Fluorescence probe for microenvironments: anomalous viscosity dependence of the fluorescence quantum yield of p-N,N-dialkylaminobenzylidenemalononitrile in 1-alkanols

The effect of solvent viscosity on the fluorescence quantum yield of p-N,N-dialkylaminobenzylidenemalononitrile has been studied in alcoholic solvents with viscosities ranging from 0.55 to 115 cP. The observed effect is shown to be a direct consequence of the molecular rotation of surrounding solvent molecules.     

Dynamic viscosity of dilute solutions of poly(L-glutamic acid)

The dynamic viscosity η′ of a dilute solution of poly(L-glutamic acid) (DP = 1370) in a mixed solvent made up of aqueous 0.2M NaCl and dioxane (2:1 by volume) is measured over the pH range 4.2–10 and in the frequency range 2–500 kHz. The frequency dependence of η′ in the helix region (low pH) is interpreted in terms of a model molecule consisting of n rigid helical segments connected by universal joints. The steady-flow viscosity, relaxation time, and high-frequency limiting viscosity at pH 4.75 (helical content 80%) are well explained by this model with n = 5. This value of n is consistent with that estimated from the nucleation parameter σ = 1.4 × 10^?3 obtained from the relation between reduced steady-flow viscosity and helical content. The high-frequency values of η′ in the coil region (high pH) are fitted by Peterlin's theory. The internal viscosity seems to arise in part from the polyelectrolytic character of the molecule. An additional relaxation at low frequencies in the coil region is ascribed to rotation of molecules elongated by the electrostatic interaction. The lower value of reduced steady-flow viscosity in the coil region in the mixed solvent compared with that in water is interpreted in terms of the lower degree of effective ionization and the selective solvation of water by the polypeptide. No anomaly is observed in the helix–coil transition region, indicating that the relaxation time for helix–coil equilibrium is less than 10^?6sec.     

Polymer mixtures with enhanced compatibility and extremely low viscosity used as DNA separation media

Poor compatibility was the major drawback of polymer mixtures when used as DNA separation media. Using poly(ethylene oxide)‐b‐poly(N, N‐dimethylacrylamide) (PEO₄₄‐b‐PDMA₈₈) and PEO (M_w: 1.3 MDa) as an example, we demonstrated the concept that the compatibility was significantly improved when mixing a homopolymer with its copolymer. Laser light scattering indicated that the major interaction between PEO and PEO‐b‐PDMA in dilute solution was the weak hydrodynamic interaction, which showed almost no effect on the viscosity and the static scattering pattern. In semidilute or concentrated solution, viscosity measurement also suggested good compatibility between the two components. When tested as DNA separation medium by CE, the viscosity of the mixture was extremely low, only 5 cP for 5.0 m/v% PEO‐b‐PDMA+0.1 m/v% PEO at 25°C. The performance on DNA separation could be tuned by varying the concentration of each component as well as the component ratio. Good separation on both dsDNA and ssDNA was achieved.     

EFFICIENCY OF PHOTOAFFINITY LABELING DNA HOMOPOLYMERS AND COPOLYMERS WITH ETHIDIUM MONOAZIDE *

Abstract— Photoaffinity labeling of synthetic DN As with ethidium monoazide was studied to determine if the efficiency of adduct formation was related to DNA sequence. Equilibrium drug binding to DNA homopolymers and copolymers was quanitified by phase partition techniques. The amount of drug bound to a deoxypolymer at equilibrium was then compared to the fraction of ethidium analog covalently-linked following photoactivation at the same drug/DNA input ratio. There were significant sequence-related differences in the ability of the photoaffinity probe to label DNA covalently. The efficiency of covalent-adduct formation decreased in the order poly(dG-dC)^. poly(dG-dC)> poly-(dG). poly(dC)poly(dA-dT). poly(dA-dT)poly(dA). poly(dT). Ethidium monoazide was about 2-fold more efficient in labeling deoxyhomopolymers and deoxycopolymers composed of G-C pairs than the A-T base counterparts. In low ionic buffers (0.015 M Na⁺), the efficiency of photoactivation decreased with increasing ethidium monoazide concentrations. However. the base sequence effect was observed over a 40-fold range of drug concentrations. Therefore, the amount of ethidium monoazide bound to a DNA site after irradiation does not appear to represent the true affinity of the drug for that site.     

