Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

High-resolution proton magnetic resonance and infrared spectra of poly(vinyl formal) and its model compounds

High-resolution proton magnetic resonance and infrared spectra of poly(vinyl formal) were studied in comparison with those of the model formals obtained from stereoisomers of pentane-2,4-diol and heptane-2,4,6-triol in order to learn spectral changes due to differences of the steric structures of the polymer. In the NMR spectrum of transformal obtained from dl diol or dl,dl (syndiotactic) triol, all proton signals were well interpreted by assuming a rapid chair-chair inversion of the formal ring. On the other hand, no such inversion was observed spectroscopically in cis-formal obtained from the meso diol or meso,meso (isotactic) triol, and the cis-formal ring was supposed to take a diequatorial form preferentially. Consequently, dioxymethylene protons gave a single peak (equivalent) in trans-formal and an AB quartet (nonequivalent) in cis-formal. In the spectra of poly(vinyl formal), the dioxymethylene signal was an overlap of the singlet and quartet in dimethylsulfoxide solution. Observations of the spectra of various poly(vinyl formals) obtained from poly(vinyl alcohols) of different tacticities and study of temperature dependence of the signal have shown that the singlet and quartet are attributed to trans- and cis- formals, respectively, in the polymer spectrum also. In the infrared spectra of poly(vinyl formals), the 800 and 785 cm^-1 bands were found to be related to cis- and trans-formal rings respectively. A linear relationship was confirmed between D₇₈₅/D₈₀₀ and trans/cis ratios determined from the peak intensities of the dioxymethylene proton signals.     

Binding of sulfonamides to erythrocyte proteins and possible drug-drug interaction

The mode of binding of sulfonamides to erythrocyte proteins and possible drug-drug interaction between those compounds in erythrocytes resulting in changes in tissue levels were studied in rats using zonisamide (a novel antiepileptic agent possessing a sulfonamide group), several other sulfonamides and some antiepileptics without a sulfonamide group. In Michaelis-Menten plottings, the sulfonamide was found to be concentrated into erythrocytes in vitro and in vivo in a saturable high-affinity mode and in a linear low-affinity mode at ordinary therapeutic plasma levels through a simple diffusion process. Concentration in erythrocytes was affected by the presence of albumin in the extracellular medium. The cellular sulfonamide was readily replaced by extracellular sulfonamides in vitro. Even in vivo, erythrocyte levels of zonisamide were lowered by administration of other sulfonamides, although the plasma and tissue levels were not significantly changed since the plasma and tissue compartments of zonisamide were large relative to the erythrocyte compartment at ordinary therapeutic dose levels of zonisamide in animals and man. Therefore, disposition of zonisamide was not significantly influenced by other sulfonamides, but it is suggested that drug-drug interaction affecting the tissue levels may occur for a combination of sulfonamides with extremely different affinities for erythrocytes and low therapeutic plasma levels.     

Production of poly(methyl methacrylate) particles by dispersion polymerization with mercaptopropyl terminated poly(dimethylsiloxane) stabilizer in supercritical carbon dioxide

Poly(methyl methacrylate) (PMMA) particles were produced by dispersion polymerization of methyl methacrylate in the presence of mercaptopropyl terminated poly(dimethylsiloxane) (MP-PDMS) in supercritical carbon dioxide at about 30 MPa for 24 h at 65 °C. The particle diameter could be controlled in a size range of submicron to micron by varying MP-PDMS concentration. The MP-PDMS worked as not only a chain transfer agent but also a colloidal stabilizer, which was named tran stab.Part CCLI of the series Studies on suspension and emulsion     

Controlled-rate thermal analysis

Controlled-rate thermal analysis (CRTA) and differential scanning calorimetry (DSC) were used to investigate the adsorbed water layers and the surface properties of different commercial activated carbons. A simple method is proposed to obtain information on the properties of the adsorbed water film and the surface heterogeneity of the materials studied. This method utilizes TG mass loss and the first derivative of the DTG mass loss curves with respect to temperature and time, obtained during programmed liquid thermodesorption. The obtained TG mass loss curves, which reflect the energetic heterogeneity, consisted of steps and inflections which were associated with the mechanism of wetting of the solid surfaces. The heights of these steps and inflections depend on the adsorption capacity, the adsorption potential and the nature and number of the active centers of the carbon samples studied. The values of the total porosity and the surface phase capacity obtained by this method are in good agreement with those estimated on the basis of independent methods. The behaviour of water/carbon samples was studied by means of DSC at subambient and elevated temperatures. The experimental results provided novel data on the structural heterogeneity, the thermal stability of the water/carbon interface and its phase and structural transitions.Support from the Research Council of Kent State University (Ohio, USA) is acknowledged. The author is pleased to thank Drs M. Jaroniec, R. K. Gilpin, J. Choma and R. Dobrowolski for fruitful discussions and the active carbon samples.     

