Modeling the gel electrophoresis of short duplex DNA by Brownian dynamics: cubic gel lattice with direct interaction

The technique of Brownian dynamics is used to model the electrophoretic mobility of spherical and rod-like particles in a three-dimensional cubic gel lattice. In addition to excluded volume interactions between the migrating particle and the gel, direct interactions are also included. The methodology is first applied to spherical particles in the absence of direct interactions and the resulting mobilities are shown to agree with independent studies. The methodology is then applied to rod-like models of short duplex DNA fragments 10-50 base pairs in length. In the absence of direct interactions between gel and DNA, calculated mobilities show a much weaker dependence on gel concentration than observed in experiments of DNA in Tris-acetate buffer and polyacrylamide gels. When an attractive interaction between gel and DNA of approximately -0.3 k(B)T per base pair at contact is included, good agreement between calculated and experimental mobilities is achieved.     

Seasonal fluctuation of DNA photodamage in marine plankton assemblages at Palmer Station, Antarctica

Ultraviolet radiation-induced DNA damage frequencies were measured in DNA dosimeters and natural plankton communities during the austral spring at Palmer Station, Antarctica, during the 1999-2000 field season. We found that the fluence of solar ultraviolet-B radiation (UV-B) at the earth's surface correlated with stratospheric ozone concentrations, with significant ozone depletion observed because of "ozone hole" conditions. To verify the interdependence of ozone depletion and DNA damage in natural microbial communities, seawater was collected daily or weekly from Arthur Harbor at Palmer Station, Antarctica, throughout "ozone season," exposed to ambient sunlight between 0600 and 1800 h and fractionated using membrane filtration to separate phytoplankton and bacterioplankton populations. DNA from these fractions was isolated and DNA damage measured using radioimmunoassay. Under low-ozone conditions cyclobutane dimer concentrations in bacterioplankton and phytoplankton communities were maximal. DNA damage measured in dosimeters correlated closely with ozone concentrations and UV-B fluence. Our studies offer further support to the theory that stratospheric deozonation is detrimental to marine planktonic organisms in the Southern Ocean.     

Efficient synthesis of tertiary amines from secondary amines

Reliable N-alkylations of secondary amines have been developed. By using DIAD and TPP (or PS-TPP) a variety of secondary amines can be converted to the corresponding tertiary amines in good to excellent yields with diverse alkylhalides; no formation of quaternary amine salts are observed. These protocols are amenable to combinatorial chemistry libraries, and are also useful for the syntheses of secondary amines by an acid lysis of the cleavable tertiary amino resins.     

Linear free energy relationship of the energy of the CTTS transition of Halide ions with the solvatochromic parameter α

A linear free energy relationship was found betweenv _max, the energy of the absorption maximum of chloride, bromide, or iodide ion in various solvents, and the solvatochromic parameter which is a measure of the hydrogen bond donor ability of the solvent. The relationships are: for chloride,v _max=6.99+50.16 kK; for bromide,v _max=5.52+45.20 kK; for iodide,v _max=5.02+40.33 kK. The correlation ofv _max for iodide ion with gave a larger correlation coefficient and smaller standard deviation than a correlation with the E _T (30) parameter of Dimroth. From the values ofv _max for iodide ion and the solvated electron in liquid ammonia at 25°C, these correlations indicate a preliminary value of 0.00 for the parameter of liquid ammonia. This had not been reported before and is lower than expected from a general knowledge of the physical and chemical properties of liquid ammonia but is consistent with a more detailed consideration and recent gas phase measurements of hydrogen bond donor strength.     

Particle circulation and oxygen mass transfer in an immobilized cell bioreactor

Two important considerations in the design of an aerobic particulate immobilized cell bioreactor are the provision of sufficient oxygen to maintain the desired metabolism of the immobilized organism, and the biomass holdup (which is proportional to the number of immobilized cell particles in the reactor). The Circulating Bed Reactor, a reactor developed for use with those forms of immobilization that result in particles of essentially neutral buoyancy, operates with an expanded bed of circulating particles. The particle number density attainable in such a reactor has been found to be dependent upon the circulation cell aspect ratio, the individual particle properties, the static bed voidage of the particles, and the superficial gas velocity. The oxygen mass transfer characteristics have been found to be dependent upon the circulatory nature of the system, the particle (solids) holdup, the particle porosity, and the superficial gas velocity.     