The mode of binding ACMA-DNA relies on the base-pair nature

A thermodynamic and kinetic study on the mode of binding of 9-amino-6-chloro-2-methoxi-acridine (ACMA) to poly(dA-dT)·poly(dA-dT) and poly(dG-dC)·poly(dG-dC) has been undertaken at pH = 7.0 and I = 0.1 M. The spectrophotometric, kinetic (T-jump), circular dichroism, viscometric and calorimetric information gathered point to formation of a fully intercalated ACMA complex with poly(dA-dT)·poly(dA-dT) and another one only partially intercalated (7%) with poly(dG-dC)·poly(dG-dC). The ACMA affinity with the A-T bases was higher than with the G-C bases. The two polynucleotide sequences give rise to external complexes when the ACMA concentration is raised, namely, the electrostatic complex poly(dA-dT)·poly(dA-dT)-ACMA and the major groove binding complex poly(dG-dC)·poly(dG-dC)-ACMA. A considerable quenching effect of the ACMA fluorescence is observed with poly(dA-dT)·poly(dA-dT), ascribable to face-to-face location in the intercalated A-T-ACMA base-pairs. The even stronger effect observed in the presence of poly(dG-dC)·poly(dG-dC) is related to the guanine residue from on- and off-slot ACMA positions.     

Bimolecular self-reactions of 2-arylindandione- 1,3-yl radicals studied by flash photolysis

Kinetic and thermodynamic data for reaction (1) of certain C-centered aromatic radicals (referred to in this paper by the numbers I to X) in chlorobenzene: have been obtained. The k₁ values of radicals varied between (1.1 ± 0.2) × 10⁶M^?1·sec^?1 (radical VIII) and (3.6 ± 0.7) × 10⁹M^?1 sec^?1 (radical VI) at 20°C. An investigation of the relationship between the recombination rates of radicals I–VIII and X and the solvent viscosity (mixture of toluene and dibutylphthalate, 0.6 < η < 18.4 cP) has shown that the recombination reactions involving radicals I–IV are limited by diffusion in solvents having a viscosity η> 10 cP and are activation reactions in solvents having a viscosity η < 10 cP. The recombination of radicals VIII and IX is an activation reaction, while that of radicals V–VII is diffusion-controlled in the entire viscosity range. The recombination of radical X is limited, in the viscosity range of 18.4 to 2 cP, by intrusion into the first coordination sphere of the partner, the effect of viscosity on the radical X recombination rate in the specified range being the same as its effect on diffusion-controlled reactions. The possible reasons of the discrepancies between the experimental fast recombination rate constants and the theoretical values calculated by the Debye–Smoluchowski theory are discussed. The equilibrium constant depends strongly on the nature of the substituent in the phenyl fragment: the substituents which increase unpaired electron delocalization in the radical intensify the dissociation of the respective dimer. Long-wave absorption bands have been recorded for radicals I–X and their extinction coefficients obtained. Dimers I–V are thermo- and photochromic compounds.     

Spectroscopic identification of binding modes of anthracene probes and DNA sequence recognition

The binding properties of two anthracene derivatives with calf thymus DNA (CT DNA), poly(dA-dT), and poly(dG) x poly(dC) are reported. One contained bulky, cyclic cationic substituents at the 9 and 10 positions, and the other carried acylic, branched, cationic substituents. Binding of the probes to the DNA was examined by calorimetry, spectroscopy and helix melting studies. The cyclic derivative indicated exothermic binding, strong hypochromism, bathochromism, positive induced circular dichroism (CD, 300-400 nm), significant unwinding of the helix, large increases in the helix melting temperature, strong but negative linear dichroism (LD, 300-400 nm) and considerable stabilization of the helix. In contrast, the acyclic analog indicated thermoneutral binding, smaller hypochromism, no bathochromism, very weak induced CD, and no change in the helix melting temperature with any of the DNA polymers. A sharp distinction between the binding properties of the two probes is indicated, and both have intrinsic binding constants of approximately 10(6) M(-1) for the three polymers. However, when the ionic strength of the medium was lowered (10 mM NaCl), the absorption as well as CD spectral changes associated with the binding of the acyclic derivative corresponded with those of the cyclic derivative. The acyclic derivative showed large preference (10-fold) for poly(dG) x poly(dC) over poly(dA-dT), whereas the cyclic analog showed no preference. The characteristic spectroscopic signatures of the two distinct binding modes of these probes will be helpful in deciphering the interaction of other anthracene derivatives with DNA.     

