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.     

Reductive PET cycloreversion of oxetanes: singlet multiplicity, regioselectivity, and detection of olefin radical anion

Cycloreversion of 2-(p-cyanophenyl)-4-methyl-3-phenyloxetane (1) is achieved using 1-methoxynaphthalene (2) as electron-transfer photosensitizer. The experimental results are consistent with the reaction taking place from the singlet excited state of the sensitizer. Ring splitting of the radical anion 1*- occurs with cleavage of O-C2 and C3-C4 bonds, leading to products (acetaldehyde and p-cyanostilbene) different from the reagents used in the Paterno-Büchi synthesis of 1. The olefin radical anion involved in the electron-transfer process has been detected by means of laser flash photolysis.     

The effect of the "inert" counteranions in the deprotonation of the dihydrogen complex trans-[FeH(eta 2-H2)(dppe)2]+: kinetic and theoretical studies

Kinetic studies indicate that trans-[FeH(H2)(dppe)2]+ reacts with an excess of NEt3 to form cis-[FeH2(dppe)2] in a single kinetic step. The second-order rate constant is strongly affected by the presence of added salts, an acceleration being observed with BF4- and PF6- salts and a deceleration with BPh4-. Theoretical calculations indicate that the role of the accelerating anions consists of the formation of ion pairs that provide a more effective reaction pathway for deprotonation. However, for the ion pair with the bulky BPh4- anion, steric crowding in the proximities of the dihydrogen ligand hinders the approach of the base, and the reaction is decelerated.     

(+)- and (-)-2-aminocyclobutane-1-carboxylic acids and their incorporation into highly rigid beta-peptides: stereoselective synthesis and a structural study

[Chemical reaction: See text] Several derivatives of (+)- and (-)-2-aminocyclobutane-1-carboxylic acid, 1, have been prepared through enantiodivergent synthetic sequences. The stereoselective synthesis of free amino acid (+)-1 has been achieved, and this product has been fully characterized for the first time. Stereocontrolled alternative synthetic methodologies have been developed for the preparation of bis(cyclobutane) beta-dipeptides in high yields. Among them, enantio and diastereomers have been synthesized. beta,beta- and beta,delta-Dimers resulting from the coupling of a cyclobutane residue and a linear amino acid have also been prepared. The ability of the cyclobutane ring as a structure-promoting unit both in the monomers and in the dimers has been manifested. The NMR structural study and DFT theoretical calculations evidence the formation of strong intramolecular hydrogen bonds giving rise to cis-fused [4.2.0]octane structural units that confer high rigidity on these molecules both in solution and in the gas phase. The contribution of a cis-trans conformational equilibrium derived from the rotation around the carbamate N-C(O) bond has also been observed, the trans form being the major conformer. In the solid state, this equilibrium does not exist, and moreover, intermolecular hydrogen bonds are present.     

Baeyer-Villiger oxidation with potassium peroxomonosulfate supported on acidic silica gel

[reaction: see text] Potassium peroxomonosulfate deposited onto silica SiO2 x KHSO5 efficiently reacts with ketones in dichloromethane at room temperature to give the corresponding esters or lactones in quantitative yields. This method avoids hydrolysis of the reaction products. The Baeyer-Villiger reaction is catalyzed by potassium hydrogensulfate present in the supported reagent.     

Thermodynamic evidence for Ca2+-mediated self-aggregation of Lewis X gold glyconanoparticles. A model for cell adhesion via carbohydrate-carbohydrate interaction

Thermodynamic evidence for the selective Ca(2+)-mediated self-aggregation via carbohydrate-carbohydrate interactions of gold glyconanoparticles functionalized with the disaccharides lactose (lacto-Au) and maltose (malto-Au), or the biologically relevant trisaccharide Lewis X (Le(X)-Au), was obtained by isothermal titration calorimetry. The aggregation process was also directly visualized by atomic force microscopy. It was shown in the case of the trisaccharide Lewis X that the Ca(2+)-mediated aggregation is a slow process that takes place with a decrease in enthalpy of 160 +/- 30 kcal mol(-)(1), while the heat evolved in the case of lactose and maltose glyconanoparticles was very low and thermal equilibrium was quickly achieved. Measurements in the presence of Mg(2+) and Na(+) cations confirm the selectivity for Ca(2+) of Le(X)-Au glyconanoparticles. The relevance of this result to cell-cell adhesion process mediated by carbohydrate-carbohydrate interactions is discussed.     

