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.     

Photophysical properties of oligo(2,3-thienyleneethynylene)s

Photophysical properties of oligo(2,3-thienyleneethynylene)s (nTE, n denotes the number of thiophene rings, n = 2, 3) in benzene were investigated using steady-state, time-resolved fluorescence, and transient absorption spectroscopies. For 2TE, generation of the radiative S2 and nonradiative S1 states was confirmed. Upon excitation, the S2 state was initially generated and deactivated to the S1 state within 10 ps. The S1 state exhibited the transient absorption band at 470 nm, of which the lifetime was estimated to be 5.3 ns. In the case of 3TE, on the other hand, it was revealed that the radiative S1 state with a transient absorption peak at 650 nm was generated upon excitation. The T1 states of nTE were generated from the S1 states. The quantum yields were estimated to be 0.52 and 0.54 for 2TE and 3TE, respectively. Extremely fast reactions in the higher triplet excited state were indicated for both 2TE and 3TE.     

Direct observation of the one-electron reduction of methyl viologen mediated by the CO2 radical anion during TiO2 photocatalytic reactions

The one-electron reduction of methyl viologen (MV(2+)) mediated by the carbon dioxide radical anion (CO(2)(*-)) during photocatalytic reactions in a colloidal TiO(2) aqueous solution (pH 2) has been investigated by time-resolved absorption spectroscopy. The formation of MV(*+) generated from the one-electron reduction reaction with CO(2)(*-), which is generated from the one-electron oxidation reactions with the photogenerated holes (h(+)), was directly observed. The spectral features of the photogenerated charge carriers and the kinetic analysis of the formation process of MV(*+) revealed that the CO(2)(*-), desorbed from the surface, reacts with MV(2+) via a homogeneous electron-transfer process in the bulk solution.     

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.     

Kinetics of transient end-to-end contact of single-stranded DNAs

The formation of the pyrene (Py) dimer radical cation (Py(2)(*+)) was used to measure the kinetics of the intrastrand end-to-end contact rates of single-stranded DNAs (ssDNAs) in the 10 nanoseconds to the tens of microseconds time range. ssDNAs labeled with Py at both ends with the lengths of 3, 6, and 9 mer were synthesized, and the two-photon ionization method was employed to generate a Py(*+), which enables the measurements of the end-to-end contact rates from 10 ns. The formation rate of Py(2)(*+) depended on the length and the sequence of the ssDNAs, and about 1 order of magnitude faster rates were observed for the T-rich ssDNAs compared to those for the corresponding length of A-rich ssDNAs, showing that ssDNA made from adenines is much more rigid than that composed of thymidines. As for the T-rich ssDNAs, the formation of Py(2)(*+) attributed to the misfolded structures was also observed, which is consistent with the configurational diffusion model suggested by Ansari and co-workers.     

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.