Intrinsic viscosity of polydisperse branched polymers

The relationships between molecular weight distribution and structure in polymerizations with long-chain branching were reviewed and extended. Results were applied to an experimental examination of intrinsic viscosity in polydisperse, trifunctionally branched systems. Several samples of poly(vinyl acetate) were prepared by bulk polymerization under conditions of very low radical concentration. The relative rate constants for monomer transfer, polymer transfer, and terminal double-bond polymerization were established from the variation of M _n and M _w with the extent of conversion. Average branching densities were then calculated for each sample and ranged as high as 1.5 branch points/molecule. Intrinsic viscosities [η]_B were measured in three systems: a theta-solvent, a good solvent, and one that was intermediate in solvent interaction. These results were compared with calculated viscosities, [η]_L, which would have been observed if all the molecules had been linear. The values of [η]_B/[η]_L were substantially the same in all three solvents. The variation of this ratio with branching density was compared with the theory of Zimm and Kilb as adapted to polydisperse systems. Discrepancies were noted, and the adequacy of present model distribution functions for branched polymers was questioned.     

Excited-State Properties of Thymidine and Their Relevance to Its Heterogeneous Emission in Double-Stranded DNA

Published results on synthetic polynucleotides point to T as the major emitting fluorophore in DNA. We have reported also that the bases of the nonalternating polynucleotide poly(dA).poly(dT), in which T was selectively excited, undergo large-amplitude motions on the picosecond-nanosecond time scales (S. Georghiou et al., Biophys. J. 70, 1909-1922, 1996). In that study, the fluorescence decay profile of the T bases of this polynucleotide was found to contain a number of components; these may be considered to be the result of the motions of the bases that give rise to a distribution of stacked geometries of varying rigidity as well as dispersion and polar interactions. Here, we report the results of a study that we have undertaken in order to test this hypothesis. To this effect, we have studied the photophysical properties of thymidine (1) in aqueous buffer and in a number of organic solvents and (2) in aqueous sucrose solutions of viscosity extending to 149 cP. The results suggest that the fluorescence quantum yield decreases with an increase in the polarizability of the solvent, whereas it increases with an increase in the solvent polarity (on the basis of the empirical parameter of solvent polarity ETN) or viscosity. These findings suggest the following for the photophysical properties of the T bases in DNA: (1) Base stacking results in two antagonistic effects, namely it causes a reduction in fluorescence as a result of dispersion interactions and an enhancement as a result of a reduction in the motions of the bases and (2) exposure of the bases to the aqueous environment results in fluorescence enhancement.     

Generalized correlations for molecular weight and concentration dependence of zero-shear viscosity of high polymer solutions

Data are presented to show that two correlations of viscosity–concentration data are useful representations for data over wide ranges of molecular weight and up to at least moderately high concentrations for both good and fair solvents. Low molecular weight polymer solutions (below the critical entanglement molecular weight M_c) generally have higher viscosities than predicted by the correlations. One correlation is η_sp/c[η] versus k′[η], where η_sp is specific viscosity, c is polymer concentration, [η] is intrinsic viscosity, and k′ is the Huggins constant. A standard curve for good solvent systems has been defined up to k′[η]c ≈? 3. It can also be used for fair solvents up to k′[η]c ≈? 1.25· low estimates are obtained at higher values. A simpler and more useful correlation is η_R versus c[η], where η_R is relative viscosity. Fair solvent viscosities can be predicted from the good solvent curve up to c[η] ≈? 3, above which estimates are low. Poor solvent data can also be correlated as η_R versus c[η] for molecular weights below 1 to 2 × 10⁵.     

