Counter-ion dependence in salt-free,aqueous solutions of heparin

Chiroptical properties of heparin for various degrees of neutralization of the sulfate and carboxylic groups and for different counter-ions in salt-free aqueous solutions were investigated. Variations of optical rotation and ellipticity values at given wavelengths are compared to simultaneous pH and viscosity changes observed during the neutralization of heparin by sodium and calcium hydroxide. For Na⁺, variations of ellipticity at 210 nm are related to acid—base properties of uronic carboxylic groups. C.d. characteristics found for alkaline-earth counter-ions (Mg²⁺, Ca²⁺ and Ba²⁺), as compared to Na⁺, are assigned to effects of divalent ions on the ionization behavior of carboxylic groups. Among the divalent counter-ions considered, Ca²⁺ gave the strongest interaction with the heparin polyanion, but no specific complex formation was observed. O.r.d. and c.d. data are discussed on the basis of a randomly coiled structure for macromolecules composed of rigid, heterocyclic repeating-units that are independent of each other in so far as electronic transitions of chromophore groups contributing to optical activity are concerned.     

Interactions of mono- and divalent counterions with alkali- and enzyme-deesterified pectins in salt-free solutions

The free fractions of monovalent and divalent counterions were determined on salt-free solutions of pectins. The effects of charge density, distribution of the carboxyl groups, polymer concentration, and the nature of the counterion were investigated by determinating the calcium and sodium activity coefficients (with specific electrodes) and by measuring the transport parameters (by conductimetry). Poor agreement for calcium ions was found with the Manning theory. The strong binding of these ions to highly charged polymers, which is ascribed to a dimerization process was demonstrated in very dilute solutions.     

The equivalent conductivity of aqueous solutions of alkali metal salts of a number of ionic polysaccharides

Measurements of the equivalent conductivity of aqueous solutions of alkalimetal salts of a number of ionic polysaccharides at 25 degrees C are reported. The polysaccharides studied are: (1) three carboxymethylcelluloses of various degrees of substitution (Li+, Na+, Cs+ salts) in the concentration range 4 X 10(-4) - 6 X 10(-2) equivalents alkali ion per liter, (2) Polypectate (Li+, Na+, K+, Cs+ salts) in the range 1.5 X 10(-4) - 2 X 10(-2) equivalent alkali ion per liter, and (3) Dextransulfate (Li+, Na+, K+ salts) in the range 3 X 10(-4) - 10(-1) equivalent alkali ion per liter. The results are compared to some earlier data and to a limiting law for conductance of rod-like polyions derived by Manning. It is concluded that although qualitative agreement is obtained between observed data and the limiting law when various polyions of different charge densities are compared at a given concentration, the concentration dependence predicted by the limiting law is in agreement with the observed curves only for polyions of a relatively low charge density. At higher charge densities appreciable deviations occur, and dextransulfate which does not have the rod-like polyion structure required by theory does not conform to the predicted concentration dependence at all.     

Dielectric properties of poly-L-glutamic acid in salt-free aqueous solutions

The electric permittivity of poly-L-glutamic acid (PGA) in salt-free aqueous solutions was measured in the frequency range 2.5 kHz – 100 MHz at different concentrations and degrees of ionization. Two samples of different molecular weight were investigated. The experimental results could under most circumstances be described by a superposition of two dispersion curves of the Cole-Cole type. The low-frequency dielectric parameters were strongly molecular weight dependent, the high-frequency ones not. Strong concentration effects were observed resulting in increasing specific dielectric increments and relaxation times with decreasing concentration. Using the theory proposed by Van der Touw and Mandel to interpret the experimental results these concentration effects could be ascribed to the influence of the polyion interactions on the average dimensions and the rigidity of the polyelectrolyte chains. The change in the total dielectric increment and low-frequency relaxation time with degree of ionization correctly reflects the helix-coil transition of PGA occurring in ths region α = 0.3–0.5. The effect of counterion size and charge on the dielectric behaviour was also found to be consistent with the theoretical model.     

Adsorption characteristics of lignosulfonates in salt-free and salt-added aqueous solutions

Five sodium lignosulfonate (SL) fractions with narrow molecular weight distribution and known salt content were used as the polyanion to build up layer-by-layer self-assembly multilayers with poly(diallyldimethylammonium chloride) (PDAC) as polycation. It is interesting to find that the salt-free SL is hardly adsorbed on the PDAC surface, but the SL in salt-added solutions can be self-assembled well with PDAC to form SL/PDAC multilayers. When the five SL fractions dissolved in saline solutions are adsorbed on the PDAC surface by a self-assembly technique, SL with higher M(w) shows a higher adsorption amount than does SL with lower M(w). The driving forces of self-assembly of SL and PDAC are discussed based on the solution behaviors and adsorption characteristics of SL in salt-free and salt-added aqueous solutions. A possible self-assembled mechanism of SL and PDAC is electrostatic or cation-π interactions, but the SL cannot be adsorbed onto the PDAC surface without a hydrophobic interaction. With the addition of enough salt, the Coulomb interaction of SL becomes negligible, but the adsorption amount increases, indicating that the electrostatic interaction is not the main driving force of SL/PDAC self-assembly. For adsorption of SL in saline solution onto the PDAC surface, the cation-π interaction is the main driving force, and the hydrophobic interaction plays an important role in the adsorbed amount.     