A convenient enantioselective synthesis of (S)-alpha-trifluoromethylisoserine

[reaction: see text] This report describes two straightforward synthetic methodologies to obtain alpha-CF3-isoserine, a new alpha,alpha-disubstituted beta-amino acid, from alpha-(trifluoromethyl)acrylic acid. The routes involve the synthesis of five-membered cyclic sulfates (using sulfuryl chloride) or sulfamidates (using the Burgess reagent) from the corresponding chiral diols, which are obtained by a catalytic asymmetric dihydroxylation (AD) reaction.     

Differential pulse polarographic determination of salicylaldehyde as its Girard-P derivative

A method for the determination of salicylaldehyde (2 × 10^–6–10^–4 M) by differential-pulse polarography, based on the in situ formation of its Girard-P derivative in aqueous solution at pH 2.5, is proposed. The relative standard deviation was 1.5% (ten determinations of 4 × 10^–5 M level). The applicability of this method was checked in synthetic samples containing salicyl alcohol,o-aminophenol, 2-methylphenol, salicylic acid and 4-aminobenzoic acid.     

Stability study of simvastatin under hydrolytic conditions assessed by liquid chromatography

In this work, a liquid chromatography stability-indicating method was developed and applied to study the hydrolytic behavior of simvastatin in different pH values and temperatures. The selected chromatographic conditions were a C18 column; acetonitrile-28 mM phosphate buffer solution, pH 4 (65 + 35) as the mobile phase; 251 degrees C column temperature; and flow rate 1 mL/min. The developed method exhibited an adequate repeatability and reproducibility (coefficient of variation 0.54 and 0.74%, respectively) and a recovery higher than 98%. Furthermore, the detection and quantification limits were 9.1 x 10(-7) and 2.8 x 10(-6) M, respectively. The degradation of simvastatin fitted to pseudo-first order kinetics. The degradation was pH dependent, being much higher at alkaline pH than at acid pH. Activation energy, kinetic rate constants (k) at different temperatures, the half life (t1/2) and the time for 10% degradation to occur (t90) values are also reported.     

Automatation of an analytical laboratory for the determination of drug levels in body fluids

Summary For the specific determination of drug levels in body fluids selective chromatographic methods are now widely used. Because these methods are time-consuming, there is a need for automatation, especially when many samples are to be run. This automatation needs special precautions so that the quality of analyses is controlled and maintained. Possibilities for automatation of chromatographic methods and solutions of the attendant problems are discussed.

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Automatisierung der Bestimmung von Arzneispiegeln in Körperflüssigkeiten

Zusammenfassung Die spezifische Bestimmung von Arzneimittelspiegeln in Körperflüssigkeiten erfolgt heute überwiegend mit chromatographischen Methoden. Besonders bei der Bestimmung größerer Serien wird es notwendig, diese zu automatisieren. Dazu sind jedoch spezielle Vorkehrungen zur Kontrolle und Aufrechterhaltung der Qualität der Analysenergebnisse zu treffen. Möglichkeiten zur Automatisierung chromatographischer Bestimmungsmethoden und Vorschläge zur Lösung der damit zusammenhängenden Probleme werden diskutiert.

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Herrn Prof. Dr. Eberhard von Wasielewski zu seinem 60. Geburtstag gewidmet.

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Presented at the 8th International Microchemical Symposium, Graz, August 25–30, 1980.