Analysis of the release process of phenylpropanolamine hydrochloride from ethylcellulose matrix granules

The release properties of phenylpropanolamine hydrochloride (PPA) from ethylcellulose (EC, ethylcellulose 10 cps (EC#10) and/or 100 cps (EC#100)) matrix granules prepared by the extrusion granulation method were examined. The release process could be divided into two parts, and was well analyzed by applying square-root time law and cube root law equations, respectively. The validity of the treatments was confirmed by the fitness of the simulation curve with the measured curve. At the initial stage, PPA was released from the gel layer of swollen EC in the matrix granules. At the second stage, the drug existing below the gel layer dissolved, and was released through the gel layer. Also, the time and release ratio at the connection point of the simulation curves was examined to determine the validity of the analysis. Comparing the release properties of PPA from the two types of EC matrix granules, EC#100 showed more effective sustained release than EC#10. On the other hand, changes in the release property of the EC#10 matrix granule were relatively more clear than that of the EC#100 matrix granule. Thus, it was supposed that EC#10 is more available for controlled and sustained release formulations than EC#100.     

Synthesis of polystyrene/poly[2-(dimethylamino)ethyl methacrylate-stat-ethylene glycol dimethacrylate] core-shell latex particles by seeded emulsion polymerization and their application as stimulus-responsive particulate emulsifiers for oil-in-water emulsions

Surfactant-stabilized polystyrene (PS) latex particles with a mean hydrodynamic diameter of 155 nm were prepared by aqueous emulsion polymerization using 2,2'-azobis(2-amidinopropane) hydrochloride as a cationic radical initiator. Seeded aqueous emulsion copolymerizations of 2-(dimethylamino)ethyl methacrylate (DMA) and ethylene glycol dimethacrylate (EGDMA) were conducted in the presence of these PS particles to produce two batches of colloidally stable core-shell latex particles, in which the shell comprised a cross-linked P(DMA-stat-EGDMA) overlayer. Both the PS and PS/P(DMA-stat-EGDMA) latexes were characterized in terms of their particle size, morphology, and composition using dynamic light scattering, electron microscopy, and FT-IR spectroscopy, respectively. Using the PS/P(DMA-stat-EGDMA) latex particles as a pH-responsive particulate ('Pickering'-type) emulsifier, polydisperse n-dodecane-in-water emulsions were prepared at pH 8 that could be partially broken (demulsified) on lowering the solution pH to 3. These emulsions were characterized in terms of their emulsion type, mean droplet diameter, and morphology using electrical conductivity and Mastersizer measurements, optical microscopy, and scanning electron microscopy (using critical point drying for sample preparation).     

Site-selective RNA cleavage by DNA bearing a base pair-mimic nucleoside

We have synthesized the deoxyadenosine derivative tethering a phenyl group (X), which mimics the Watson-Crick A/T base pair. The RNA/DNA hybrid duplexes containing X in the middle of the DNA sequence showed a similar thermal stability regardless of the ribonucleotide species (A, G, C, or U) opposite to X, probably because of the phenyl group stacking inside of the duplex accompanied by the opposite ribonucleotide base flipped in an extrahelical position. The RNA strand hybridized with the DNA strand bearing X was cleaved on the 3'-side of the ribonucleotide opposite to X in the presence of MgCl2, and the RNA sequence to be cleaved was not restricted. The site-specific RNA hydrolysis suggests that the DNA strand bearing X has the advantage of the site-selective base flipping in the target sequence and the development of a "universal deoxyribozyme" to exclusively cleave a target RNA sequence.     

Mechanism of antioxidant action of pueraria glycoside (PG)-1 (an isoflavonoid) and mangiferin (a xanthonoid).

The antioxidant activities of pueraria glycoside (PG)-1 (isoflavonoid) and mangiferin (xanthonoid) were studied and compared with PG-3 and daidzein (isoflavonoids) and with wogonin (flavonoid). PG-1 and mangiferin rapidly scavenged 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical, and inhibited lipid peroxidation which was initiated enzymatically by reduced nicotinamide adenine dinucleotide phosphate (NADPH) or non-enzymatically by ascorbic acid or Fenton's reagent (H2O2 + Fe2+) in rat liver microsomes. Wogonin inhibited the enzymatically induced lipid peroxidation but had no scavenging effect on DPPH radical or on the non-enzymatic peroxidation. PG-3 and daidzein did not show any of these effects. Formation of Fe2+ by NADPH-dependent cytochrome P-450 reductase was inhibited by wogonin, but not by PG-1 or mangiferin. PG-1 and mangiferin had no effect on terminating radical chain reaction during the lipid peroxidation in the enzymatic system of microsomes or in the linoleic acid hydroperoxide-induced peroxidation system. These results suggest that PG-1 and mangiferin have an antioxidant activity, probably due to their ability to scavenge free radicals involved in initiation of lipid peroxidation. In contrast, wogonin may affect NADPH-dependent cytochrome P-450 reductase action, since it inhibited only the enzymatically induced lipid peroxidation.