Thermal denaturation of DNA in concentrated salt-free solutions: comparison of microcalorimetric and spectrophotometric data

Scanning microcalorimetry and spectrophotometry were used to study the dependence of melting enthalpy (delta Hm) and temperature (Tm) on DNA concentration in salt free solutions and on NaCl concentration in solutions with constant DNA concentration. This data is used to calculate the Manning's charge density parameter which is found to be equal 1.8. The linear dependence of Tm on the logarithm of DNA concentration in salt free solution was obtained. An approximate evaluation of dissociation degree in native DNA at different concentrations was made by comparison of straight lines in the Tm = f(lg CNaCl) and Tm = f(lg Cp) coordinates.     

The release of monovalent counterions by addition of divalent countemons to aqueous solutions of maleic acid copolymer

Divalent cation binding and the release of monovalent cations accompanying the cation binding were experimentally studied by ion-selective electrode methods in aqueous solutions of copolymer of maleic acid and ethyl vinyl ether. It was found that in the process of Ca2+ addition, all the Ca2+ added was bound to polyions and the initially condensed Na+ was released in proportion to the concentration of the added Ca2+ up to the critical concentration of added Ca2+ at which the condensation of Ca2+ ceases. Values of the structural charge density parameter xi(s), were determined from the end-points of condensation of Ca2+. The process of Na+ release by adding Ca2+ was analyzed on the basis of the counterion condensation theory by using these xi(s) values. In addition, the relationship between the activity coefficient gamma-- of Ca2+ and degree of neutralization alpha in salt-free solutions was obtained from the Manning theory. Agreement between the calculated and experimental values was excellent in both cases.     

Electric conductivity changes in salt-free solutions in connection with the formation of polyriboadenylic and polyribouridylic acid complexes

Conductometric and spectrophotometric investigations of concentrated salt-free solutions of poly(A) -- poly(U) demonstrated the 1:1 complex formation. It was accomplished by the increase of solution conductivity in contrast to the situation when DNA redenaturation takes place.     

Proton relaxation in aqueous DNA solutions

By use of D₂O we found that the shortening of the longitudinal proton relaxation time which occurs in the investigated aqueous yeast DNA solutions (≦ 2.4% with 2% protein) was not based on a hydration effect, but was caused by magnetic impurities only. An estimate shows that the mobility of the hydrated water molecules is reduced by less than two orders of magnitude in comparison with the free water molecules.     

Influence of amino acid and peptide counterions on the conformation of DNA

We describe fibre diffraction studies on the interaction of DNA with different amino acids and peptides. The B form of DNA, with ten base-pairs per turn, is always found at high levels of humidity. We suggest that this pitch is observed because the DNA molecules are maintained in a straight position. In solution, the DNA molecules are bent and may have a larger pitch. The A form of DNA is never found upon dehydration. Instead, the B form may be either stabilized by the counterions or altered so that the number of base-pairs per helical turn decreases upon dehydration. Alteration is favoured either by small counterions that have a single charge or by large basic polypeptides and proteins. Stabilization is favoured by small counterions that have several charged groups. A third type of behaviour is found with some amino acids that contain hydrophobic groups, which destabilize the secondary structure of DNA, probably due to a modification of its intramolecular interactions. We have not detected any specific effect of amino acid side-chains, although the amino acid sequence has a clear influence on the interaction. We think that these observations are of interest in the pursuit of more detailed crystallographic studies on protein-DNA interactions.     

The DNA melting transition in aqueous magnesium salt solutions.

The melting transition of the magnesium salt of DNA has been systematically examined in the presence of various types of anions. The addition of ClO4- to a concentration of 3.0 N results in the biphasic optical transition, with the first phase exhibiting rapid reversibility and independence of the DNA concentration. This subtransition, which is interpreted as an intramolecular condensation to a collapsed form of DNA, is followed by a DNA concentration-dependent aggregation reaction. The aggregation can be reversed by increasing the ClO4- concentration to 6.0 N while elevating the temperature to post-transition levels. Alternatively, both the collapse and the aggregation can be prevented by melting in the presence of trichloroacetate, the most strongly chaotropic solvent for DNA which has been reported (K. Hamaguchi and E. P. Geiduschek (1962), J. Am. Chem. Soc. 84, 1329). The forces responsible for mediating both the collapse and the aggregation are superficially similar to those involved in maintaining duplex stability. The collapsed form, in particular, possibly possesses features in common with the condensed structures which can be produced in aqueous solution of certain polymers, such as polyethylene glycol (Lerman, L.S. (1971), Proc. Natl. Acad. Sci. U.S.A. 68, 1886).     

