Onset of DNA aggregation in presence of monovalent and multivalent counterions

We address theoretically aggregation of DNA segments by multivalent polyamines such as spermine and spermidine. In experiments, the aggregation occurs above a certain threshold concentration of multivalent ions. We demonstrate that the dependence of this threshold on the concentration of DNA has a simple form. When the DNA concentration c(DNA) is smaller than the monovalent salt concentration, the threshold multivalent ion concentration depends linearly on c(DNA), having the form alphac(DNA) + beta. The coefficients alpha and beta are related to the density profile of multivalent counterions around isolated DNA chains, at the onset of their aggregation. This analysis agrees extremely well with recent detailed measurements on DNA aggregation in the presence of spermine. From the fit to the experimental data, the number of condensed multivalent counterions per DNA chain can be deduced. A few other conclusions can then be reached: 1), the number of condensed spermine ions at the onset of aggregation decreases with the addition of monovalent salt; 2), the Poisson-Boltzmann theory overestimates the number of condensed multivalent ions at high monovalent salt concentrations; and 3), our analysis of the data indicates that the DNA charge is not overcompensated by spermine at the onset of aggregation.     

Effect of D2O on maize plasmalemma ATPase and electron transport coupled proton pumping.

Heavy water (D2O) has been used as a putative inhibitor of the plasma membrane H(+)-ATPase and the plasma membrane redox system. Concentrations above 50% D2O inhibited H+ secretion and the plasma membrane redox system of Zea mays L. roots. Inhibition of H+ secretion by vanadate was reduced in presence of D2O. The plasma membrane of roots was transiently depolarized after the addition of heavy water in concentrations above 5%. The repolarization of the plasma membrane that takes place while the H+ secretion is still reduced by heavy water indicates that, despite the overall inhibiting effect of D2O, the plant is still able to regulate the membrane potential.     

Synthesis of chitosan-based polymeric surfactants and their adsorption properties for heavy metals and fatty acids

Chitosan-based polymeric surfactants (CBPSs) were prepared by N-acylation of chitosans (chitosan 10 and 500) with several acid anhydrides such as hexanoic (C6), lauric (C12), and palmitic (C16) anhydrides. Among the CBPS samples, CBPSs having a good solubility at pH 4.0 were selected and observed for viscosity, surface tension, and adsorption of heavy metals (Cd2+, Co2+, Cr2O7(2-), and Pb2+) as well as the fatty acid (n-octanoic acid). The 1H NMR spectrum of chitosan 10 modified with C16 at the substitution ratio of 0.4 (CBPS10-C16,0.4) showed 85% of acylation in 1% DCl/D2O solutions. CBPS10 with the substitution ratio less than 0.4 showed a good solubility because of shorter repeating units and lesser amounts of hydrophobic substituents. The intrinsic viscosity of CBPS10 was slightly increased, while that of CBPS500 was decreased. As the substitution ratio and length of the carbon chain increased, the surface tension of CBPS10 tended to decrease. CBPS10-C16,0.2 had high adsorption ability for cationic metal ions such as Cd2+, Co2+, and Pb2+ comparable to chitosan. Interestingly, CBPS(10)-C(16,0.2) showed a unique pH optimum for the anionic metal ion such as Cr2O7(2-). In addition, CBPS10-C16,0.2 exhibited the highest adsorption ability for n-octanoic acid among the tested CBPS10 with different carbon chains.     

Protection of DNA by salts against thermodegradation at temperatures typical for hyperthermophiles

The effect of physiological concentrations of KCl and MgCl₂ on the chemical stability of double-stranded and single-stranded DNA has been studied at temperatures typical for hyperthermophiles. These two salts protect both double and single-stranded DNA against heat-induced cleavage by inhibiting depurination. High KCl concentrations also protect DNA cleavage at apurinic sites, while high MgCl₂ concentrations stimulate this cleavage. It has been previously proposed that salt protects double-stranded DNA against depurination by stabilizing the double helix. However, the inhibition of the depurination of single-stranded DNA by KCl and MgCl₂ indicates that this effect is more probably due to a direct interaction of salts with purine nucleotides. These results suggest that the number and nature of heat-induced DNA lesions which have to be repaired might be quite different from one hyperthermophile to another, depending on their intracellular salt concentration. High salt concentrations might be also useful to protect DNA in long polymerase chain reaction (PCR) experiments and for long-term preservation. Received: October 12, 1997 / Accepted: January 29, 1998     

