Molecular dynamics simulations of the oligonucleotide with the modified phosphate/phosphonate internucleotide linkage

Impact of the internucleotide linkage modification by inserting a methylene group to the P-O bond (—O—PO ₂ ^— —O— chain changed for —O—PO ₂ ^— —CH₂—O—), on the modified oligonucleotide binding ability to the natural DNA strand was studied by molecular dynamics simulation. Complex of (dT)₁₁ with a deoxyadenosine undecamer containing alternating modified and natural internucleotide linkage was studied as a model system. The Amber force field was completed by a set of new parameters needed to model the modified part of the nucleotide. The simulations confirmed existence of a double-helical complex the melting point of which is considerably higher than 300 K. While the thymidine (unmodified) strand possesses a B-type secondary structure, the conformation of the adenosine (modified) strand is not stable at 300 K. The -ggt conformation of the modified linkages is highly preferred, temporary jumps to the -g-gt and ggt conformations were, however, observed.     

Quadratic Functionals with General Boundary Conditions

The purpose of this paper is to give the Reid ``Roundabout Theorem' for quadratic functionals with general boundary conditions. In particular, we describe the so-called coupled point and regularity condition introduced in [16] in terms of Riccati equation solutions. Accepted 27 February 1996     

RANDOM EDGE can be exponential on abstract cubes

We prove that RANDOM EDGE, the simplex algorithm that always chooses a random improving edge to proceed on, can take a mildly exponential number of steps in the model of abstract objective functions (introduced by Williamson Hoke [Completely unimodal numberings of a simple polytope, Discrete Appl. Math. 20 (1988) 69-81.] and by Kalai [A simple way to tell a simple polytope from its graph, J. Combin. Theory Ser. A 49(2) (1988) 381-383.] under different names). We define an abstract objective function on the n-dimensional cube for which the algorithm, started at a random vertex, needs at least exp(const·n^1/3) steps with high probability. The best previous lower bound was quadratic. So in order for RANDOM EDGE to succeed in polynomial time, geometry must help.     

Fatty acid binding site of mitochondrial uncoupling protein UCP2 as probed by EPR spectroscopy of spin-labeled fatty acids

Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled fatty acids was used to investigate their interaction withEscherichia coli-expressed human mitochondrial uncoupling protein UCP2 refolded from inclusion bodies in nonaethylene glycol monododecyl ether (C₁₂E₉) micelles. 5-DOXYL-stearic acid and 4-PROXYL-palmitic acid bound to UCP2 exhibited additional clearly separated h_+1I, h_?1I “immobile” peaks in the low- and high-field region, respectively, separated by 42 and 44 Gauss, and extensively reduced h_+1M, h_?1M “mobile” peaks, separated by about 30 G, whereas with 7-DOXYL-stearic acid the I and M peaks were smoothed together into one wide peak. Competition of 4-PROXYL-palmitic acid with added palmitic acid, arachidonic acid, and all-cis-8,11,14-eicosatrienoic acid and of 7-DOXYL-stearic acid with arachidonic acid was indicated by the disappearance of the h_+1I, h_?1I “immobile” peaks, whereas redistribution in micelles without protein was indicated by the rising of the h_+1M, h_?1M “mobile” peaks. In conclusion, a competition of palmitic, arachidonic, and eicosatrienoic acid within a putative fatty acid binding site was observed for mitochondrial uncoupling protein UCP2. This finding together with the observation of EPR spectra of highly immobilized probes exclusively in the presence of the recombinant UCP2 suggest the existence of a fatty acid binding site on UCP2 which is a prerequisite of the fatty acid cycling mechanism as previously postulated for UCP1.     

Synthesis and antimycobacterial activity of alkyl 1‐heteroaryl‐1H‐1,2,3‐triazole‐4‐carboxylates

A series of alkyl l‐heteroaryl‐1H‐1,2,3‐triazole‐4‐carboxylates 6a‐u were synthesised in four steps from methyl (Z)‐2‐benzyloxycarbonylarmino‐3‐(dimethylamino)prop‐2‐enoate ( 1 ) and heterocyclic amines 2a‐s. Triazoles 6a‐o were tested against antimycobacterial activity. For the most active compound, n‐pentyl 1‐(6‐phenylpyridazin‐3‐yl)‐1H‐1,2,3‐triazole‐4‐carboxylate ( 6n ), minimum inhibitory concentration 3.13 μg/ml was determined.     

Quantification of trace elements in human serum fractions by liquid chromatography and inductively coupled plasma mass spectrometry

On‐line coupling of LC and ICP‐MS has been used for fractionation and detection of species of Cu, Fe, I, Se and Zn in human serum. It has been shown that anion exchange chromatography provided better separation capability (both intra‐ and inter‐element) than size‐exclusion chromatography. The mobile phases for ion exchange chromatography consisted of Tris–HNO₃ buffer and ammonium salt (nitrate, acetate or formate). Formate was found to be the best mobile phase counter ion, enabling good chromatographic separation, and is acceptable for mass spectrometry too. The quantitative evaluation of element concentrations adhering to individual fractions was performed by the peak area normalization method. The repeatability of results ranged from 3 to 15% (depending on the element concentration level) and represented the main part of the result uncertainty. The accuracy of Cu and Zn fraction determinations was confirmed by comparison with the isotope dilution technique. Copyright © 2006 John Wiley & Sons, Ltd.     

Complex backflow dynamics in nematic liquid crystals

Received December 31, 2001 / Published online May 21, 2002     

Material tensor parameters of LiNbO3 relevant for electro- and elasto-optics

The complete set of self-consistent parameters of nominally undoped LiNbO₃ crystals of congruent composition that describe the electro-optic, piezoelectric, elasto-optic, elastic, and dielectric response has been determined by numerically evaluating available measurements. The parameters were determined at room temperature and consist of the low-frequency clamped dielectric constants ε^S _ij, elastic stiffness constants at constant electric field C^E _ijkl, piezoelectric stress coefficients e_ijk, elasto-optic constants at constant electric field p^E _ijkl, and clamped electro-optic coefficients r^S _ijk. It is shown that the complete set is required for calculating the effective electro-optic coefficients and dielectric constants in photorefractive applications of LiNbO₃. Received: 4 January 2002 / Revised version: 1 February 2002 / Published online: 14 March 2002     

The treatment of nonhomogeneous Dirichlet boundary conditions by thep-version of the finite element method

Summary The paper addresses the problem of the implementation of nonhomogeneous essential Dirichlet type boundary conditions in thep-version of the finite element method.Partially supported by the Office of Naval Research under Grant N-00014-85-K-0169Research partially supported by the Air Force Office of Scientific Research, Air Force Systems Command, USAF, under Grant Number AFOSR 85-0322     

Angular distribution of muon pairs produced by negative pions on deuterium and tungsten in terms of coherent states

Recently published data on thep _T dependence of the angular distributions of muon pairs produced in collisions of negative pions with deuterium and tungsten nuclei reveal an unexpected tendency. We show that the quantum statistical approach involving expansions in terms of coherent states leads in this case to an exact, non-perturbative result which in the lowest order approximation describes the observed trends with sufficient accuracy. In this procedure, the non-vanishing correlations between the coordinates and momenta of dimuons play a decisive role.