Exchange of counterions in DNA condensation

We measured the fluorescence intensity of DNA-bound fluorescent dyes YO-PRO-1 (oxazole yellow) and YOYO-1 (dimer of oxazole yellow) at various spermidine concentrations to determine how counterions on DNA are exchanged in the process of DNA condensation. A decrease of fluorescence intensity was observed with an increase of spermidine. Considering the chemical equilibrium under the competition between the dye and spermidine for counterion condensation on DNA, the theoretical curve well describes the decrease of the fluorescence intensity. These results indicate that dyes are exchanged for spermidine at the binding site on DNA; that is, the exchange of counterions occurs. The parameters associated with the decrease of the fluorescence intensity show that the relative affinity of the dye and spermidine for DNA depends on the state of DNA. Moreover, YOYO-1 prevents the DNA condensation, but the effect of YO-PRO-1 on the condensation is very slight, though both dyes intercalate for DNA; the high affinity of YOYO-1 compared to YO-PRO-1 enables prevention of the condensation.     

Dielectric relaxation of DNA in aqueous solutions.

Using a four-electrode cell and a new electronic system for direct detection of the frequency differences specturm of solution impedance, the complex dielectric constant of calf thymus DNA (M_r = 4 × 10⁶) in aqueous NaCl at 10°C is measured at frequencies ranging from 0.2 Hz to 30 kHz. The DNA concentrations are C_p = 0.01% and 0.05%, and the NaCl concentrations are varied from C_s = 10^?4 M to 10^?3 M. A single relaxation regions is found in this frequency range, the relaxation frequency being 10 Hz at C_p = 0.01% and C_s = 10^?3 M. At C_p = 0.05% it is evidenced that the DNA chains have appreciable intermolecular interactions. The dielectric relaxaton time τ_d at C_p = 0.01% agrees well with the rotational relaxation time estimated from the reduced visocisty on the assumption that the DNA is not representable as a rigid rod but a coiled chain. It is concluded that the dielectric relaxiatioinis ascribed to the rotation of the molecule. Observed values of dielectric increment and other experimental findings are reasonably explained by assuming that the dipole moment of DNA results from the slow counterion fluctuation which has a longer relaxation time than τ_d.     

Effect of pH and preparation method on thermal denaturation of thymus DNA in salt-free solutions]

Thermal denaturation of calf thymus DNA was studied by scanning microcalorimetry. It has been shown that long dialysis of DNA against water causes a sharp decrease of DNA thermal stability due to biopolymer protonation. The literature data on the properties of DNA salt-free solutions obtained by dialysis are discussed.     

DNA conformation and thermostability in urea aqueous solutions

It is suggested from the character of the change of circular dichroism spectra that in the presence of urea winding of DNA double helix takes place within the bounds of B-family of forms. It is shown that the realized conformation of DNA differs from the experimentally known forms of DNA belonging to B-family. Urea destabilizes the DNA molecules without connection with helical and melt pairs of DNA nitrous bases. Urea affects the conformational state of DNA by water destruction around DNA, which is accompanied by dehydration of DNA and basic metal ions.     

DNA and its counterions: a molecular dynamics study

The behaviour of mobile counterions, Na⁺ and K⁺, was analysed around a B-DNA double helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains diffusive in the presence of DNA. Ions sample the complete space available during the simulation time, although individual ions sample only about one-third of the simulation box. Ions preferentially sample electronegative sites around DNA, but direct binding to DNA bases remains a rather rare event, with highest site occupancy values of <13%. The location of direct binding sites depends greatly on the nature of the counterion. While Na⁺ binding in both grooves is strongly sequence-dependent with the preferred binding site in the minor groove, K⁺ mainly visits the major groove and binds close to the centre of the oligomer. The electrostatic potential of an average DNA structure therefore cannot account for the ability of a site to bind a given cation; other factors must also play a role. An extensive analysis of the influence of counterions on DNA conformation showed no evidence of minor groove narrowing upon ion binding. A significant difference between the conformations of the double helix in the different simulations can be attributed to extensive α/γ transitions in the phosphate backbone during the simulation with Na⁺. These transitions, with lifetimes over tens of nanoseconds, however, appear to be correlated with ion binding to phosphates. The ion-specific conformational properties of DNA, hitherto largely overlooked, may play an important role in DNA recognition and binding.     

Atomic force microscopy of DNA in aqueous solutions.

DNA on mica can be imaged in the atomic force microscope (AFM) in water or in some buffers if the sample has first been dehydrated thoroughly with propanol or by baking in vacuum and if the sample is imaged with a tip that has been deposited in the scanning electron microscope (SEM). Without adequate dehydration or with an unmodified tip, the DNA is scraped off the substrate by AFM-imaging in aqueous solutions. The measured heights and widths of DNA are larger in aqueous solutions than in propanol. The measured lengths of DNA molecules are the same in propanol and in aqueous solutions and correspond to the base spacing for B-DNA, the hydrated form of DNA; when the DNA is again imaged in propanol after buffer, however, it shortens to the length expected for dehydrated A-DNA. Other results include the imaging of E. coli RNA polymerase bound to DNA in a propanol-water mixture and the observation that washing samples in the AFM is an effective way of disaggregating salt-DNA complexes. The ability to image DNA in aqueous solutions has potential applications for observing processes involving DNA in the AFM.