Oligodeoxyribonucleotide analogues with bridging dimethylene sulfide,sulfoxide, and sulfone groups. Toward a second-generation model of nucleic acid structure

Short DNA analogues with bridging dimethylene sulfide, sulfoxide, and sulfone groups replacing the phosphate diesters (S-DNAs) were synthesized from building blocks prepared via two routes, both starting from D-glucose. Building blocks for RNA analogues were prepared by stereoselective introduction of nucleobase into a 2'-acylated ribose analogue. The ribose analogues were converted to deoxyribose analogues by replacement of a 3'-OH group by a thioacetyl unit, followed by photolytic deoxygenation or radical-based 2'-deoxygenation. DNA analogues joined via CH(2)(-)S-CH(2) units were prepared by S(N)2 displacement of a 6'-mesyl group on one building block using a thiolate nucleophile of another. 4,4'-Dimethoxytrityl protection and deprotection schemes were established for both the thiol and hydroxyl groups. The corresponding sulfoxide DNA analogues were obtained by oxidation with hydrogen peroxide. Sulfone DNA analogues were obtained by oxidation of the sulfide DNA with persulfate or hydrogen peroxide in the presence of a titanium silicate catalyst. The physical properties of several representative oligonucleotide analogues were examined, and interpreted in light of a "second-generation" model for DNA strand-strand recognition, a model that emphasizes the role of the polyanionic backbone in diminishing unwanted tendencies of highly functionalized molecules to form "structure" in solution. Even short sulfide-linked DNA analogues displayed association properties different from those displayed by standard DNA molecules. Complex formation observed with sulfide-linked tetramers by HPLC study in different solvents suggested that the complex is formed using hydrogen bonding. Sulfone-linked dinucleotides display Watson-Crick behavior; the tetramer, however, displayed self-structure. Self-structure and self-aggregation become more prominent as the length of the oligonucleotide analogues increases. The tendency to self-aggregate can be decreased by adding a charged sulfonate group to the 3'-end of the DNA analogue. Features of the second-generation model are important for many areas of nucleic acid chemistry, from the design of nucleic acid therapeutic agents to the search for life on other planets.     

Inter- and intramolecular pathways for the formation of tetrahydrofurans from beta-(Phosphatoxy)alkyl radicals. Evidence for a dissociative mechanism

beta-(Phosphatoxy)alkyl radicals generated by photolysis of Barton PTOC esters in the presence of allyl alcohol and tert-butyl mercaptan undergo nucleophilic substitution followed by 5-exo-trig radical ring closure leading to tetrahydrofurans in good yield and with high trans selectivity. beta-(Phosphatoxy)alkyl radicals obtained by intramolecular hydrogen 1,5-abstraction with an alkoxyl radical undergo nucleophilic displacement providing tetrahydrofurans. The ensemble of results, including the effects of leaving groups and substituents, strongly support a dissociative mechanism for these radical nucleophilic displacement reactions.     

Molecular weight distribution studies. I. Radiation-induced polymerization of liquid α-methylstyrene

The concentration of water in purified and BaO-dried α-methylstyrene was found to be 1.1 × 10^?4M. The radiation-induced bulk polymerization of the α-methylstyrene thus prepared was studied in the temperature range of ?20°C to 35°C. The polymerization rate varied as the 0.55 power of the dose rate. The theoretical molecular weights and molecular weight distribution were calculated from a proposed kinetic scheme and these values were then compared with those found experimentally. The agreement between these two was reasonably close, and therefore it was concluded that, from the molecular weight distribution point of view, the proposed kinetic scheme for the cationic polymerization of α-methylstyrene is an acceptable one. The rate constant for chain transfer to monomer k_f changed with temperature and was found to be responsible for the decrease in the molecular weight of the polymer with increase in temperature. k_f and k_p at 20°C were found to be 0.95 × 10⁴ l./mole-sec and 0.99 × 10⁶ l./mole-sec, respectively.     

Synthesis and optical resolution of a series of inherently chiral calix[4]crowns with cone and partial cone conformations

A series of inherently chiral calix[4]arenes with cone and partial cone conformations and with crown ether moieties of variable size have been readily synthesized. By taking advantage of the carboxy appendage on the lower rim, these were condensed with the chiral auxiliary (S)-BINOL to form diastereomers which, in most cases, could be separated by preparative TLC, or more desirably, by column chromatography on silica gel (diastereomeric excess >99 % based on HPLC analysis). Seven enantiopure antipodes of inherently chiral calix[4]crowns were obtained after hydrolysis. It has been found that both the size of the crown moiety and alkylation of the last phenolic hydroxy group (accompanied with or without a change in the conformation) affect the separation of the diastereomers.     