Capillary electrochromatography of Triton X-100

Nonionic surfactants such as Triton X-100 (TX-100) are comprised of a mixture of oligomers with a varying degree of length in the ethoxylate chain. The development of chromatographic methods for resolution of the various oligomers of TX-100 is of environmental importance, and can be useful for quality control and characterization in industrial manufacture. Capillary electrochromatography (CEC) is fast becoming a capable separation technique that combines the benefits of both high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE). This report presents a novel CEC method for separation of the various TX-100 oligomers. A comparison of monomeric vs. polymeric stationary phases for separation of TX-100 was conducted. Since the oligomers of TX-100 were better resolved on a monomeric phase as compared to polymeric phase, a systematic mobile phase tuning was performed utilizing a monomeric CEC-C18-3 microm-100 A stationary phase. Various mobile phase parameters such as acetonitrile (ACN) content, Tris concentration, pH, voltage, and temperature were manipulated in order to achieve the optimum separation of oligomers in less than 30 min.     

Understanding ion deceleration lenses: What are the simplicity/performance trade-offs?

The traditional approach for obtaining highly collimated low energy (<200 eV) beams from high-energy (1–10 keV) sector mass spectrometers involves the use of a complex exponential deceleration lens assembly. Through ion optical modeling of the exponential lens and other less-complex lens designs, the fundamental features that contribute to deceleration lens performance are investigated. From this evaluation, a simple high-performance lens was designed, constructed, and characterized. The novel lens described here decelerates a 3-keV ion beam down to the 3-200-eV range while providing low angular divergence, excellent focusing, and good transmission.     

DNA-templated three-branched nanostructures for nanoelectronic devices

Three-branched DNA molecules have been designed and assembled from oligonucleotide components. These nucleic acid constructs contain double- and single-stranded regions that control the hybridization behavior of the assembly. Specific localization of a single streptavidin molecule at the center of the DNA complex has been investigated as a model system for the directed placement of nanostructures. Highly selective silver and copper metallization of the DNA template has also been characterized. Specific hybridization of these DNA complexes to oligonucleotide-coupled nanostructures followed by metallization should provide a bottom-up self-assembly route for the fabrication and characterization of discrete three-terminal nanodevices.     

Synthesis and chemistry of some pyridazine nucleosides related to certain 5-substituted pyrimidine nucleosides

Condensation of 3,4-dichloro-6-[(trimethylsilyl)oxy] pyridazine ( 3 ) with 1-O-acetyl-2,3,5-tri-O-benzoyl-β- D -ribofuranose ( 4 ), by the stannic chloride catalyzed procedure, has furnished 3,4-dichloro-1-(2,3,5-tri-O-benzoyl-β- D -ribofuranosyl) pyridazin-6-one ( 5 ). Nucleophilic displacement of the chloro groups and removal of the benzoyl blocking groups from 5 has furnished 3-chloro-4-methoxy-, 3,4-dimethoxy-, 4-amino-3-chloro-, 3-chloro-4-methylamino-, 3-chloro-4-hydroxy-, and 4-hydroxy-3-methoxy-1-β- D -ribofuranosylpyridazin-6-one. An unusual reaction of 5 with dimethylamine is reported. Condensation of 4,5-dichloro-3-nitro-6-[(trimethylsilyl)oxy]pyridazine with 4 yielded 4,5-dichloro-3-nitro-1-(2,3,5-tri-O-benzoyl-β- D -ribofuranosyl)pyridazin-6-one ( 24 ). Nucleophilic displacement of the aromatic nitro groups from 24 is discussed. Condensation of 3 with 3,5-di-O-p-toluoyl 2-deoxy- D -erythro-pentofuranosyl chloride ( 28 ) afforded an α, β mixture of 2-deoxy nucleosides. The synthesis of certain 3-substituted pyridazine 2′-deoxy necleosides are reported.