H/D isotope effects on protein hydration and interaction in solution

An approach has been suggested to study the H/D isotope effect on protein-water and protein-protein intermolecular interactions by determining the content of non-freezing water using low-temperature (1)H NMR in mixed (H2O/D2O) water solutions. Direct data are obtained on the amount of H2O adsorbed (absolute hydration) in presence of the heavy isotope (deuterium D), and isothermals of H2O/D2O fractionation at protein surface groups are presented for temperatures between -10 degrees C and -35 degrees C and solutions of varying composition. The fractionation factor, phi = [x/(1 - x)]/[x(0)/(1 - x(0))], where x and x(0) are the fractions of deuterons in hydration and bulk water, respectively, appeared to be extremely high: phi > 1 at 0.03 < x(0) < 0.10. The high values of phi indicate a decrease in apparent hydration of protein molecules. A probable reason of the effect can be an inter-protein molecular solvent-mediated interaction induced by D2O. The excess of phi over 1 appears to provide a quantitative estimate of the fraction of hydration water affected by such interaction.     

Deuterium oxide effects upon three parameters characterizing the activity of glycerol-extracted muscle: phosphate release, ATP-induced shortening, and 22Na+ distribution

ATP splitting activity is progressively reduced with increasing heavy water (D2)) concentration. In contrast, sarcomere shorteining inhibition produced by D2O does not significantly depend on its concentration. Even at low concentration, the presence of D2O does reduce the excessive accumulation of radioactive sodium within glycerinated frog muscle. These heavy water effects on muscular contraction and soidum distribution can be interpreted to indicate adsorbed water within the cells. Evaluation of these experimental results in terms of Gibbs free enthalpy of binding at the adsorption sites of D20 or H20 is in good agreement with the data in the literature.     

Exchange of H1 histone depends on aggregation of chromatin, not simply on ionic strength

Chromatin solubility was observed at several concentrations of various cations. Spermine and spermidine precipitated (50%) chromatin at about 0.2 mM, Ca2+ and Mg2+ at about 1-2 mM, and Na+ at about 100 mM. Further increases in cation concentration induced more aggregation, but eventually excess cation increased chromatin solubility so that 50% solubility was observed again at 60 mM Mg2+ and 180 mM Na+. H1 histone was 50% released by 80 mM MgCl2 or 425 mM NaCl. Combinations of MgCl2 and NaCl showed that Mg2+ and Na+ are synergistic in the induction of aggregation in lower concentrations (less than 2 mM) of Mg2+ but antagonistic at higher concentrations, and a similar effect of NaCl on spermidine-induced precipitation was shown below and above about 0.2 mM spermidine. At 5 mM, MgCl2 proved capable of precipitating chromatin depleted of H1 histone, but no concentration of NaCl was capable of doing so. These phenomena can be rationalized by supposing that neutralization of chromatin by any cation (including H1 histone) favors aggregation and also that cross-linking of chromatin fibers by multivalent cations (including H1 histone) is also critically important. The exchange of H1 histone between chromatin fragments was tested in various concentrations of different salts. H1 exchange was correlated with chromatin aggregation rather than with ionic strength and thus appears to depend on fiber to fiber contact. Under conditions where H1 exchanges between chromatin fibers that are permitted to make contact with each other, no H1 exchange occurred between chromatin inside the nucleus and chromatin outside, even though H1 histone is capable of passage through the nuclear membrane.     

Role of the C-terminal extremities of the smooth muscle myosin heavy chains: implication for assembly properties.

The two light meromyosin isoforms from rabbit smooth muscle were prepared as recombinant proteins in Escherichia coli. These species which differed only by their C-terminal extremity showed the same circular dichroism spectra and endotherms in measurements of differential scanning calorimetry. Their solubility properties were different at pH 7.0 in the absence of monovalent salts. Their paracrystals formed at low pH differed by their aspect and number. These data suggest a role for the C-terminal extremity of myosin heavy chains in the assembly of myosin molecules in filaments and consequently in the contractility of smooth muscles.     

