Letter: The magnitude of intramolecular DNA optical absorbance with variation in (Na+) and GC base composition: for special application to DNA reassociation studies.

The magnitude of intramolecular DNA optical absorbance is presented as a function of [Na⁺] and GC composition of the DNA. The data are presented as a ratio of absorbances A₀/A₀ for the DNA at the denaturing temperature (T_d) and renaturing temperature (T_r) under the given conditions. All ratios were determined for T_r corresponding to the temperature optimum (T_m ? T_r = 25°C) in DNA reassociation rate. This fact, coupled with the convenient A₀/A₀ ratio representation, permits the quick estimation of the magnitude of this optical effect in DNA reassociation reactions over a wide range of experimental conditions.     

Biopolymer–surfactant interaction. I. Kinetics of binding of cetyltrimethyl ammonium bromide with carboxymethyl cellulose (Na Salt)

The kinetics of binding of the cationic surfactant cetyltrimethyl ammonium bromide with the Na salt of carboxymethyl cellulose was studied by the electrometric method using cetyltrimetlyl ammonium⁺ (CTA⁺) ion-selective polyvinyl chloride membrane electrode. The binding process followed the first-order kinetics and occurred in three stages. Its affinity increased with increasing CTA bromide concentration and decreased with ionic strength. The activation process comprised moderate E and ΔH^≠ and negative ΔS^≠ for all three stages with a ΔH^≠ < TδS^≠ trend proving it to be entropy controlled. The ΔG^≠ values followed the trend ΔG < ΔG < ΔG (in accordance with k₁ > k₂ > k₃). The enthalpies (ΔH^≠) and entropies (ΔS^≠) of activation followed a systematic and interdependent trend. The multiple-stage binding kinetics is grossly comparable with the kinetics of binding of proteins to solid surfaces. © 1995 John Wiley & Sons, Inc.     

Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: effects of DNA packing density

The kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration, the results can be described as first-order binding with two different rate constants, k (= k₁ + k_?1) and k (= k₂ + k_?2). The larger rate constant (k) was at least four orders of magnitude smaller than the comparable first-order forward rate constant for binding to DNA released from its capsid. At 25°C values of k decreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA-containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots of kM are biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate that k s are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.     

On the “filterable aggregates and other particles” interpretation of the extraordinary regime of polyelectrolytes

Quasi-elastic light scattering studies on some polyelectrolyte systems exhibit a somewhat “bizarre” behavior in the profile of the apparent diffusion coefficient D_app as a function of the salt concentration C_s. As C_s is decreased, D_app first increases in accordance with polyelectrolyte theories, and then undergoes a precipitous drop in value by over an order of magnitude at a well-defined critical value C_s = C. This “transition” from C_s > C (ordinary) to C_s < C (extraordinary) is referred to as the “ordinary-extraordinary” (o-e) transition. Ghosh, Peitzsch, and Reed [(1992) Biopolymers, Vol. 32, pp. 1105–1122] proposed a “filterable aggregate” (FA) and “other particle” interpretation for the o-e transition and its reversibility in regard to ionic strength changes. The present communication examines in detail the FA model as applied to the o-e transition. It is shown that the FA model fails to account of the established characteristics of the o-e transition. © 1993 John Wiley & Sons, Inc.     

Conformation study of poly(γ-methyl-L-glutamate) in helicogenic solvents by small-angle X-ray scattering

Small-angle x-ray scattering of poly(γ-methyl-L -glutamate), [Glu(OMe)]_n, in m-cresol and in pyridine was measured to determine the mass per unit length, M_q, and the radius of gyration of the cross section, 〈S〉^1/2. It was confirmed from the values of M_q that [Glu(OMe)]_n exists in an α-helical conformation in these solvents. It was elucidated from the calculations on 〈S〉^1/2 that the side chains come in moderately close contact with the main chain in these solvents. It was indicated from the analysis of the outer portion of the scattering curves that the side-chain conformation varied depending on the solvent.     

Cation effects on the nonlinear electrical properties of DNA solutions

The nonlinear electrical properties of DNA solutions were measured when different monovalent cations were added to DNA. The influence of different parameters has been examined: fundamental frequency, field strength, and concentration. A linear relationship between the harmonic current I_h and the DNA concentration is shown, even for higher concentration values (400 mg/l.). The frequency dispersion of I_h has the same shape for all the cations and the low-frequency amplitude of I_h increases in the following order: Li⁺ < Na⁺ < K⁺ < NH < Cs⁺. The nonlinear polarizability values are compared with the linear ones determined using the very low field electric birefringence technique. Both linear and nonlinear values are of the same order of magnitude. It is thought that the nonlinear electrical property of high-molecular-weight DNA mainly results from the deformation of the DNA coils by the electric field.     

