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.     

Dynamic light scattering of aqueous solutions of linear aggregates induced by thermal denaturation of ovalbumin

Dynamic light scattering measurements were performed on dilute aqueous solutions of native ovalbumin (OA) and on those of linear OA aggregates induced by thermal denaturation at low ionic strength and neutral pH. The weight-average molecular weight M_w of four aggregates tested ranged from 1,700,000 to 5,500,000. The translational diffusion coefficient D₀ of native OA at infinite dilution was estimated as 8.70 × 10 ^?7 cm²/s, which gave 56.0 Å as the diameter of the rigid spherical particle. The intensity autocorrelation function of linear OA polymers was analyzed with the cumulant method to obtain the first cumulant Λ_e. The dependence of Λ_e on the scattering vector q at very low polymer concentration was found intermediate between those of a flexible chain and a rigid rod. The translational diffusion coefficient D_tr [≡ (T_e/q²)_{q → 0}] was in proportion to M, and the magnitude was in good agreement with a value calculated from the wormlike cylinder model with values of three parameters determined in an earlier study, M_L = 1600 Å^?1, d = 120 Å, and Q = 230 Å, where M_L, d, and Q are the molecular weight per unit length, diameter, and persistence length, respectively. Based on these results, a new model, to be called as the dimer model, was proposed to interpret the formation mechanism of linear OA polymers induced by thermal denaturation. © 1993 John Wiley & Sons, Inc.     

Sedimentation and viscosity of bacteriophage T7 DNA in presence of CH3HgOH

The effects of increasing concentartions of methylmercuric hydroxide (CH₃HgOH) on the rate of sedimentation, S⁰, and intrinsic viscosity, [η], of T7 DNA have been studied at 20°C in 0.005, 0.05, and 0.5M Na₂SO₄, respectively, whereby each salt solvent conatined, in addition, 0.005M sodium borate, pH 9.18, as a buffer. Both S⁰ and [η] are independent of organomercurial concentration as long as DNA remains native. Denaturation, brought about by the complexing of CH₃HgOH with the polymer, produces large changes in S⁰ as wll as [η]. The sedimentation coefficient increases strongly with increasing oragnomercurial concentration once strand separation has occured. Experimental difficulties prevented measuring of [η] in the posttransition region. The data on S⁰ have been used, in combination with available information on the so-called density increment (?ρ/?c₂), to obtain information on the frictional properties of single-stranded and methylmercurated T7 DNA. The frictional coefficient, defined as f′₂ = M₂(?p/?c₂)/S⁰ηN_A, where M₂ is the molecular wieght of T7 DNA, c₂ is the concentration of DNA in g/ml of solution, η_r the realtive viscosity of the salt solvents, and N_A is Avogadro's number, was evaluated for all three salt media as a function of organomercurial concentration. f′₂ of native T7 DNA was found not to be sensitive to changes in ionic strngth; but f′₂ of single-stranded and methylmercurated T7 DNA varied strongly with salt concentration. Since f′₂ of single-stranded T7 DNA was barely affected by organomercurial concentration at a given ionic strength, it is concluded that the dramatic variations of S⁰ with pM (pM ≡ -log[CH₃HgOH]) observed in the posttransition zone reflect only changes in the thermodynamic interactions (“preferential interactions”) existing between DNA and the vatious other solution components, but not changes in the coil dimensions of the polymer.     

Order–Disorder conformation change of xanthan in 0.01M aqueous sodium chloride: Dimensional behavior

Weight-average molecular weights M_w, second virial coefficients, and z-average radii of gyration 〈S²〉 were determined by light scattering as a function of temperature T for four sodium salt samples of xanthan in 0.01M aqueous NaCl, in which the polysaccharide undergoes an order–disorder conformation change with increasing T. The data for 〈S²〉 and M_w at 25 and 80°C, the lowest and highest temperatures studied, confirmed the previous conclusion that the predominant conformation at the former T, i.e., in the ordered state, is a double helix, while that at the latter T, i.e., in the disordered state, is a dimerized coil expanded by electrostatic repulsions between charged groups of the polymer. As T was increased from 25 to 80°C, 〈S²〉 sigmoidally decreased or increased depending on the dimer's molecular weight. This temperature dependence of 〈S²〉 and that determined elsewhere for a high molecular weight sample were found to be described almost quantitatively by a simple dimer model in which the double helix melts from both ends, when the double-helical fraction in the dimer at a given T estimated previously from optical rotation data was used.     

