water-soluble, non-volatile, aromatic nitroso spin trap, combined with ESR, was used for the detection of sonochemically induced radicals. Spin adducts were also generated by OH radicals produced by UV photolysis of aqueous solution containing H2O2. ESR spectra observed from these photolysis experiments were identical to those after sonolysis. The ESR spectra of the spin adducts suggest that the major spin-trapped radical of thymine and thymidine was the 5-yl radical, and that of cytosine, cytidine, uracil, and uridine was the 6-yl radical. To compare the radicals induced by sonolysis and photolysis, the decay of the ESR spectra of the thymine and thymidine spin adducts was investigated. The decay curves of thymine and thymidine after sonolysis indicated biphasic decay. However, after photolysis the spin adducts from both compounds showed very little decay. These results suggest that the observed spin adducts in the sonolysis of pyrimidine bases and nucleosides were formed by OH radical and H atom addition to the 5,6 double-bond.     

Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration.

The data and approach reported in paper I (Hanlon et al., 1975, preceding paper) have been used to calculate the fractional changes in secondary structure of calf thymus deoxyribonucleic acid which occur in aqueous solutions as a function of the concentration of NaCl, KCl, LiCl, CsCl, and NH4Cl. There is a continuous loss in the "B" character of the nucleic acid with concomitant production of the C and, in some instances, an A form, as well, as the salt concentration increases. Sedimentation velocity studies suggest that there is an accompanying change in the hydrodynamic characteristics of the DNA molecules, as well. Utilizing the existing hydration data in the literature (Hearst and Vinograd, 1961a,b; Hearst, 1965; Tunis and Hearst, 1968a; Cohen and Eisenberg, 1968; Falk et al., 1962, 1963a,b), we have found that a gradual loss of "B" character and a decrease in the frictional coefficient of DNA occur as the net hydration of DNA is reduced from the fully hydrated from (60-80 mol of H2O/mol of nucleotide) to values of ca. 12-14 mol of H2O/mol of nucleotide. Below that value, a more precipitous decrease in these properties occurs. Extrapolation of the linear relationship observed between the fractional B content and the net hydration in the latter regions yield values of ca. 18 mol of H2O/mol of nucleotide at 100% B and ca. 4 mol of H2O/mol of nucleotide at 0% B (i.e., 100% C or C + A) for the alkali metal salts of DNA. The ammonium salt retains somewhat more H2O in the C and A forms (ca. 7). These results together with the hydration site assignments of Falk et al. (1962, 1963a,b) are interpreted in terms of a hydration model for DNA in aqueous solution in which an intact primary hydration shell of ca. 18 mol of H2O/mol of nucleotide is required for the maintenance of the "B" conformation. Removal of all but those water molecules solvating the phosphate groups results in the conversion to the C forms, predominantly, with a small amount of A structure formed as well in some salts. The accompanying changes in the sedimentation coefficients suggest that the DNA molecule assumes a more compact and/or flexible form under these conditions in which it is mainly in the C and A structures. The combination of these two events which ensue upon dehydration create a polymeric structure which can be more easily packaged in biological systems.     

Thermodynamics of some nucleic acid bases and nucleosides in water, and their transfer to aqueous glucose and sucrose solutions at 298.15 K

The partial molar heat capacities and volumes of some of the constituents of nucleic acids have been determined in water and 1 molal aqueous glucose and sucrose solutions in order to elucidate the nature of interactions occurring between various nucleic acid bases, nucleosides and the sugar (glucose and sucrose) molecules. The results have been explained in terms of the contributions from hydrophobic interactions, hydrophilic interactions and the hydrogen bonding between the solute and solvent molecules. The results have also been compared with those of amino acids and peptides in aqueous glucose and sucrose solutions.     