Adsorption of toxic mercury(II) by an extracellular biopolymer poly(gamma-glutamic acid)

Adsorption of mercury(II) by an extracellular biopolymer, poly(gamma-glutamic acid) (gamma-PGA), was studied as a function of pH, temperature, agitation time, ionic strength, light and heavy metal ions. An appreciable adsorption occurred at pH>3 and reached a maximum at pH 6. Isotherms were well predicted by Redlich-Peterson model with a dominating Freundlich behavior, implying the heterogeneous nature of mercury(II) adsorption. The adsorption followed an exothermic and spontaneous process with increased orderliness at solid/solution interface. The adsorption was rapid with 90% being attained within 5 min for a 80 mg/L mercury(II) solution, and the kinetic data were precisely described by pseudo second order model. Ionic strength due to added sodium salts reduced the mercury(II) binding with the coordinating ligands following the order: Cl(-) >SO(4)(2-) >NO(3)(-). Both light and heavy metal ions decreased mercury(II) binding by gamma-PGA, with calcium(II) ions showing a more pronounced effect than monovalent sodium and potassium ions, while the interfering heavy metal ions followed the order: Cu(2+) > Cd(2+) > Zn(2+). Distilled water adjusted to pH 2 using hydrochloric acid recovered 98.8% of mercury(II), and gamma-PGA reuse for five cycles of operation showed a loss of only 6.5%. IR spectra of gamma-PGA and Hg(II)-gamma-PGA revealed binding of mercury(II) with carboxylate and amide groups on gamma-PGA.     

Spermine-induced aggregation of DNA, nucleosome, and chromatin.

We have analyzed the conditions of aggregation or precipitation of DNA in four different states: double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), mononucleosome core particles (NCP), and H1-depleted chromatin fragments (ChF) in the presence of the multivalent cation spermine (4+). In an intermediate regime of DNA concentration, these conditions are identical for the four states. This result demonstrates that the mechanism involved is general from flexible chains to rigid rods and quasi-colloidal states. It is dominated by local electrostatic attractions that are considered, for instance, by the "ion-bridging" model. The onset of precipitation does not require the electroneutrality of the DNA chains. Above a given spermine concentration dsDNA aggregates remain neutral, whereas NCP aggregates turn positively charged. The difference is thought to originate from the extension of the positively charged proteic tails of the NCP. This suggests that local fluctuations of polyamine concentrations can induce either positively or negatively charged chromatin domains.     

Effects of neutral salts on the conformational state of glycogen, interacting with iodine

The effects of salts on helix formation of linear (outer) chains of branched alpha-glucane, muscle glycogen, was judged upon by the state of polyiodine chromophore of the iodine reaction surrounded by a polysaccharide asymmetric helix and recorded by the circular dichroism method. It was demonstrated that apart from the known changes in the absorption of the iodine-glycogen complex the salts induce changes in the ellipticity by affecting the helix formation of the linear chains of the polysaccharide. The nature of these effects depends on the type and concentration of the salt used. Monovalent metal salts produce a more favourable effect on helix formation than the divalent metal salts. Among divalent metal salts transient metal salts produce a weaker effect. The action of neutral salts on helix formation is of dual nature: helix formation and helix destruction. The helix formation is largely impaired by high concentrations of LiCl (greater than 6 M) or CaCl2 (greater than 2M). It was shown that a certain role in the mechanism of neutral salt action on helix formation belongs both to electrostatic and lyotropic effects. The latter determine the effects of salts on helix formation at concentrations above the monomolar one, when the specific effect of a salt is especially well-pronounced. The salts which enhance the orderliness of H2O structure produce a favourable effect on helix formation of the linear polysaccharide chains and, consequently, on the iodine reaction. In terms of molar efficiency of their action on the iodine reaction the salts correspond to the Hofmeister lyotropic sequence.     

DNA hairpin structures in solution: 500-MHz two-dimensional 1H NMR studies on d(CGCCGCAGC) and d(CGCCGTAGC)

A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz 1H NMR studies in H2O and D2O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2", it was concluded that in d(CGCCGCAGC) and d(CGCCGTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins.     