Calorimetric and thermal analysis studies on the binding of phenothiazinium dye thionine with DNA polynucleotides

Binding of the phenothaizinium dye thionine with four sequence specific deoxyribopolynucleotides, poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT), and poly(dA).poly(dT) has been investigated by means of thermal helix melting, isothermal titration calorimetry, and differential scanning calorimetry experiments. The binding affinity values evaluated from isothermal titration calorimetry suggests that thionine exhibits the highest binding affinity to poly(dG-dC).poly(dG-dC). The binding to poly(dG-dC).poly(dG-dC), poly(dA-dT).poly(dA-dT), and poly(dG).poly(dC) is exothermic and favoured by negative enthalpy changes while binding to poly(dA).poly(dT) is endothermic and anomalous. The values of heat capacity changes of the interaction are negative and in the range (?0.4 to ?0.5) kJ · K^?1 · mol^?1. The binding is characterized by strong stabilization of the polynucleotides against thermal strand separation. The binding affinity values derived from thermal melting data are in excellent agreement with those obtained from isothermal titration calorimetry data. Insights into the energetic aspects and guanine–cytosine selectivity of the DNA interaction of thionine have been obtained from these studies.     

Conformational Kinetics in Chiral Poly(diphenylacetylene)s: A Dynamic P/M Memory Effect

Dynamic P/M (plus/minus) helical memory in chiral dissymmetric poly(diphenylacetylene)s (PDPA) is shown using a PDPA that bears the benzamide of (L)-alanine methyl ester as pendant. For a single chiral polymer, it is possible to obtain either P or M helical structures in a specific solvent without the presence of any chiral external stimuli. To do that, it is necessary to combine the conformational control at the pendant group with a high steric hindrance at the backbone. In this case, by thermal annealing in low-polar solvents, an anti-conformer is stabilized at the pendant which commands a P helix in the PDPA. Next, solvent removal followed by addition of a polar solvent such as dimethyl sulfoxide (DMSO), results in the kinetic conformationally trapped P helix. However, in this medium, the preferred handedness and the thermodynamic macromolecular helix for poly-(L)- 1 is M. This process also occurs in the opposite way. Electronic circular dichroism (ECD) and circularly polarized luminescence (CPL) studies show that the dynamic memory effect is present both in ground and excited states.     

Experimental evidence to support viscosity dependence of rates of Diels-Alder reactions in solvent media

This note is aimed at ascertaining whether rates of Diels-Alder reactions depend on the viscosity of solvent media in which the reactions are performed. On the basis of the data collected from the literature and in this laboratory, it is seen in general that the rates increase in the solvents with their viscosities ranging up to approximately 1.2 cP. In solvents possessing viscosities above 1.2 cP, a drop in the reaction rates is observed in all cases. The effect of temperature on the above phenomena is also examined.     

Synthesis and conformation of poly(L-azetidine-2-carboxylic acid-L-proline) and poly([L-proline]3-L-azetidine-2-carboxylic acid)

The synthesis, characterization, and conformational assessment of poL y(L -Aze-L -Pro) and poly[(L -Pro)₃-L -Aze] are reported. The polymers were prepared by using the pentachlorophenol active ester as the polymerizable tetrapeptide derivatives. The copolymer, poly(L -Aze-L -Pro), assumes a Form II helix in polar solvents, and is converted into a form I-like helix at a critical solvent composition of ethanol to trifluoroethanol. The CD spectrum of this Form I-like conformation of poly(L -Aze-L -Pro) is similar to that of poly(trans-5-isopropyl-L -proline), indicating that the rigid four-membered ring at the alternating position can lock in the structure by a mechanism similar to that of a bulky substituent at the trans-5-position of proline. The helix conformation of this copolymer was unfolded in a 0.2M CaCl₂ aqueous solution. In contrast to poly(L -Aze-L -Pro), the copolymer of poly[(L -Pro)₃-L -Aze] contains both cis and trans peptide bond geometry when dissolved in a 90:10 ETOH-H₂O mixture. The conversion of the mixed conformation of poly[(L -Pro)₃-L -Aze)] into a polyproline Form II-like structure occurred in highly polar solvent environments such as water.     

Determination of Chain Transfer Constant for Solvent When the Viscosity of the Polymerizing System Is Considered Important

Abstract

The chain transfer constant of the polymethyl methacrylate radical for N,N-dimethylaniline was determined in two solvents, benzene and dimethyl phthalate. Plots were made using1/P_n=k_t°R_p/k_p ²[M]²η + C_S1 [S₁]/[M] + C_S2 [S₂]/[M] +C_M where η=viscosity of monomer-solvents mixture, k_t°=rate coefficient of termination when η=1 cP, S₁=benzene or dimethyl phthalate, S₂=N,N-dimethylaniline, and other symbols have their usual meanings. The plots agreed well for the two solvents. If the plots were made without considering the viscosity term, two separate lines resulted for the two solvents. Thus it is essential to consider the viscosity of the polymerizing system in the analysis of chain transfer reactions when the termination reaction is diffusion-controlled and the viscosities of the monomer and solvent differ markedly.     

