Analysis of DNA-phosphate adducts in vitro using miniaturized LC-ESI-MS/MS and column switching: Phosphotriesters and alkyl cobalamins

DNA-phosphate adducts are known to be formed by a variety of alkylating agents. Due to little or no repair of DNA-phosphate adducts, these adducts may offer increased possibilities of both identifying and quantifying DNA adducts. The formation of DNA-phosphate adducts leads to a complete esterification of the phosphate group giving rise to a phosphotriester configuration. This work consists of the characterization of ethyl phosphotriesters (Ethyl PTE) using miniaturized LC-ESI-MS/MS and column switching in enzymatic hydrolysate of DNA treated in vitro with the model compound N-ethyl-N-nitrosourea (ENU). In vitro ENU-treated DNA was enzymatically degraded using nuclease P1, phosphodiesterase, and alkaline phosphatase. The use of column switch allowed for large-volume injections, where unmodified nucleosides were discarded in the loading step. The analytes were forward flushed to the analytical column in the eluting step and separated using a linear gradient. Ten different ethyl PTEs (dGpEtdG, dApEtdA, dCpEtdC, TpEtT, dGpEtdA, dGpEtdC, dGpEtT, dApEtdC, dApEtT, and dCpEtT) were characterized by their masses and CAD product ion spectra. Measurements of accurate masses were carried out yielding experimental masses within 5 ppm of the calculated masses for 9 of the 10 ethyl PTEs. For comparison, the enzymatic hydrolysate of ENU-treated DNA was subjected to transalkylation of the DNA-phosphate adducts by cob(I)alamin. Formed ethyl-cobalamins were analyzed according to earlier developed methods. The limit of detection of an alkyl-cobalamin standard and an alkyl PTE standard was 2 fmol and 5 fmol, respectively.     

Potentiometric discrimination of neutral forms of nitrophenol isomers by liquid membrane electrodes incorporated with corroles

The results of studies on the use of corrole derivatives as a host ligand in the PVC liquid membrane electrodes and their ability for the potentiometric high-throughput discrimination of nitrophenol guests have been presented. The significance of parameters which govern the mechanism of generation of potentiometric signals such as the attachment of substituents in the corrole structure, acidity and lipophilicity of the guests, and pH of the aqueous solutions has been discussed in details. Supramolecular recognition processes between corroles and para-nitrophenol molecules have been confirmed by independent NMR measurements.     

Determination of Inner and Outer Bounds of Reachable Sets Through Subpavings

The computation of the reachable set of states of a given dynamic system is an important step to verify its safety during operation. There are different methods of computing reachable sets, namely interval integration, capture basin, methods involving the minimum time to reach function, and level set methods. This work deals with interval integration to compute subpavings to over or under approximate reachable sets of low dimensional systems. The main advantage of this method is that, compared to guaranteed integration, it allows to control the amount of over-estimation at the cost of increased computational effort. An algorithm to over and under estimate sets through subpavings, which potentially reduces the computational load when the test function or the contractor is computationally heavy, is implemented and tested. This algorithm is used to compute inner and outer approximations of reachable sets. The test function and the contractors used in this work to obtain the subpavings involve guaranteed integration, provided either by the Euler method or by another guaranteed integration method. The methods developed were applied to compute inner and outer approximations of reachable sets for the double integrator example. From the results it was observed that using contractors instead of test functions yields much tighter results. It was also confirmed that for a given minimum box size there is an optimum time step such that with a greater or smaller time step worse results are obtained.     

On Ranges and Moore�CPenrose Inverses Related to Matrix Carath��odory and Schur Functions

By Cayley transformation, there is an interplay between matrix-valued Carathéodory and Schur functions in the unit disk. One of the main aims of the paper is to study this interplay with a view to the fact that the matrix function given by the values of a Carathéodory function via Moore–Penrose inverses is also a Carathéodory function. In doing so, we also analyze ranges and null spaces of the values of the matrix function in question and get some results of independence concerning the concretely chosen point of the domain.     