Small angle neutron scattering, total cross-sections and mass density measurements of concentrated NaCl and KCl solutions in H2O or D2O

The mass densities, total cold neutron cross sections and small angle scattering of concentrated NaCl and KCl solutions in H2O or D2O (2H2O) were measured at 20 degrees C. The partial specific volumes of both salts increase with salt concentration and are significantly smaller in D2O than in H2O, showing that these salt solutions cannot be considered as isomorphous in H2O and D2O. As salt concentration increases for both salts, the total coherent cross sections for neutrons of the solutions also increase while the coherent small angle scattering decreases-observations that are consistent, respectively, with increasing correlations involving the ion and water components and a decrease in the particle number density and/or concentration fluctuations, in the solutions. Changes in incoherent scattering with salt concentration are essentially those expected from the solution compositions and densities.     

Mono- and divalent competitive adsorption to a charged membrane in a closed system: A comparative study

Competitive adsorption to a negative surface between monovalent and divalent cations is studied in a closed system. A self-consistent theory is presented for the cases when the divalent cation binds to two negative sites (1:2 binding) and to one negative site (1:1 binding). It is demonstrated that these two cases are distinguishable when the relative difference in total divalent concentrations determined at fixed bulk divalent concentrations is plotted as a function of the bulk monovalent concentration. The 1:2 binding case yields a sigmoidal curve while the 1:1 binding curve is hyperbolic. The comparison between the 1:2 and 1:1 binding cases of the divalent cation is extended to include; (1) the existence of a surface charge to which no binding occurs, and (2) the case when an additional non-binding monovalent cation is present.     

Formation and properties of polyelectrolyte complexes of chitosan hydrochloride and sodium dextransulfate

Methods of potentiometry, turbidimetry, colorimetry, IR spectroscopy, and element analysis were used to investigate the conditions of formation and the properties of non-stoichiometric polyelectrolyte complexes of chitosan hydrochloride (CHC) and sodium dextransulfate (the molecules of both polysaccharides appear as semirigid chains, but their charges are opposite). It was determined that the complexes' formation of polyelectrolytes studied is predominantly electrostatic in the presence of urea. As was also found turbidity and stability of the polycomplexes solutions depended markedly on pH value of CHC and a nature of the low-molecular-weight salts added. The complexes obtained were soluble in water, aqueous urea, and water-organic mixtures. The extent of solubility depended on the composition of the complexes and could be influenced by addition of appropriate concentrations of certain low-molecular-weight salts.     

Solubility of cyclomaltooligosaccharides (cyclodextrins) in H2O and D2O: a comparative study

Cyclomaltooligosaccharides (cyclodextrins, CDs) are cyclic oligomers having six, seven, or eight units of alpha-D-glucose, named as cyclomaltohexaose (alpha-CD), cyclomaltoheptaose (beta-CD) and cyclomaltooctaose (gamma-CD), respectively. The molecule of CD has a cavity in which the interior is hydrophobic relative to its outer surface. The solubility of cyclodextrins in water is unusual, as an irregular trend is observed in the series of the cyclic oligomers of glucose. beta-CD is at least nine times less soluble than the others CDs. This intriguing behavior has been investigated, and some interesting explanations in terms of the effect caused by CD on the water lattice structure have been proposed. In this work a comparative study on the solubility of alpha, beta, and gamma-cyclodextrins was carried out in H2O and D2O and reveals a much lower solubility of the three CDs in D2O. The solid-phase structure of the CDs in equilibrium with the solution is quite similar with both solvents. The results are discussed in terms of the CD molecular structure and the differences in the hydrogen bonds formed between H2O and D2O.     

Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability

Interactions of the solutes glycine betaine (GB) and urea with mononucleosomal calf thymus DNA in aqueous salt solutions are characterized by vapor pressure osmometry (VPO). Analysis of osmolality as a function of solute and DNA concentration yields the effect of the solute on the chemical potential, mu(2), of the DNA. Although both GB and urea generally are nucleic acid denaturants and therefore must interact favorably with the nucleic acid surface exposed upon melting, VPO demonstrates that neither interacts favorably with duplex DNA. Addition of GB greatly increases mu(2) of DNA, indicating that the average local concentration of GB in the vicinity of the double helix is much less than its bulk concentration. By contrast, addition of urea has almost no effect on mu(2) of duplex DNA, indicating that the average local concentration of urea in the vicinity of duplex DNA is almost the same as in bulk solution. Qualitatively, we conclude that the nonuniform distribution of GB occurs primarily because duplex DNA and GB prefer to interact with water rather than with each other. Comparison with thermodynamic data for the interaction of GB with various protein surfaces (Felitsky et al., Biochemistry, 43, 14732-14743) shows that GB is excluded primarily from anionic DNA surface and that the hydration of anionic DNA phosphate oxygen surface (>or approximately 17 H(2)O per nucleotide or >or approximately 0.22 H(2)O A(-)(2)) involves at least two layers of water. From analysis of literature data for effects of urea and of GB on DNA melting, we propose that urea is an effective nonspecific nucleic acid denaturant because of its favorable interactions with the polar amide-like surface of G, C, and especially T or U bases exposed in denaturation, whereas GB is a specific GC denaturant because of its favorable interaction with G and/or C surface in the single-stranded state.     