Thermodynamics of stabilization of RNA pseudoknots by cobalt(III) hexaammine

Equilibrium unfolding (folding) studies reveal that the autoregulatory RNA pseudoknots derived from the bacteriophage T2 and T4 gene 32 mRNAs exhibit significant stabilization by increasing concentrations of divalent metal ions in solution. In this report, the apparent affinities of exchange inert trivalent Co(NH₃) have been determined, relative to divalent Mg²⁺, for the folded, partially folded (K_f), and fully unfolded (K_u) conformations of these molecules. A general nonspecific, delocalized ion binding model was developed and applied to the analysis of the metal ion concentration dependence of individual two‐state unfolding transitions. Trivalent Co(NH₃) was found to associate with the fully folded and partially unfolded pseudoknotted forms of these RNAs with a K_f of 5–8 × 10⁴ M⁻¹ in a background of 0.10 M K⁺, or 3‐ to 5‐fold larger than the K_f obtained for two model RNA hairpins and hairpin unfolding intermediates, and ≈ 40–50‐fold larger than K_f for Mg²⁺. The magnitude of K_f was found to be strongly dependent on the monovalent salt concentration in a manner qualitatively consistent with polyelectrolyte theory, with K_f reaching 1.2 × 10⁵ M⁻¹ in 50 mM K⁺. Two RNA hairpins were found to have affinities for Co(NH₃) and Ru(NH₃) of 1–2 ×10⁴ M⁻¹, or ≈ 15‐fold larger than the K_f of ∼ 1000 M⁻¹ observed for Mg²⁺. Additionally, the K_u of 4,800 M⁻¹ for the trivalent ligands is ≈ 8‐fold larger than the K_u of 600 M⁻¹ observed for Mg²⁺. These findings suggest that the T2 and T4 gene 32 mRNA pseudoknots possess a site(s) for Mg²⁺ and Co(NH₃) binding of significantly higher affinity than a “duplexlike” delocalized ion binding site that is strongly linked to the thermodynamic stability of these molecules. Imino proton perturbation nmr spectroscopy suggests that this site(s) lies near the base of the pseudoknot stem S2, near a patch of high negative electrostatic potential associated with the region where the single loop L1 adenosine crosses the major groove of stem S2. © 1999 John Wiley & Sons, Inc. Biopoly 50: 443–458, 1999     

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.     

Laser light-scattering analysis of the dimerization of transfer ribonucleic acids with complementary anticodons

Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA and yeast tRNA^Phe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 10⁵M^?1 in the absence of magnesium to 1.5 × 10⁶M^?1 in 10 mM Mg⁺². The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.     

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.     

Effects of cavity-creating mutations on conformational stability and structure of the dimeric 4-α-helical protein ROP: Thermal unfolding studies

The structural and energetic perturbations caused by cavity-creating mutations (Leu-41 → Val and Leu-41 → Ala) in the dimeric 4-α-helical-bundle protein ROP have been characterized by CD spectroscopy and differential scanning calorimetry (DSC). Deconvolution of the CD spectra showed a decrease in α -helicity as a result of the amino acid exchanges that follows qualitatively the overall decrease in conformational stability. Transition enthalpies are sensitive probes of the energetic change associated with point mutations. ΔH⁰ values at the respective transition temperatures, T_1/2 (71.0, 65.3, and 52.9°C at 0.5 mg/ml) decrease from 580 ± 20 to 461 ± 20 kJ/(mol of dimmer) and 335 ± 20 kJ/(mol of dimmer) for wildtype ROP (Steif, C., Weber, P., Hinz, H.-J., Flossdorf, J., Cesareni, G., Kokkinidis, M. Biochemistry 32:3867-3876, 1993), L⁴¹V, and L⁴¹A, respectively. The conformational stabilities at 25°C expressed by the standard Gibbs energies of denaturation, ΔG, are 71.7, 61.1, and 46.1 kJ/(mol of dimmer). The corresponding transition enthalpies have been obtained from extrapolation using the c(T)and c(T) functions. Their values at 25°C are 176.3, 101.9, and 141.7 kJ/(mol of dimmer) for wild-type ROP, L⁴¹V, and L⁴¹A, respectively. When the stability perturbation resulting from the cavity creating mutations is referred to the exchange of 1 mol of CH₂ group, the average ΔΔG value is ?5.0 ± 1 kJ/(mol of CH₂ group). This decrease in conformation stability suggests that dimeric ROP exhibits the same susceptibility to Leu → Yal and Leu → Ala exchanges as small monomeric proteins. Careful determinations of the partial specific heat capacities of wild-type and mutated protein solutions suggest that the mutational effects are predominantly manifested in the native rather than the unfolded state. © 1995 Wiley-Liss, Inc.     

