Electrostatic interactions in ionic homopolypeptides in solutions of moderate ionic strength

At sufficiently high ionic strength, long-range electrostatic interactions in a polyelectrolyte such as poly(L -glutamic acid) might be adequately approximated in matrix calculations by use of statistical weights representing second-order interactions. The validity of this assumption has been investigated making use of experimental observations (CD spectra and titration curves) for poly(L -glutamic acid) as a function of temperature in 0.1–0.5M sodium chloride. Theoretical analysis, using a statistical weight matrix proposed by Warashina and Ikegami, is based on the Zimm-Rice theory. Implementation differs from that of Warashina and Ikegami in one respect. Refinement of the initial estimates is achieved using a form of the configuration partition function which does not assume diagonalization of the statistical weight matrix. This difference is of no consequence for the values of σ and s, but it does produce somewhat different values for the statistical weights used to represent the electrostatic interactions. The method used to treat electrostatic interactions in poly(L -glutamic acid) in 0.1M sodium chloride can be viewed as successful in that it properly reproduces the helix–coil transition and titration curves in this solvent and the molecular-weight dependence of the titration curves yields values for s in harmony with those obtained using a treatment which is independent of model, and gives a reasonable ionic-strength dependence for the electrostatic parameters. Furthermore, the model can account for measured helix–coil transitions and titration curves in homopolypeptides in which the side chain is —(CH₂)_xNHCO(CH₂)_yCOOH. The model, however, is not exact. It does not properly account for the molecular-weight dependence of the helical content for polymers of low degree of polymerization.     

Theory of melting of the triple helix poly (A + 2U) for a 1 : 2 mixture of Poly A to Poly U

The Zimm-Bragg theory is extended to treat the melting of the triple helix poly (A + 2U) for a solution with a 1 : 2 mole ratio of poly A to poly U. Only the case for long chains is considered. For a given set of parameters the theory predicts the fraction of segments in the triple helix, double helix, and random coil states as a function of temperature. Four nucleation parameters are introduced to describe the two order–disorder transitions (poly (A + 2U) ? poly A + 2 poly U and poly (A + U) ? poly A + poly U) and the single order–order transition (poly (A + 2U) ? poly (A + U) + poly U). A relation between the nucleation parameters is obtained which reduces the number of independent parameters to three. A method for determining these parameters from experiment is presented. From the previously published data of Blake, Massoulié and Fresco⁸ for [Na⁺] = 0.04, we find σ_T = 6.0 × 10^?4, σ_D = 1.0 × 10^?3, and σσ* = 1.5 × 10^?3. σ_T and σ_D are the nucleation parameters for nucleating a triple helix and double helix, respectively, from a random coil region. σσ* is the nucleation parameter for nucleating a triple helix from a double helix and a single strand. Melting curves are generated from the theory and compared with the experimental melting curves.     

A unified theory of the B-Z transition of DNA in high and low concentrations of multivalent ions

We showed recently that the high-salt transition of poly[d(G-C)]. poly[d(G-C)] between B-DNA and Z-DNA (at [NaCl] = 2.25 M or [MgCl(2)] = 0.7 M) can be ascribed to the lesser electrostatic free energy of the B form, due to better immersion of the phosphates in the solution. This property was incorporated in cylindrical DNA models that were analyzed by Poisson-Boltzmann theory. The results are insensitive to details of the models, and in fair agreement with experiment. In contrast, the Z form of the poly[d(G-m5C)] duplex is stabilized by very small concentrations of magnesium. We now show that this striking difference is accommodated quantitatively by the same electrostatic theory, without any adjustable parameter. The different responses to magnesium of the methylated and nonmethylated polymers do not come from stereospecific cation-DNA interactions: they stem from an experimentally derived, modest difference in the nonelectrostatic component of the free energy difference (or NFED) between the Z and B forms. The NFED is derived from circular DNA measurements. The differences between alkaline earth and transition metal ions are explained by weak coordination of the latter. The theory also explains the induction of the transition by micromolar concentrations of cobalt hexammine, again without specific binding or adjustable parameters. Hence, in the case of the B-Z transition as in others (e.g., the folding of tRNA and of ribozymes), the effect of multivalent cations on nucleic acid structure is mediated primarily by nonspecific ion-polyelectrolyte interactions. We propose this as a general rule for which convincing counter-examples are lacking.     

Competitive cooperative bindings of a small ligand to a linear polymer. II. Investigations on the mechanisms of proflavine binding to poly (A) and DNA.