Studies on the reactions of silyl enol ether with perfluoroorganic compounds1 III. Synthesis of perfluoroalkylated α, β-unsaturated aldehydes and their derivatives

Per- and poly-fluoroalkylated α, β-unsaturated alkenals were synthesized by the reaction of silyl enol ether of alkanals with per- and poly-fluoroalkyl iodide initiated by Na₂S₂O₄ conveniently in high yield. Their corresponding alkenol and 2,4-dinitrophenylhydrazone were also synthesized.     

Increased throughput in quantitative bioanalysis using parallel-column liquid chromatography with mass spectrometric detection

The feasibility of quantitative bioanalysis by parallel-column liquid chromatography in conjunction with a conventional single-source electrospray mass spectrometer has been investigated using plasma samples containing a drug and its three metabolites. Within a single chromatographic run time, sample injections were made alternately onto each of two analytical columns in parallel at specified intervals, with a mass spectrometer data file opened at every injection. Thus, the mass spectrometer collected data from two sample injections into separate data files within a single chromatographic run time. Therefore, without sacrificing the chromatographic separation or the selected reaction monitoring (SRM) dwell time, the sample throughput was increased by a factor of two. Comparing the method validation results obtained using the two-column system with those obtained using the corresponding conventional single-column approach, the methods on the two systems were found to be equivalent in terms of accuracy and precision. The parallel-column system is simple and can be implemented using existing laboratory equipment with no additional capital outlays. A parallel-column system configured in this manner can be used not only for the within-a-run analysis of two samples containing two different sets of chemical entities, but also for the within-a-run analysis of two samples containing the same set of chemical entities.     

Topography of the free-energy landscape probed via mechanical unfolding of proteins

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.     

Kinetics of zinc and cadmium dissociation of metallothionein in the presence of chelating agents

The dissociation kinetics of metal ions from native metallothionein (Cd₅Zn₂-MT) of rat liver has been studied in the presence of external ligands including amino acids, peptide and polyamino polycarboxylic acids at 25°C. The study shows that the solution pH affects the metal dissociation process. Different ligands present different multiphasic kinetics. The possible mechanism of metal dissociation from metallothionein has been proposed.     

The neomycin biosynthetic gene cluster of Streptomyces fradiae NCIMB 8233: characterisation of an aminotransferase involved in the formation of 2-deoxystreptamine

The biosynthetic gene cluster of the 2-deoxystreptamine (DOS)-containing aminoglycoside antibiotic neomycin has been cloned for the first time by screening of a cosmid library of Streptomyces fradiae NCIMB 8233. Sequence analysis has identified 21 putative open reading frames (ORFs) in the neomycin gene cluster (neo) with significant protein sequence similarity to gene products involved in the biosynthesis of other DOS-containing aminoglycosides, namely butirosin (btr), gentamycin (gnt), tobramycin (tbm) and kanamycin (kan). Located at the 5'-end of the neo gene cluster is the previously-characterised neomycin phosphotransferase gene (apH). Three genes unique to the neo and btr clusters have been revealed by comparison of the neo cluster to btr, gnt, tbm and kan clusters. This suggests that these three genes may be involved in the transfer of a ribose moiety to the DOS ring during the antibiotic biosynthesis. The product of the neo-6 gene is characterised here as the L-glutamine : 2-deoxy-scyllo-inosose aminotransferase responsible for the first transamination in DOS biosynthesis, which supports the assignment of the gene cluster.     

Force acting on the microparticles in electrorheological solids under the application of a nonuniform ac electric field

Under the application of electric fields, the structure of electrorheological (ER) solids can be changed from the body-centered tetragonal lattice to other lattices. We have derived the dipole factor for the lattice by taking into account the local-field effect through the Ewald–Kornfeld formulation, and expressed it in the spectral representation exactly. It is found that when the ER solid is subject to a nonuniform ac electric field, the force acting on the microparticle can be affected by the structure transformation, and local-field effect as well as field frequency. Our results are very well understood in the spectral representation theory.