β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new stereochemical probes for DNA polymerases

Deoxynucleoside 5'-triphosphate analogues in which the β,γ-bridging oxygen has been replaced with a CXY group are useful chemical probes to investigate DNA polymerase catalytic and base-selection mechanisms. A limitation of such probes has been that conventional synthetic methods generate a mixture of diastereomers when the bridging carbon substitution is nonequivalent (X ≠ Y). We report here a general solution to this long-standing problem with four examples of β,γ-CXY dNTP diastereomers: (S)- and (R)-β,γ-CHCl-dGTP (12a-1/12a-2) and (S)- and (R)-β,γ-CHF-dGTP (12b-1/12b-2). Central to their preparation was conversion of the prochiral parent bisphosphonic acids to the P,C-dimorpholinamide derivatives 7 of their (R)-mandelic acid monoesters, which provided access to the individual diastereomers 7a-1, 7a-2, 7b-1, and 7b-2 by preparative HPLC. Selective acidic hydrolysis of the P-N bond then afforded "portal" diastereomers, which were readily coupled to morpholine-activated dGMP. Removal of the chiral auxiliary by H(2) (Pd/C) gave the four individual diastereomeric nucleotides 12, which were characterized by (31)P, (1)H, and (19)F NMR spectroscopy and by mass spectrometry. After treatment with Chelex-100 to remove traces of paramagnetic ions, at pH ~10 the diastereomer pairs 12a,b exhibit discrete P(α) and P(β)(31)P resonances. The more upfield P(α) and more downfield P(β) resonances (and also the more upfield (19)F NMR resonance in 12b) are assigned to the R configuration at the P(β)-CHX-P(γ) carbons on the basis of the absolute configurations of the individual diastereomers as determined from the X-ray crystallographic structures of their ternary complexes with DNA and polymerase β.     

The Evans Lemma of Differential Geometry

A rigorous proof is given of the Evans lemma of general relativity and differential geometry. The lemma is the subsidiary proposition leading to the Evans wave equation and proves that the eigenvalues of the d'Alembertian operator, acting on any differential form, are scalar curvatures. The Evans wave equation shows that the eigenvalues of the d'Alembertian operator, acting on any differential form, are eigenvalues of the index-contracted canonical energy momentum tensor T multiplied by the Einstein constant k. The lemma is a rigorous and general result in differential geometry, and the wave equation is a rigorous and general result for all radiated and matter fields in physics. The wave equation reduces to the main equations of physics in the appropriate limits, and unifies the four types of radiated fields thought to exist in nature: gravitational, electromagnetic, weak and strong.     

Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

Understanding the chemical step in the catalytic reaction of DNA polymerases is essential for elucidating the molecular basis of the fidelity of DNA replication. The present work evaluates the free energy surface for the nucleotide transfer reaction of T7 polymerase by free energy perturbation/empirical valence bond (FEP/EVB) calculations. A key aspect of the enzyme simulation is a comparison of enzymatic free energy profiles with the corresponding reference reactions in water using the same computational methodology, thereby enabling a quantitative estimate for the free energy of the nucleotide insertion reaction. The reaction is driven by the FEP/EVB methodology between valence bond structures representing the reactant, pentacovalent intermediate, and the product states. This pathway corresponds to three microscopic chemical steps, deprotonation of the attacking group, a nucleophilic attack on the P(alpha) atom of the dNTP substrate, and departure of the leaving group. Three different mechanisms for the first microscopic step, the generation of the RO(-) nucleophile from the 3'-OH hydroxyl of the primer, are examined: (i) proton transfer to the bulk solvent, (ii) proton transfer to one of the ionic oxygens of the P(alpha) phosphate group, and (iii) proton transfer to the ionized Asp654 residue. The most favorable reaction mechanism in T7 pol is predicted to involve the proton transfer to Asp654. This finding sheds light on the long standing issue of the actual role of conserved aspartates. The structural preorganization that helps to catalyze the reaction is also considered and analyzed. The overall calculated mechanism consists of three subsequent steps with a similar activation free energy of about 12 kcal/mol. The similarity of the activation barriers of the three microscopic chemical steps indicates that the T7 polymerase may select against the incorrect dNTP substrate by raising any of these barriers. The relative height of these barriers comparing right and wrong dNTP substrates should therefore be a primary focus of future computational studies of the fidelity of DNA polymerases.     

Comparison of sample preparation methods for stable isotope analysis of dissolved sulphate in forested watersheds

Pretreatment methods for measuring stable sulphur (δ³⁴S) and oxygen (δ¹⁸O) isotope ratios of dissolved sulphate from watersheds have evolved throughout the last few decades. The current study evaluated if there are differences in the measured stable S and O isotope values of dissolved sulphate from forested watersheds when pretreated using three different methods: Method 1 (M1): adsorb sulphate on anion exchange resins and send directly to isotope facility; Method 2 (M2): adsorb sulphate on anion exchange resins, extract sulphate from anion exchange resins, and send the produced BaSO₄ to the isotope facility; and Method 3 (M3): directly precipitate BaSO₄ without anion exchange resins with the precipitates being sent to the isotope facility. We found an excellent agreement of the δ³⁴S_sulphate values among all the three methods. However, some differences were observed in the δ¹⁸O_sulphate values (M1 versus M2:?1.5 ‰; M1 versus M3:?1.2 ‰) associated with possible O contamination before isotope measurement. Several approaches are recommended to improve the pretreatment procedures for δ¹⁸O_sulphate analysis.     

National school on neutron and x-ray scattering

Human habitation is dependent on the chemical and physical processes that shape Earth's surface environment and control the transport, cycling, and chemical form of elements. The challenges facing society concerning water, energy, climate change, and health require a molecular-scale understanding of these processes. It is not surprising therefore that synchrotron radiation (SR) techniques have become essential research tools for the molecular environmental science (MES) and low-temperature geochemistry (LTG) communities as they address critical needs for society.     

Tautomerism in some quinaldyl sulfones

A series of quinaldyl sulfones was synthesized and their tautomeric composition was determined by ¹H nmr.     

The isostrophisms of planar ternary rings Part II

In Part I the family of ternary rings determined with respect to the base points A,B,C,D of a projective plane was considered, when the different members of the family are determined by permutations of A,B,C,D. Some of the algebraic relationships between the different rings were studied. In Part II these results are applied to problems of collineations. There is a large body of results relating the properties of ternary rings to collineations, and relating the existence of one set of collineations to the existence of others. Once several basic theorems are established many theorems involving collineations follow quite easily. The usual method of determining what a given collineation implies about a ternary ring is to compute the image points and image lines and see what results. That is not necessary for the collineations presented here using the techniques of isostrophisms.This research is included in the author's doctoral dissertation submitted to Temple University. The author would like to express his appreciation to Professor R. Artzy for his assistance in completing this work.