Experimental binding isotherms relative to the interactions between proflavine and poly(A) or DNA are analyzed by comparison with theoretical models dealing with competitive cooperative bindings. In the case of poly(A), there are apparently no specific binding sites for the positive co-operative binding (complex I) leading to dye aggregation along the polyanionic chain. The second complex (complex II) seems to involve specific base-dye interactions, but it cannot be said whether this binding displays negative cooperativity or noncooperativity. None of the two simpler theoretical models agree quantitatively with all experimental data. A plausible interpretation can be given if it is assumed that (i) the electrostatic binding of one isolated bound dye molecule (nucleus of complex I) involves a definite interaction between a phosphate group and the positive charge of the dye; (ii) the structure of complex II is such that a dye–phosphate ionic interaction is maintained. In the case of DNA, our model of monoexclusive interactions fits the data more closely than does the model of biexclusive interactions. This gives experimental support for structural models in which the intercalated molecule interacts preferentially with one strand of the double helix and blocks only one phosphate for electrostatic binding. In order to propose a mechanism consistent with equilibrium and relaxation kinetic data, a modified reaction scheme is considered which takes account of the cooperativity effects in external binding and extends previous models.     

Halogenated nucleic acids: effects of 5-fluorouracil on the conformation and properties of a polyribonucleotide and its constituents

The conformational properties of 5-fluorouracil derivatives are compared to uracil derivatives. FUrd, 5′-FUMP, and poly(FU) are studied as a function of pH and temperature by ¹⁹F- and ¹H-nmr spectroscopy, and the corresponding uracil derivatives by ¹H-nmr spectroscopy. FUrd exhibits no significant conformational changes with solution pH (5–10). In contrast, at low pH (6–7) 5′-FUMP and 5′-UMP show similar conformational features, while at high pH (9) 5′-FUMP shows significant conformational alterations. Also, poly(U) and poly(FU) are conformationally similar at low pH, but increasing pH induces changes in poly(FU). These changes are observed in the backbone [γ(C4′-C5′)], furanose, and furanose-base conformations. The apparent pK_a of N3-H ionization of the FUra base is determined by ¹H- and ¹⁹F-nmr to range from 7.5 to 8.2 [FUrd < 5′-FUMP < 5′-FUDP < poly(FU)]. These observations are interpreted as a result of electrostatic interactions generated between the ionized phosphate group and the negatively charged base moiety as the pH is raised. The interaction properties of poly(FU) with ApA are studied by ¹H- and ¹⁹F-nmr spectroscopy, and these properties compared to those published for poly(U). Poly(FU) forms a complex with ApA inducing upfield ¹H-shifts in both components, and downfield ¹⁹F- shifts in poly(FU). The base stoichiometry of the complex for poly(U)·ApA is 2U:1A at various U/A ratios. In contrast, the base stoichiometry of the poly(FU)·ApA complex appears to be dependent on the FU/A ratio. At high FU/A ratio, the complex is 2FU:1A, and as the FU/A ratio approaches unity the complex becomes 1FU:1A.     

Protonated polynucleotide structures. 16. Thermodynamics of the melting of the acid form of polycytidylic acid

A phase diagram (pH, ionic strength, temperature) for the double helical form of poly(C) is presented. The thermo-dynamic analysis of these data shows that poly(C) behaves essentially as cytidine, if the electrostatic (ionic strength) contributions and the free energy of double helix formation are considered and taken into account.     

Stable and metastable forms of poly(G)

Poly(G) is shown by ir spectroscopy to be capable of existence in a metastable form which is converted spontaneously at ambient temperature, or more rapidly on heating, to a stable form. The metastable form can be regenerated by freezing and thawing the solution. The high-charge density of four-stranded poly(G) makes it especially susceptible to electrostatic destabilization by use of Et₄N⁺ counterions, which screen electrostatic repulsion of multiple strands less effectively than alkali metal ions. Poly(G) has been obtained for the first time in the single-stranded form in aqueous solution and shown to undergo a fully reversible helix–coil transition on heating.     