Intrinsic viscosity of solutions of rigid particles at high shear rates

The results of a numerical calculation which extends Scheraga's calculation on the non-Newtonian behavior of the viscosity factor v of rigid ellipsoid solutions are given here and compared to experimental data obtained on different poly(γ-benzyl L -glutamate) samples in helical configuration, over a wide range of molecular weight, up to 980,000. Relations for the axial ratio p, the rotary diffusion constant D, and a test of the deformability of the polymer under shear, are given as functions of the shear-rate dependence of the intrinsic viscosity. The experimental behavior under shear shows that PBLG becomes somewhat flexible in dichloroethane, but not in m-cresol. The dimensions calculated from the viscometric results suggest discrete changes in the length per monomeric unit of the helix at different well defined molecular weights.     

Theoretical Study of β‐Peptide Models: Intrinsic Preferences of Helical Structures

β‐Peptides form various secondary structures, such as 14‐helix, 12‐helix, 10/12‐helix, 10‐helix, 2₈‐ribbon, C6‐ribbon, and pleated‐sheet. Thus, it is useful to understand the intrinsic backbone conformational preferences of these basic structures. By using a simple repeating‐unit method, we have calculated the preferences of C6‐ribbon, β‐strand, 10/12‐helix, 14‐helix, 12‐helix, 10‐helix, and 2₈‐ribbon of a series of poly‐β‐alanine models, Ac‐(β‐Ala)_n‐NH₂, with n=1–9. Interactions among single amino acids result in cooperative residue energies. This is not found for the formations of β‐strands, 2₈‐ribbons, and C6‐ribbons, which possess constant residue energies. In contrast, the 12‐helix, 10‐helix, and 14‐helix are characterized by increasing residue energies as the peptide elongates. Therefore, there is a considerable positive cooperative impetus in the gas phase for their formation. The residue energy of the 10/12‐helix increases significantly for n=2 and 3, and then displays a zigzag pattern. Meanwhile, there is a good correlation between calculated residue energies and residue dipole moments, indicating the importance of long‐range electrostatic interactions to the cooperative residue energy. Efforts have been made to separate the electrostatic and torsional interactions between residues. Thereby, the 12‐, 10‐, and 10/12‐helices all benefit from electrostatic interactions, while the 14‐helix has the most intrinsic preference in terms of torsional interaction. The effect of MeOH on the secondary structures has also been evaluated by SCIPCM solvent model calculations.     

Aggregation of sulfonated poly(p-phenylene terephthalamide) in dilute solutions

The viscosities of dilute solutions of poly(p-phenylene terephthalamide), PPTS, in dimethylacetamide, water, and their mixtures were determined. The reduced viscosity plot in dimethylacetamide shows a negative slope. When the water content in the mixed solvent in 90% or higher, there is an upswing in the reduced viscosity values at concentrations below 0.1 g/dL. The latter behavior suggests a “polyelectrolyte” effect. However, an association model was found to be able to explain the viscosity behaviors in both solvents. ©1995 John Wiley & Sons, Inc.     

Intermolecular Forces of Sugars in Water

Summary. Apparent molar volume and viscosities of fructose, glucose, mannose, and sucrose have been measured in dilute aqueous solution, concentration range 0.028–0.336 M at 293 K. The viscosity coefficient B and A were calculated from the viscosity data using the Jones-Dole equation for all the studied sugars. The data were also analysed for Stauarding equation. The structure making behavior was obtained for all the sugars. A modified Jone-Dole equation was proposed by using ratio of mole fractions of solute and solvent in place of concentrations of solute.     

Intermolecular Forces of Sugars in Water

Apparent molar volume and viscosities of fructose, glucose, mannose, and sucrose have been measured in dilute aqueous solution, concentration range 0.028–0.336 M at 293 K. The viscosity coefficient B and A were calculated from the viscosity data using the Jones-Dole equation for all the studied sugars. The data were also analysed for Stauarding equation. The structure making behavior was obtained for all the sugars. A modified Jone-Dole equation was proposed by using ratio of mole fractions of solute and solvent in place of concentrations of solute.