Water-sensitive low-frequency vibrations of reaction intermediates during S-state cycling in photosynthetic water oxidation

In photosynthetic water oxidation, two water molecules are converted to an oxygen molecule through five reaction intermediates, designated S(n) (n = 0-4), at the catalytic Mn cluster of photosystem II. To understand the mechanism of water oxidation, changes in the chemical nature of the substrate water as well as the Mn cluster need to be defined during S-state cycling. Here, we report for the first time a complete set of Fourier transform infrared difference spectra during S-state cycling in the low-frequency (670-350 cm(-1)) region, in which interactions between the Mn cluster and its ligands can be detected directly, in PS II core particles from Thermosynechococcus elongatus. Furthermore, vibrations from oxygen and/or hydrogen derived from the substrate water and changes in them during S-state cycling were identified using multiplex isotope-labeled water, including H2(18)O, D2(16)O, and D2(18)O. Each water isotope affected the low-frequency S-state cycling spectra, characteristically. The bands sensitive only to (16)O/(18)O exchange were assigned to the modes from structures involving Mn and oxygen having no interactions with hydrogen, while the bands sensitive only to H/D exchange were assigned to modes from amino acid side chains and/or polypeptide backbones that associate with water hydrogen. The bands sensitive to both (16)O/(18)O and H/D exchanges were attributed to the structure involving Mn and oxygen structurally coupled with hydrogen in a direct or an indirect manner through hydrogen bonds. These bands include the changes of intermediate species derived from substrate water during the process of photosynthetic water oxidation.     

Adsorption of biopolymers at hydrophilic cellulose-water interface

The extent of adsorption (Gamma2(1)) of bovine serum albumin (BSA), beta-lactoglobulin, lysozyme, gelatin, and DNA from aqueous solution onto the hydrophilic surface of cellulose has been measured as function of biopolymer concentration at different temperatures, pHs, and ionic strengths, and in the presence of a high concentration of inorganic salts and denaturants. In all cases, the value of Gamma2(1) increases with the increase of biopolymer concentration (X2) in bulk and it attains a maximum value at a critical mole fraction concentration X2m. The value of Gamma2m depends upon the nature of protein, temperature, pH, and ionic strength, as well as the nature of neutral salts present in excess. Gamma2m for proteins at a fixed physicochemical condition stands in the following order: Gelatin>betalactoglobulin>lysozyme>BSA. The isotherms for adsorption of DNA nucleotides on cellulose surface at pH 4.0 have been compared at different temperatures and ionic strengths, and in the presence of high concentration of inorganic salts LiCl, NaCl, KCl, and Na2SO4. Values of Gamma2m for different systems have been evaluated and critically compared. At pH 6.0 and 8.0, Gamma2(1) values of DNA nucleotides on cellulose are all negative due to the excess positive hydration of cellulose. At pH 4.0, adsorption of nucleotides of acid, alkali, and heat-denatured DNA widely differ from each other and in the presence of excess concentration of urea becomes negative. The probable mechanisms of biopolymer-cellulose adsorption in terms of polymer hydration, steric interaction, London-van der Waals, hydrophobic, and other types of interactions have been discussed qualitatively. The standard free energy change for the adsorption of protein and DNA nucleotides on the cellulose surface at the state of adsorption saturation has been calculated in kJ per kg of cellulose using an integrated form of the Gibbs adsorption equation. The relation between DeltaG degrees and maximum affinities between biopolymers and the polysaccharide interface have been discussed for various systems.