Thermodynamic analysis of micellization in PEO–PPO–PEO block copolymer solutions from the hydrogen bonding point of view

A thermodynamic approach is suggested to study the micellization mechanism of poly(ethylene oxide)–poly(propylene oxide)–poly(ethylene oxide) (PEO–PPO–PEO) triblock copolymers solutions from the hydrogen bonding point of view. Using Flory–Huggins theory, an association model is presented to describe hydrogen bonded (HB) chains, which are bridged by hydrogen bonds between water molecules and segments of the copolymer. The entropic change due to hydrogen bonding is formulated and the individual contribution of EO–water (EO–W) and PO–water (PO–W) hydrogen bonding to the micellization are derived respectively. Fourier transform infrared (FTIR) spectroscopy is applied to obtain the information of hydrogen bonds. During the temperature-dependent micellization of P105 block copolymer solutions, rapid disruption of PO–W hydrogen bonds is observed by FTIR and the calculated entropy relating to PO–W hydrogen bonds increases drastically compared with that of EO–W hydrogen bonds. The results demonstrate that PO–W hydrogen bonds play a dominant role in micellization.     

Quantum-mechanical study of the hypochromic effect in polynucleotides. Intra- and interstrand interaction contributions.

The first uv absorption band hypochromism of poly(dA) · poly(dT), poly(dG) · poly(dC), poly(dA), poly(dT), poly(dG), and poly(dC) is calculated with the help of perturbation theory on the basis of monomer characteristics computed by the Pariser-Parr-Pople method taking into account all singly excited configurations. The theoretical results obtained are in good agreement with experimental values of hypochromism. The origin of the hypochromic effect in the double-stranded polynucleotides is investigated. It is shown that intrastrand interactions between the bases make the main contribution to hypochromism (60–76%), while the contribution of the Watson–Crick-pair formation is small (2–12%). The essential part of hypochromism (22–28%) is due to the interstrand interactions between the bases that are not coupled by hydrogen bonds. The discussion of the experimental data shows that the present theoretical investigation could serve as a basis for the correct treatment of experimental data.     

Interaction of poly(A) with different adsorbents for affinity chromatography of nucleic acids

Chromatography on adsorbents for separation of mRNA containing poly(A) has given interesting results, even if the nature of the occurring interaction was not always well understood. In the present study we report the chromatographic behaviour of poly(A) homopolynucleotides on different substituted matrices: poly(U)-: poly(A)-: phenyl-, octyl-, ethanolamine-, acriflarin- and DNA-Sepharose: oligo-dT and MN-cellulose. Using different experimental conditions as ionic strength, neutral salt, pH, temperature, buffer composition it was possible to evaluate the participation of electrostatic, hydrophobic hydrogen-bonding, and/or charge-transfer interaction. Furthermore, it is shown that poly(A) interacts non-specifically with matrices like acriflavin or DNA-Sepharose, as well as with oligo-dT cellulose or poly(U)-Sepharose.     

Light scattering from solutions of a semi-flexible polymer and a polyelectrolyte both having sharp molecular weight distributions

The particle scattering factor in light scattering is determined for poly(tert-butyl crotonate) in n-butyl chloride and also for partially neutralized poly (acrylic acid) in aqueous solution in the presence of added neutral salt (NaBr). The former is a wormlike chain which is extended due to stiffness of the polymer chain, while the latter is extended due to the electrostatic repulsive force which is a kind of excluded volume effect. A clear difference is found between P(theta) of both polymers.     

Preferential binding of the chemical carcinogen N-hydroxy-2-aminofluorene to B-DNA as compared to Z-DNA

The reaction between the chemical carcinogen N-hydroxy-2-aminofluorene and poly (dG-dC) . poly (dG-dC) (B-form), poly (dG-m5dC) . poly (dG-m5dC) (B-or Z-form), poly(dG-br5dC) . poly (dG-br5dC) (Z-form) has been studied. The carcinogen binds covalently to B-DNA but does not bind significantly to Z-DNA. These results are discussed as related to the accessibility, the electrostatic potential and the dynamic structure of DNA. The accessibility and the electrostatic potential of DNA do not explain the difference in reactivity of the carcinogen since a related carcinogen N-acetoxy-N-acetyl-2-aminofluorene binds equally well to both B and Z-DNA. On the other hand, poly (dG-dC) . poly(dG-dC) and poly (dG-br5dC) . poly(dG-br5dC), in presence of ethidium bromide binds equally well to N-hydroxy-2-aminofluorene. It is suggested that the very low binding of this carcinogen to Z-DNA as compared to B-DNA is due to differences in the dynamic structures of these two forms of DNA.     