Collapse of DNA caused by trivalent cations: pH and ionic specificity effects

A comparison of the condensation of T4 phage DNA by spermidine and Co(NH₃) at pH values between 5.1 and 10.2 has been made using quasielastic light scattering to determine translational diffusion coefficients and Stokes radii. Co(NH₃) is more effective than spermidine in causing condensation at all pH, indicating that the differences observed in previous work were not due to pH effects, as might have been inferred from recent theories of intermolecular forces. The DNA particles collapsed with Co(NH₃) are smaller than those obtained with spermidine. The hydrodynamic radius of spermide-collapsed structures decreases slightly with increasing pH, while the size of the Co(NH₃)collapsed structures is almost independent of pH. These results confirm that there are specific ion effects in DNA condensation by oligocations, in addition to the dominant general polyelectrolyte effects.     

On the blue color of triiodide ions in starch and starch fractions. I. Characterization and assignment of absorption and circular dichroism spectra of triiodide ions in amylose

Four fundamental Raman lines were observed at 159, 111, 55 and 27 cm^-1 corresponding to the I bound (I) in amyloses with DP from 20 to 100, regardless of the degree of polymerization of I and the excitation wavelength. The spectral resolution was based on the molar extinction coefficient and molar ellipticity spectra of I. Eight bands, named, S₁, S₂, ?, S₈ from long to short wavelength, were isolated. These were found regardless of the DP. By a resonance excitation Raman study, the characteristics of S₃ and S₄, comprising the shoulder around 480 nm, were found to be different from those of S₁ and S₂, comprising the blue band. The assignment of the spectra was based on the electronic states of the monomeric I in the exciton-coupled dimeric unit. It was concluded that the blue band (S₁,S₂) belonged to the long-axis transitions and the shoulder band (S₃,S₄) to the short-axis ones on the monmeric coordinate system.     

Conformational analysis of acetyl-L-phenylalanine p-acetyl and p-valeryl anilides

Empirical force-field calculations and ir and ¹H-nmr spectra indicate that five-membered (C₅) and seven-membered (C) hydrogen-bonded rings are the preferred conformations of acetyl-L -Phe p-acetyl and p-valeryl anilides in nonpolar media. The C₅/C ratio was found to be dependent on the dryness of the solute and the solvent. This fact and the results from conformational-energy calculations suggest that a molecule of water participates in the stabilization of the C conformation.     

Heat capacity changes and partial molal heat capacities of some di- and tripeptides in water

Integral enthalpies of solution of several dipeptides and tripeptides in water at low concentrations have been determined at 25 and 35°C. These data have been used to derive the changes in heat capacity on dissolution at infinite dilution ΔC at 30°C. Limiting partial molal heat capacities ΔC have been determined by combining ΔC with C_p2 (heat capacity of pure solid peptides). Using the data on ω-amino acids and these peptides, the partial molal heat capacity of a peptide group ? CONH? was semiquantitatively estimated.     

Intrinsic viscosity of native and single-stranded T7 DNA and its relationship to sedimentation coefficient

The intrinsic viscosity and sedimentation coefficient, of native and single-stranded T7 DNA have been determined at 25°C as a function of ionic strength in neutral and alkaline NaCl. The relationship between [η] and S_,w is well represented by the Mandelkern-Flory equation over the entire range of conditions between 0.0013 and 1M Na⁺. An apparent discrepancy between the two methods at moderate to high ionic strengths is probably due to a change in V with ionic strength. It appears that [η] is a more sensitive and reliable measure of molecular expansion for native DNA, S_,w but is a better index of conformational change in single strands, since [η] becomes too small to measure conveniently at high ionic strengths. At moderate to high ionic strengths, denaturation leads to a decrease in [η], although unfolded single strands retain considerable viscosity. At sufficiently low ionic strength, the intrinsic viscosity of the single strands becomes higher than that of native DNA, and the effective volume of a single strand approaches that of the native molecule.     

Apparent molar volumes of some amino acids and peptides in aqueous urea solutions

Densities of solutions of several α-amino acids and peptides in 3 and 6m aqueous urea solvents have been determined at 298.15 K. These data have been used to evaluate the infinite-dilution apparent molar volumes of the solutes and the volume changes due to transfer (V ) of the α-amino acids and peptides at infinite dilution from water to aqueous urea solutions. The sign and magnitude of the V values have been rationalized in the framework of Friedman's cosphere-overlap model. The V values for the glycyl group (? CH₂CONH? ) and alkyl side chains have been estimated.     

Physical association of two simple alkylators to some DNA sequences

Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az⁺) and a CH prototype test probe with B-form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH-like ion interacting with (G-C)₄, (A-T)₄, and [(G-C)·(A-T)]₂ deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH-like ion is near known alkylation sites. The results of the Az⁺ … [(G-C)·(A-T)]₂ interaction are virtually identical to those found for the CH-like ion. Aqueous solvation energetics have little effect on the physical association of Az⁺ with [(G-C)·(A-T)]₂.     