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°C, the apparent molar volumes ΦV and the apparent molar compressibilities ΦK_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) ≈ 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. © 1999 John Wiley & Sons, Inc. Biopoly 50: 459–471, 1999     

Ordering in aqueous polysaccharide solutions. II. Optical rotation and heat capacity of aqueous solutions of a triple-helical polysaccharide schizophyllan

Deuterium oxide solutions of schizophyllan, a triple-helical polysaccharide, undergoing an order-disorder transition centered at 17 degrees C, were studied by optical rotation (OR) and heat capacity (C(p)) to elucidate the molecular mechanism of the transition and water structure in the solution and frozen states. The ordered structure at low temperature consisted of the side chains and water in the vicinity forming an ordered hydrogen-bonded network surrounding the helix core and was disordered at higher temperature. In the solution state appeared clearly defined transition curves in both the OR and C(p) data. The results for three samples of different molecular weights were analyzed theoretically, treating this transition as a typical linear cooperative transition from the ordered to disordered states and explained quantitatively if the molecular weight polydispersity of the sample was considered. The excess heat capacity C(EX)(p) defined as the C(p) minus the contributions from schizophyllan and D(2)O was estimated. In the frozen state it increased with raising temperature above 150 K until the mixture melted. This was compared with the dielectric increment observed in this temperature range and ascribed to unfreezable water. From the heat capacity and dielectric data, unfreezable water is mobile but more ordered than free water. In the solution state, the excess heat capacity originates from the interactions of D(2)O molecules as bound water and structured water, and so forth. Thus the schizophyllan triple helix molds water into various structures of differing orders in solution and in the solid state.     

A mechanistic analysis of the increase in the thermal stability of proteins in aqueous carboxylic acid salt solutions

The stability of proteins is known to be affected significantly in the presence of high concentration of salts and is highly pH dependent. Extensive studies have been carried out on the stability of proteins in the presence of simple electrolytes and evaluated in terms of preferential interactions and increase in the surface tension of the medium. We have carried out an in-depth study of the effects of a series of carboxylic acid salts: ethylene diamine tetra acetate, butane tetra carboxylate, propane tricarballylate, citrate, succinate, tartarate, malonate, and gluconate on the thermal stability of five different proteins that vary in their physico-chemical properties: RNase A, cytochrome c, trypsin inhibitor, myoglobin, and lysozyme. Surface tension measurements of aqueous solutions of the salts indicate an increase in the surface tension of the medium that is very strongly correlated with the increase in the thermal stability of proteins. There is also a linear correlation of the increase in thermal stability with the number of carboxylic groups in the salt. Thermal stability has been found to increase by as much as 22 C at 1 M concentration of salt. Such a high thermal stability at identical concentrations has not been reported before. The differences in the heat capacities of denaturation, deltaCp for RNase A, deduced from the transition curves obtained in the presence of varying concentrations of GdmCl and that of carboxylic acid salts as a function of pH, indicate that the nature of the solvent medium and its interactions with the two end states of the protein control the thermodynamics of protein denaturation. Among the physico-chemical properties of proteins, there seems to be an interplay of the hydrophobic and electrostatic interactions that lead to an overall stabilizing effect. Increase in surface free energy of the solvent medium upon addition of the carboxylic acid salts appears to be the dominant factor in governing the thermal stability of proteins.     

Phagostimulation of larval Culexpipiens L. by nucleic acid nucleotides, nucleosides and bases

ABSTRACT. The influence of nucleic acid constituents on the rate of ingestion of charcoal powder filtered from ambient water by larvae of Culex pipiens L. was examined. All nucleotides tested stimulated ingestion to some extent. Various mono-, di- and tri-phosphates of adenosine were most effective and at concentrations of 1 mM stimulated ingestion nearly as well as yeast extract, a powerful phagostimu-lant. Guanylic, thymidylic, cytidylic and uridylic acids were less stimulatory, the latter two even at 10 mM. Cyclic AMP and deoxyadenylic acid were less effective than other adenine nucleotides. The nucleosides adenosine, guanosine and uridine were almost as effective as their corresponding nucleotides (adenylic, guanylic and uridylic acids); thymidine was less effective than thymidylic acids, whereas cytidine was non-stimulatory. Adenine, guanine, uracil and cytosine, the bases of the ribose nucleotides, were non-phagostimulatory, whereas thymine, base of the deoxynucleotide, thymidylic acid, caused low but significantly increased ingestion. These findings are compared with the reported phagostimulation by nucleic acid constituents of certain plant feeding insects and with the stimulation of engorgement of the blood meal by many blood feeding insects.