Differential fixation of poly(L-arginine) and poly(L-lysine) by tannic acid and its application to the fixation of collagen in electron microscopy

A differential fixation of poly(L-arginine) and poly(L-lysine) has been demonstrated by means of cellulose acetate electrophoresis and colorimetric titration. Electrophoresis showed that at pH 3.0 and concentrations between 0.025% and 2% the reagent interacts with poly(L-arginine) but not with poly(L-lysine). at pH 7.5, however, poly(L-lysine) also reacts, although at a higher concentration of tannic acid than was required to fix poly(L-arginine) at this pH. Colorimetric titration revealed that for poly(L-arginine) the reaction with tannic acid commences at pH 3.0 and is complete at pH 4.1 whereas for poly(L-lysine) the reaction commences at pH 3.5 and is complete at pH 4.9. It is suggested that the reaction is predominantly electrostatic. The results are discussed in relation to the use of tannic acid as a protein fixative in electron microscopy.     

Complexity and characterization of polyadenylated RNA in the mouse brain

The complexity of nuclear RNA, poly(A)hnRNA, poly(A)mRNA, and total poly(A)RNA from mouse brain has been measured by saturation hybridization with nonrepeated DNA. These DNA populations were complementary, respectively, to 21, 13.5, 3.8, and 13.3% of the DNA. From the RNA Cot required to achieve half-sturation, it was estimated that about 2.5–3% of the mass of total nuclear RNA constituted most of the complexity. Similarly, complexity driver molecules constituted 6–7% of the mass of the poly(A)hnRNA. 75–80% of the poly(A)mRNA diversity is contained in an estimated 4–5% of the mass of this mRNA. Poly(A)hnRNA constituted about 20% of the mass of nuclear RNA and was comprised of molecules which sedimented in DMSO-sucrose gradients largely between 16S and 60S. The number average size of poly(A)hnRNA determined by sedimentation, electron microscopy, or poly(A) content was 4200–4800 nucleotides. Poly(A)mRNA constituted about 2% of the total polysomal RNA, and the number average size was 1100–1400 nucleotides. The complexity of whole cell poly(A)RNA, which contains both poly(A)hnRNA and poly(A)mRNA populations, was the same as poly(A)hnRNA. This implies that cytoplasmic polyadenylation does not occur to any apparent qualitative extent and that poly(A)mRNA is a subset of the poly(A)hnRNA population. The complexity of poly(A)hnRNA and poly(A)mRNA in kilobases was 5 × 10⁵ and 1.4 × 10⁵, respectively. DNA which hybridized with poly(A)mRNA renatures in the presence of excess total DNA at the same rate as nonrepetitive tracer DNA. Hence saturation values are due to hybridization with nonrepeated DNA and are therefore a direct measure of the sequence complexity of poly(A)mRNA. These results indicate that the nonrepeated sequence complexity of the poly(A)mRNA population is equal to about one fourth that observed for poly(A)hnRNA.     

Pressure dependence of the helix-coil transition temperature for polynucleic acid helices

Thermal denaturation of DNA's and the corresponding helix–coil transformation of artificial polyribonucleic and polydeoxyribonucleic acids have been studied extensively both theoretically^1–13 and experimentally. ^14–30 Much less work has been carried out on the properties of these polynucleic acids at high pressure, and in particular, on the presure dependence of the helix–coil transition temperature.^31–33 Light-scattering techniques have been used in this study to measure the pressure dependence of the helix–coil transition temperature of the two- and three-stranded helices of polyriboadenylic and polyribouridilic acids and of calf thymus DNA. From the slopes of the transition temperature vs. pressure curves and heats of transition obtained from the literature,^20,34 the following volume changes from these helix–coil transitions have been obtained: (a) ?0.96 cc/mole of nucleotide base pairs for the poly (A + U) transition, (b) +0.35 cc/mole of nucleotide base trios for the poly (A + 2U) transition, and (c) +2.7 cc/mole of nucleotide base pairs for the DNA transition. The relative magnitudes and signs of these volume changes which show that poly (A + U) is destabilized by increased pressure, whereas poly (A + 2U) and calf thymus DNA are stabilized by increased pressure, indicates that further development of the helix–coil transition theory for polynucleotides is needed.     

A calorimetric investigation of the heats of binding of Mg ++ to poly A, to poly U, and to their complexes

The heats of binding of Mg⁺⁺ ions to poly A, poly U, and to their complexes, in the presence of Na⁺ ions, have been measurd calorimetrically. In all cases the heat, ΔH(θ), exhibitis a distinct dependence on the extent of binding, θ, and in the cases of poly A and poly U also on the Na⁺ concentration. The values of ΔH(θ) range from +2 to +3 kcal/mole of Mg⁺⁺ bound at θ = 0 to 1.3 kcal/mole at θ = 0.5 except in poly A where at θ = 0 ΔH(θ) = ?2 to ?3 kcal/mole. This is interpreted as being due to a facilitation of base stacking by the binding of Mg⁺⁺. The extent of facilitation is consistent with current estimates of base stacking. A similar effect but of much smaller magnitude is believed to obtain in poly A poly U. An interpretation of the dependence of ΔH(θ) on θ in terms of simple electrostatic interactions, but neglecting solvent effects, was attempted and found to be inadequate.     