Contribution of synthetic polymers of amino acids to knowledge of immune response

The synthetic random polymers poly(Glu,Lys,Phe), poly(Glu,Phe) and poly(Glu,Lys,Tyr), have been used to study some parameters associated with the genetic control of the immune response (Ir) of mice. Mice of haplotypes d and q respond well to GLPhe. Mice of haplotypes k and b were previously shown to be nonresponders, whereas the F₁ (k × b) responded via a phenomenon involving “complementation” between 2 Ir genes, i.e., one gene product from IA, and another from IE form the requisite two-chain Ia “receptor” macromolecules (EE). When it was determined that mice of haplotypes q and k respond to GPhe, and the controlling gene maps to IA, (A_α A_β), we tested the theory that mice having q and k alleles in IA might respond to GLPhe via recognition of GPhe determinants in the terpolymer. Employing the in vitro proliferative response to T-cells from mice immunized with GLPhe and stimulated with GPhe and GLT (cross-reaction), it was determined that different determinant selection patterns exist in the recognition of GLPhe. Mice having q and k alleles in IA can respond to GLPhe via one mechanism, and other mice having d and f alleles respond via other mechanisms. The F₁ of the appropriate nonresponder strains forming the Ia molecule (EE) still exhibit the “complementation” phenomenon. Rabbit antibody against anti-GPhe (ID) from SWR mice (H-2^q)(anti-ID) was prepared. This anti-ID strongly inhibited the binding of ¹²⁵I-GPhe by anti-GPhe antisera produced only in mice of H-2^q haplotype and had no effect on the binding of GPhe by anti-GPhe antisera produced in mice of other haplotypes. The anti-ID also inhibited the binding of ¹²⁵I-GLPhe and ¹²⁵I-GPhe by anti-GLPhe antisera produced only in mice of H-2^q haplotype. These specificities were also confirmed by the inhibition of the plaque-forming cells. It was concluded that the antibodies produced in mice of H-2^q haplotype against GPhe and GLPhe share common idiotypic determinants that are recognized by the anti-idiotypic antiserum.     

The effects of Cu2+ and Pb2+ on the solution structure of calf thymus DNA: DNA condensation and denaturation studied by fourier transform IR difference spectroscopy

The interaction of calf thymus DNA with Cu²⁺and Pb²⁺ was studied in aqueous solution at pH 6.5 with metal/DNA (P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform ir (FTIR) spectroscopy. Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established. Spectroscopic evidence has shown that at low metal/DNA (P) molar rations 1/80 and 1/40, copper and lead ions bind mainly to the PO of the backbone, resulting in increased base-stacking interaction and duplex stability. The major copper ion base binding via G-C base pairs begins at r > 1/40, while the lead ion base binding occurs at r > 1/20 with the A-T base pairs. The denaturation of DNA begins at r = 1/10 and continues up to r = 1/2 in the presence of copper ions, whereas a partial destabilization of the helical structure was observed for the lead ion at high metal ion concentration (r = 1/2). Metal-DNA binding also results in DNA condensation. No major departure from the B-family structure was observed, upon DNA interaction with these metal ions. © 1993 John Wiley & Sons, Inc.     

DNA condensation by cobalt hexaammine(III) in alcohol–water mixtures: Dielectric constant and other solvent effects

