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.     

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.     

Dextran-modified iron oxide nanoparticles

Dextran-modified iron oxide nanoparticles were prepared by precipitation of Fe（Ⅱ） and Fe（Ⅲ） salts with ammonium hydroxide by two methods. Iron oxide was precipitated either in the presence of dextran solution, or the dextran solution was added after precipitation. In the second method, the iron oxide particle size and size distribution could be controlled depending on the concentration of dextran in the solution. The nanoparticles were characterized by size-exclusion chromatography, transmission electron microscopy and dynamic light scattering. Optimal conditions for preparation of stable iron oxide colloid particles were determined, The dextran/iron oxide ratio 0-0,16 used in precipitation of iron salts can be recommended for synthesis of nanoparticles suitable for biomedical applications, as the colloid does not contain excess dextran and does not coagulate.     

Preface

This issue of Journal of Thermal Analysis and Calorimetry contains selected papers based on presentations in the field of thermal characteristics of advanced polymer systems presented at the 8^th International Symposium on Polymers for Advanced Technologies (PAT 2005) held in Budapest, September 2005. Guest Editors     

Students' Verification Strategies for Combinatorial Problems

We focus on a major difficulty in solving combinatorial problems, namely, on the verification of a solution. Our study aimed at identifying undergraduate students' tendencies to verify their solutions, and the verification strategies that they employ when solving these problems. In addition, an attempt was made to evaluate the level of efficiency of the students' various verification strategies in terms of their contribution to reaching a correct solution. 14 undergraduate students, who had taken at least 1 course in combinatorics, participated in the study. None of the students had prior direct learning experience with combinatorial verification strategies. Data were collected through interviews with individual or pairs of participants as they solved, 1 by 1, 10 combinatorial problems. 5 types of verification strategies were identified, 2 of which were more frequent and more helpful than others. Students' verifications proved most efficient in terms of reaching a correct solution when they were informed that their solution was incorrect. Implications for teaching and learning combinatorics are discussed.     

Projectivep-algebras

Presented by R. Freese.     

Multiple-scattering-theory analysis of XANES spectra of SO2 adsorbed on Cu(100)

The sulphur K-edge x-ray absorption spectra of SO₂ multilayer and of SO₂ submonolayer adsorbed on Cu(100) are analysed. It is found that the dominant spectral features are of a molecular origin. The results support earlier findings that the SO₂ molecule stands perpendicular to the surface. Use of non-selfconsistent potentials does not lead to a good quantitative agreement between theory and experiment.