Interaction of a dimeric distamycin analog with poly(dA)poly(dT), poly[d(A–T)]poly[d(A–T)], and duplex O<Subscript>23</Subscript> at the origin of replication of the herpes simplex virus

The binding of a dimeric distamycin analog (Pt–bis–Dst) to poly[d(A–T)]poly[d(A–T)], poly(dA)poly(dT), and duplex O₂₃ with the sequence 5’-GCCAATATATATATATTATTAGG-3’, which occurs at the origin of replication (OriS) of the herpes simplex virus, was studied via UV and CD spectroscopy. The synthetic polyamide differs from the natural antibiotic in having two distamycin moieties that are linked via a glycine cis-diamino platinum group. The Pt–bis–Dst binding to poly[d(A–T)]poly[d(A–T)] and poly(dA)poly(dT) reached saturation at approximately one ligand molecule per eight bp. As the ligand–base pair ratio further increased, the maximum wavelength band tended to shift toward longer wavelengths in the CD spectra of complexes with poly[d(A–T)]poly[d(A–T)] and a shoulder appeared in the 290–310 nm spectral region that was absent from the CD spectra of complexes with lower ligand coverages. At higher ligand–oligonucleotide molar ratios, Pt–bis–Dst could bind to poly[d(A–T)]poly[d(A–T)] in the form of hairpins or associations that result from interactions between the distamycin moieties of two neighbor Pt–bis–Dst molecules. The structures of the complexes were stabilized by interactions between the pirrolcarboxamide moieties of two Pt–bis–Dst molecules absorbed on adjacent overlapping binding sites. The interactions could also be responsible for the concentration-dependent spectral changes that were observed during the formation of a complex between Pt–bis–Dst and poly[d(A–T)]poly[d(A–T)]. Spectral changes were almost absent in the case of Pt–bis–Dst binding to poly(dA)poly(dT). The binding of Pt–bis–Dst to duplex O₂₃ reached saturation at two ligand molecules per duplex, which contained a cluster of 18 AT pairs. At higher molar-concentration ratios, duplex CD spectra underwent changes similar to those that were observed for Pt–bis–Dst binding to poly[d(A–T)]poly[d(A–T)]. Testing Pt–bis–Dst for antiviral activity identified 1.5 μg/mL as a concentration that halved the cytopathic effect of the herpes simplex virus on Vero E6 cells; the selectivity index of antiviral action was 65; cytotoxicity was relatively low. The Pt–bis–Dst concentration that caused the death of approximately half of the cells was estimated at 100 μg/mL.     

Electrostatic effects on polynucleotide transitions. II. Behavior of titrated systems

The theory developed in the previous paper to discuss changes in electrostatic free energies in polynucleotide order–disorder transitions is extended to cases where one or more of the participating species is titrated to some degree α. It is shown that, for any class of transition, the melting temperature T_m at constant pH is a linear function of the logarithm of the monovalent counterion concentration M, that at high salt the logarithm of the depression of the melting temperature by pH titration is proportional to the pH change, and that the stability of the ordered form as measured by its melting temperature at neutral pH, is a monotonic function of the quantity pH_m – pK, where pH_m and pK are the pH of melting and the monomer base pK, both measured under similar conditions of temperature and ionic strength. For the transition from double helix to coil, the dependences of T_m and dT_m/d log M on pH are determined experimentally and compared with the qualitative predictions of the theory. It is found that dT_m/dlog M, a measure of – ΔF?^el (the negative of the electrostatic free energy change in the transition), decreases with increasing pH. In acid solution, where the coil is more extensively prolonated than the helix, the change in electrostatic free energy in the transition is larger than at neutral pH. Conversely, in alkali the electrostatic five energy change is smaller than at neutral pH. Hence (dT_m/d log M)_acid > (dT_m/d log M _neutral) > (dT_m/d log M)_alkali. At Suffeciently high pH, dT_m/d log M is observed to become negative, indicating that the electrostatic free energy change is positive in the transition of this region. Date from the literature on the ionic strength dependence of the melting temperature for the acid helices of poly rA, poly rC, and poly dC are also considered from the standpoint of the theory.