Heteronuclear proton assisted recoupling

We describe a theoretical framework for understanding the heteronuclear version of the third spin assisted recoupling polarization transfer mechanism and demonstrate its potential for detecting long-distance intramolecular and intermolecular (15)N-(13)C contacts in biomolecular systems. The pulse sequence, proton assisted insensitive nuclei cross polarization (PAIN-CP) relies on a cross term between (1)H-(15)N and (1)H-(13)C dipolar couplings to mediate zero- and∕or double-quantum (15)N-(13)C recoupling. In particular, using average Hamiltonian theory we derive effective Hamiltonians for PAIN-CP and show that the transfer is mediated by trilinear terms of the form N(±)C(?)H(z) (ZQ) or N(±)C(±)H(z) (DQ) depending on the rf field strengths employed. We use analytical and numerical simulations to explain the structure of the PAIN-CP optimization maps and to delineate the appropriate matching conditions. We also detail the dependence of the PAIN-CP polarization transfer with respect to local molecular geometry and explain the observed reduction in dipolar truncation. In addition, we demonstrate the utility of PAIN-CP in structural studies with (15)N-(13)C spectra of two uniformly (13)C,(15)N labeled model microcrystalline proteins-GB1, a 56 amino acid peptide, and Crh, a 85 amino acid domain swapped dimer (MW=2×10.4 kDa). The spectra acquired at high magic angle spinning frequencies (ω(r)∕2π>20 kHz) and magnetic fields (ω(0H)∕2π=700-900 MHz) using moderate rf fields, yield multiple long-distance intramonomer and intermonomer (15)N-(13)C contacts. We use these distance restraints, in combination with the available x-ray structure as a homology model, to perform a calculation of the monomer subunit of the Crh protein.     

THE USE OF SULFINATE ANIONS IN TERPENOID SYNTHESIS

Abstract

Sulfinate anions of type 2 have proved to be excellent building blocks for the construction of isoprenoid polyenes, starting from haloalkyl 2-methylbutadienylsulfone1.     

Reply to A Computational Evaluation of the Evidence for the Synthesis of 1,3‐Dimethylcyclobutadiene in Solid State and Aqueous Solution—Beyond the Experimental Reality

Following earlier reports on the photochemical synthesis of 1,3‐dimethylcyclobutadiene 8 , 10 in a protective host matrix, theoretical calculations for the formation of that adduct have been recently performed by Rzepa. 13 The author formulated criticisms based mainly on density functional theory calculations of ¹H NMR spectra. According to Rzepa the calculated spectra do not correspond with our measured spectra, which leads him to the conclusion that our interpretation is wrong, and that mainly cyclobutadiene has not been stabilized or even synthesized; we believe, however, that the initial model that Rzepa used for his calculations does not correspond to chemical reality or is at the very least a crude simplification of it, which implies that his calculations cannot match, in every point, our experimental spectra. Rzepa′s simplified models might be ‘reasonable’ from the theoretical point of view; however, in the case of assessment in the solid state, the theoretical setup does not force the system to preserve the confined stabilizing space defined by the crystalline matrix for encapsulated hosts in the solid state. Inversely, in the case of solution modeling, the theoretical setup is too rigid to properly assess the complex equilibria occurring in solution and to accurately determine the NMR spectra of exchanging species in solution. The inconsistency between our experimental results and the results of the theoretical models proposed by Rzepa is such that his conclusions are considered to be too far from experimental reality. Accurate modeling taking in account “reasonable” experimental details would be a worthwhile endeavor.     

X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno‐oncology.     

A marked difference between two populations under mass screening of neonatal TSH and biotinidase activity

Health-associated reference values are universally needed in clinical chemistry. The aim of this study was to establish the reference intervals of two populations from data obtained by the mass screening of newborn babies and to demonstrate how to determine 95% confidence intervals around the lower and upper limits of reference values from values that are not normally distributed. Biotinidase activities from Belgian (n=260) and Turkish (n=328) populations were measured by fluorometric assay and expressed as 1 IU (1 nmol/(dl min). Neonatal thyroid-stimulating hormone (nTSH) values from Belgian (n=4186) and Turkish (n=1663) populations were also measured by the solid phase two-site fluoroimmunometric assay, the results were given as μU/ml blood. Transformation of data was performed for each parameter. A parametric method was used for determination of reference values of biotinidase activity and the Belgian population was significantly higher than the Turkish population. nTSH reference values were evaluated by an exact non-parametric method, but approximate calculation based on the central limit theorem was also performed for confidence intervals around the reference limits. nTSH values of the Turkish population were found to be significantly higher than for the Belgian population. Rank numbers were found by an exact non-parametric method based upon the assumption of a binomial distribution. This study shows a procedure to define the rank numbers for n>1000 and to obtain reference values with 95% confidence intervals for lower and upper reference limits. Received: 20 July 2002 Accepted: 27 July 2002 Acknowledgements We are grateful to Professor Per Hyloft Peterson, Clinical Biochemist, Odense University Hospital, for his valuable advice and criticism. Also we would like to thank John Pezzullo Associate Professor for Pharmacology and Biostatistics, at Georgetown University Medical Center, for his binomial and approximate calculations. We also want to thank Professor Fatma Kutay, Clinical Chemist, Ege University Medical School and Hospital, for her contributions. This investigation was supported in part by a short term FEBS (Federation European Biochemical Society) fellowship grant. Presented at the European Conference on Quality in the Spotlight in Medical Laboratories, 7–9 October 2001, Antwerp, Belgium Correspondence to T. Tanyal?ın