DNA molecules condense into compact structures in the presence of a critical concentration of multivalent cations. To probe the contribution ofelectrostatic forces to condensation, we used mixtures of water with methanol (MeOH), ethanol (EtOH), and isopropanol (iPrOH) to vary the dielectric constant ? from 80 to 50. The condensation of pUC18 plasmids by hexaammine cobalt (III), Co(NH₃), was monitored by total intensity and dynamic light scattering, electron microscopy, andCD. The total scattering intensity increased as ? went from 80 to 70, and then decreased as ? decreased further. Ultraviolet spectrophotometry confirmed that the loss of intensity at low ? was not due to the particles' settling out of solution. The rate as well as the extent of condensation increased as? was lowered from 80 to 70, and also depended on the species of alcohol (MeOH < EtOH < iPrOH). The hydrodynamic radii R_H of the particles, however, remained roughly the same at 300–350 A and was independent of the species of alcohol. R_H increased below ? = 70. The critical concentration of Co(NH₃) required to induce DNA condensation decreased from 21 μM to about 16 μM as the dielectric constant decreased from 80 to 70, and decreased moderately with the nonpolarity of the alcohol. The fraction of DNA charge neutralized at the onset of DNA condensation was calculated by a modification of Manning's two-variable counterion condensation theory to be 0.90 ± 0.01, independent of ?. By electron microscopy we observed that the condensed particles changed from about 93% toroids at ? = 80 to 89% rods at ? = 70 and 98% rods at ? = 65. At epsi; lower than 65, DNA collapsed into a network of multistranded fibers. The morphology of condensed DNA particles, whether toroids, rods, or fibers, was independent of the alcohol species. CD spectra in ethanol–water mixtures indicated that both closed circular and linearized plasmids were in the B conformation when condensed with Co(NH₃)³⁺₆ at ?≥ 70, although the closed circular molecules exhibited a weak Ψ-DNA spectrum. A transition from the B to A formtook place between ? = 70 and 60, well above the normal dielectric constant of ? = 40 for this transition, indicating that ethanol and Co(NH₃) synergistically promote the B–A transition. We interpret these results to mean that alcohols have both electrostatic and structural effects on DNA, leading to three regimes of condensation. At the lowest alcohol concentrations the B conformation is stableand condensation is relatively slow, allowing time for the packing adjustments necessary to form toroids. At intermediate alcohol concentrations condensation is faster, and the combined effects of solvent and Co(NH₃) locally destabilize the double helix, permitting DNA foldbacks that lead to rodlike condensates. Rods become shorter as wellas more numerous as ? decreases from 80 to 65–60, indicatingincreasing destabilization as alcohol increases. At the lowest dielectric constants, alcohol and Co(NH₃) produce A-DNA, which strongly self-adheres and rapidly aggregates intofibrous networks, not allowing time for more compact condensates to form. © 1995 John Wiley & Sons, Inc.     

Conformation and folding in histones H1 and H5

Denatured histones H1 and H5 can be readily refolded on salt addition. Their digestion by trypsin leads to limit peptides of about 80 residues having the same nmr and CD spectra as those of the intact parent histones. Scanning microcalorimetry shows that (1) the folded structures of H1 and H5 are located entirely in their limit peptides; (2) both have values of the specific denaturation enthalpy typical for small globular proteins; and that (3) both exhibit a classic “2-state” transition (ΔH = ΔH). The heat-denaturation profiles of H5 measured using intrinsic and extrinsic Cotton effect and side-chain nmr peaks do not coincide at all. Only the intrinsic Cotton effects give a T_m and ΔH close to that from microcalorimetry. We conclude that these proteins exhibit large-scale side-chain motions that precede the macroscopic cooperative transition.     

Characterization of the transition state of Lysozyme unfolding. I. Effect of protein-solvent interactions on the transition state

The influence of proline cis-trans isomerization on the kinetics of lysozyme unfolding was examined carefully according to the theory of Hagerman and Baldwin [(1976) Biochemistry 15, 1462–1473]. As a result, the kinetics of lysozyme unfolding was found to follow the two-state transition model well. The temperature dependencies of k_uf and k_f over a wide temperature range showed that ΔC = 0 and ΔC = ?6.7 kJ K^?1 mol^?1 in solutions of different concentrations of GuHCl. The data observed in solutions containing other denaturants also supported the conclusion that ΔC is nearly equal to zero. The activation enthalpies of unfolding (ΔH) were observed at various concentrations of several kinds of denaturants. They were independent of species and concentrations of denaturants ΔH = 200 kJ mol^?1). These facts indicate that the aspect of interaction between protein and different kinds of solvent molecules varies only slightly during the unfolding to the transition state, that is, the transition state is at compact as the native one. Therefore, it is also suggested that ΔH of 200 kJ mol^?1 is primarily required for the disruption of long-range interactions among different structural domains through a subtle conformational change. We compared the effects of several kinds of denaturants on the unfolding rate. The addition of PrOH more remarkably increases the unfolding rate than do other hydrophilic denaturants. This is probably because PrOH molecules can penetrate into the hydrophobic core of lysozyme, but hydrophilic reagents cannot because of the compactness of the transition state.     

Calorimetric investigation of the helix-coil conversion of polyuridylic acid

The heats of the conformational conversion ΔH_c of polyuridylic acid (polyU) in the presence of various cations were determined using a differential scanning microcalorimeter and an isothermal mixing calorimeter. The first method yields a value of ΔH_c = 5.2 kcal/mol of base pairs, the second one a value of ΔH_c = 6.4 kcal/mol of base pairs. Knowing ΔH_c and the maximal slope of the degree of conversion, which was determined from the temperature dependence of the absorbance of polyU solutions at 260 nm, we were able to evaluate the parameter of cooperativity σ. From the relation σ = e the stacking free energy ΔF_stack could be calculated. Dividing the apparent enthalpy of conversion by the calorimetrically measured enthalpy yields the cooperative length N₀ of one helical segment at the midpoint of conversion. The results show that the type of the cation has no influence on the magnitude of ΔH_c, whereas the cooperativity of polyU is influenced by the various cations.