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.     

Compressibility studies of three proteins in CsCI solutions in the analytical ultracentrifuge

The compositional buoyant densities, ρ;, of human γ-immunoglobulin, bovine serum mercaptalbumin, and egg albumin have been measured in CsCl solutions in the analytical ultracentrifuge as a function or pressure. Standard pressure coefficients, ψ⁰, and standard partial specific volumes of the solvated proteins, υ ,0, have been computed from these data. The ψ⁰ values obtained are strikingly different from each other and from the only other pressure coefficients which have been measured, those values obtained for nucleic acids and nucleoproteins. The ψ value for γ-immunoglobulin is negative, the first nonpositive value obtained, and suggests an unusual internal structure for this protein. The pressure coefficient of mercaptalbumin is not constant. A second-order relation is derived and utilized to interpret these data. The slope of the ρ(P) plot for egg albumin was constant and negative and yielded values of ψ⁰ which are about 20% as large as those reported for DNA. Evaluation of published isopiestic data for egg albumin in CsCl solutions provided the dependence of preferential hydration on water activity. This quantity, (dΓ′/da) as well as α, were found to be negative. The values of ψ⁰ and α were used to compute the effective density gradient from which the correct molecular weight of egg albumin was obtained. The apparent specific volume of egg albumin in a buoyant CsCl solution was measured using the Mettler-Paar densimeter.     

Thermal properties of collagen in helical and random coiled states in the temperature range from 4° to 300°K

The low-temperature heat capacity of collagen (in the hydrated and dehydrated states) and the large entropy of collagen in the coiled state relative to the same protein in the helical state were investigated. The heat capacity for collagen in the solid state in the temperature range 4°–50° K changes proportionally to the square of temperature (C_p ～ T²). Above 50°K there is a linear dependence (C_p ～ T). The differences in the character of temperature dependence of heat capacity for the hydrated and dehydrated collagen show the importance of the specific interaction of water molecules with polypeptide chains of this protein. The peculiarities of the temperature dependence of the heat capacity difference (ΔC_p) of hydrated denatured (random coiled) and hydrated native (helical) collagen are observed at 15°, 120°, and 240°K. These differences are caused by the varying degree of ordering of the hydrate water molecules in native and denatured collagen macromolecules. At all temperatures (4°–300°K) the entropy of the random coiled state is higher than that of collagen in the native state and at 298°K ΔS = ∫ (ΔC_p/T)dT = 0.8 cal/100 g °K.     

Number of binding sites of DNA and polynucleotides with tris(2,2'-dipyridyl)ruthenium(II) cations

The binding of tris(2,2′-bipyridyl)ruthenium(II) cations [Ru(bpy)] with single- and double-stranded (ss and ds) DNA, and the polynucleotides poly(A), poly(C), poly(G), poly(I), poly(I) · poly(C), and poly(U), was studied in aqueous solution. Steady-state electrical conductivity measurements with the polynucleotides, ssDNA, and dsDNA reveal that approximately three nucleotides offer one binding site. This may be compared with the ratio [nucleotide]/[Mg²⁺] of 2.4 : 1 for dsDNA. After laser excitation (353 nm), the luminescence of Ru(bpy) bound to nucleic acids shows two decay components. The contribution of the fast component, which is interpreted as resulting from quenching processes of the absorbed ruthenium complex, exhibits a maximum with increasing [nucleotide]/[Ru(bpy)] at a ratio of about three to one. Bound Ru(bpy) can be released from the strand by addition of NaClO₄ [half-concentration: 2.5 and ≤ 10 mM for poly(U) and dsDNA, respectively].     

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.     

Effects of temperature on microbial ethanol production. II. A thermodynamic interpretation of the temperature profile curve of ethanol production

An attempt is made to give a thermodynamic interpretation of the complete temperature profile curve of ethanol formation. Taking into consideration an enhancing competition between thermal activation and thermal deactivation of ethanol formation at increasing temperatures and supposing that the ethanol production is affected by a reversible and an irreversible term of thermal deactivation of a modified ARRHENIUS equation being current for the total biokinetic sphere may be derived: . The quantities ΔH and ΔH^D_2T are identical with the temperature functions of the change of entropy caused by reversible and irreversible deactivation of ethanol formation, respectively. Accordingly for the yeast strain Saccharomyces cerevisiae Sc 5 the calculated entropy coefficients of reversible and irreversible thermal deactivation of ethanol formation amount to C = (0.245± 0.013) kJ/mol · deg.² and C = (1.657 ± 0.046) kJ/mol · deg.².     

Construction of Equi-replicated Balanced Block Designs with Block Sizes Exceeding the Number of Treatments

In this note it is shown that the block design with incidence matrix Ñ = [NN… N], where N = c_1hN_h + c_oh (11′–N_h). c_oh and c_1h are any non-negative integers and N_h,h = 1, 2,…,p, are incidence matrices of balanced incomplete block designs with the same number of treatments t, is a balanced block design with the block sizes exceeding the number of treatments. In derivation the matrix M₀, introduced by CALIński (1971) is utilized.     

Quasielastic light scattering from solutions of filamentous viruses. I. Experimental

Intensity fluctuations of laser light scattered from filamentous viruses Pf1 [length L (Å) × diameter d (Å) = 20,000 × 90], M13 (9000 × 90), potato virus X (5150 × 130), and tobacco mosaic virus (3000 × 180) in sucrose density gradients were measured with a photon correlation spectrometer over a range of scattering angles from 15° to 120°. The experimental data can be approximated by two exponential decays, “slow” and “fast.” The slow decay rate constant t corresponds to the translational diffusion D of the virus, i.e., t = K²D, where K is the magnitude of the scattering vector. The amplitude of the slow component, i.e., translational diffusion, remains greater than that of the fast component, even at high KL. The fast decay rate constant t is also proportional to K² for viruses such as Pf1, M13, and even potato virus X. In the companion paper, we shall attribute the amplitude enhancement of the translational diffusion to the coupling of its anisotropy to the rotational diffusion modes. In order to explain the excessive decay rates in the fast component, we need to consider the bending mode of rodlike viruses, especially in the longer viruses such as M13 and Pf1, in addition to the usually expected rotational diffusion modes.     

Conformation of mucous glycoproteins in aqueous solvents

Light-scattering techniques have been used to measure the z-average radius of gyration R_g z-average translational diffusion coefficient D_t and weight–average molecular weight M_w of porcine submaxillary mucin (PSM) in solution. PSM isolated at low shear in the presence of protease inhibitors has a M_w about twice as large as a sample prepared without these precautions. The former sample has a M_w of 17 × 10⁶ in 0.1M NaCl, which decreases to 8 × 10⁶ in 6M guanidine hydrochloride (GdnHCl) and then to 2 × 10⁶ on addition of 0.1M mercaptoethanol to the 6M GdnHCl solution. The R_g or D values obtained for PSM in this work superimpose with those of other authors for different mucin glycoproteins, leading to linear log–log relationships to the molecular weight of the protein core. Comparison of these results with those in the literature for denatured proteins suggest that mucins are linear random coils in which the protein core is stiffened by the presence of the oligosaccharide side chains. The length of the oligosaccharides and the nature of the solvent have little effect on the extension of the protein core. This suggests that the stiffness of the protein core is maintained by steric repulsion of the residues at the beginning of the oligosaccharide chains.     

An Unbalanced Mixed Model with Random Effects Having Unequal Variances

Consider the mixed model where x_ijk's are known constants, β_k are unknown parameters and a_i, e_ij are random variables independently and normally distributed with zero means and variances σd_i and σ² respectively, where it is assumed that the d_i's are known (d_i >0). This paper presents procedures for estimating the variance components σ, σ², for testing the hypothesis σ = 0, and for making transformations to random variables with uncorrelated errors and constant variances in order to estimate as well as to test hypothesis concerning the β_k's in the model.