Optimization of unnatural base pair packing for polymerase recognition

As part of an effort to expand the genetic alphabet, we have been examining the ability of predominately hydrophobic nucleobase analogues to pair in duplex DNA and during polymerase-mediated replication. We previously reported the synthesis and thermal stability of unnatural base pairs formed between nucleotides bearing simple methyl-substituted phenyl ring nucleobase analogues. Several of these pairs are virtually as stable and selective as natural base pairs in the same sequence context. Here, we report the characterization of polymerase-mediated replication of the same unnatural base pairs. We find that every facet of replication, including correct and incorrect base pair synthesis, as well as continued primer extension beyond the unnatural base pair, is sensitive to the specific methyl substitution pattern of the nucleobase analogue. The results demonstrate that neither hydrogen bonding nor large aromatic surface area is required for polymerase recognition, and that interstrand interactions between small aromatic rings may be optimized for replication. Combined with our previous results, these studies suggest that appropriately derivatized phenyl nucleobase analogues represent a promising approach toward developing a third base pair and expanding the genetic alphabet.     

Characterization of the carrot defect in 4H-SiC epitaxial layers

Characterization of the epitaxial defect known as the carrot defect was performed in thick 4H-SiC epilayers. A large number of carrot defects have been studied using different experimental techniques such as Nomarski optical microscopy, KOH etching, cathodoluminescence and synchrotron white beam X-ray topography. This has revealed that carrot defects appear in many different shapes and structures in the epilayers. Our results support the previous assignment of the carrot defect as related to a prismatic stacking fault. However, we have observed carrot defects with and without a visible threading dislocation related etch pit in the head region, after KOH etching. Polishing of epilayers in a few μm steps in combination with etching in molten KOH and imaging using Nomarski optical microscope has been used to find the geometry and origin of the carrot defects in different epilayers. The defects were found to originate both at the epi-substrate interface and during the epitaxial growth. Different sources of the carrot defect have been observed at the epi-substrate interface, which result in different structures and surfaces appearance of the defect in the epilayer. Furthermore, termination of the carrot defect inside the epilayer and the influence of substrate surface damage and growth conditions on the density of carrot defects are studied.     

The mass spectra of small-ring hetero-cycles—II. Aziridinones (α-lactams)

The mass spectra of six aziridinones (α-lactams) are presented. The six aziridinones exhibit the same general fragmentation pattern, the primary processes being loss of the N-t-butyl group, loss of carbon monoxide and loss of t-butyl isocyanate. Several additional rearrangement or fragmentation processes are observed with specific α-lactams.     

Morphology of actinide-rich particles released from the BOMARC accident and collected from soil post remediation

The physical, chemical, and radiological characteristics of material released to the environment from accidents involving nuclear weapon components are dependent upon many factors, especially the manner in which the material is released and delivered to the environment. These characteristics will also be influenced by physical and chemical effects associated with weathering if the material remains exposed to the environment for a long period of time. This study evaluates the morphological characteristics of particles released to the environment as a result of the 1960 BOMARC incident and compares these characteristics to those described following similar incidents at Thule, Greenland (1968) and Palomares, Spain (1966). Each of these incidents involved unique circumstances and conditions that distributed actinide-rich particles to the environment with a range of distinctive morphological characteristics. Morphological and surface elemental analyses were conducted on a set of discrete particles isolated from samples of post-remediated soil collected at McGuire Air Force Base, the site of the BOMARC incident. Scanning electron microscopy and complimentary energy dispersive X-ray spectroscopy were used to perform the analyses. Non-destructive analysis of uranium and plutonium contained in each particle was measured using high-resolution gamma spectrometry. Unique characteristics of the BOMARC samples include some particles exhibiting a smooth, crystalline texture and varying elemental surface distribution of uranium and plutonium, dependent on the particle’s morphology.     

A Quantum Chemical Study of the Abnormal Reactivity of 2‐Methoxyfuran

The gas‐phase pyrolytic and oxidative chemistry of furans has received much attention recently because of their potential as platform chemicals and biofuels. Typically these compounds exhibit very strong ring carbon to H or CH₃ bonds. 2‐Methoxyfuran had been reported to be exceptionally unstable in comparison to related substituted heterocycles in pyrolytic experiments. The origins of its reactivity are shown to be due to the very weak O–CH₃, which at 189.5 ± 1.9 kJ mol^?1 is some 200 kJ mol^?1 weaker than C–H bonds in the molecule. We show that the reported reactivity is somewhat overestimated but that does not alter the fact that 2‐methoxyfuran is exceptionally unstable. It may prove to be a useful alternative to azomethane as a thermal source of methyl radicals.     

Coordination Chemistry of Lipoic Acid and Related Compounds V [1]. New Heteroditopic Ligands Derived from Monoazacrown Ethers and Lipoic Acid

Summary.  Lipoyl imidazolide reacts with aza-15-crown-5 (1,4,7,10-tetraoxa-13-azacyclopentadecane) or aza-18-crown-6 (1,4,7,10,13-pentaoxa-16-azacyclooctadecane) to afford new N-lipoylated azacrown compounds in good yields. These compounds can be transformed into 1,3-dithiols and amines by reduction with complex hydrides of the disulfide and/or amide group of the lipoyl chain. The new pendant-arm macrocycles react as heteroditopic ligands by forming dithiolate and disulfide complexes with the ‘soft’ metal ions Ni²⁺ and Pd²⁺, respectively, and an amine complex with the ‘hard’ Li⁺ ion. Semiempirical and DFT calculations on the complexation of a lithium ion give a most favourable structure in which the azacrown and two solvent molecules are in contact with the metal but not the pendant arm. Received January 29, 2002; accepted (revised) March 25, 2002     

Acid digestion of geological and environmental samples using open-vessel focused microwave digestion

The application of open vessel focused microwave acid digestion is described for the preparation of geological and environmental samples for analysis using inductively coupled plasma-mass spectrometry (ICP-MS). The method is compared to conventional closed-vessel high pressure methods which are limited in the use of HF to break down silicates. Open-vessel acid digestion more conveniently enables the use of HF to remove Si from geological and plant samples as volatile SiF4, as well as evaporation-to-dryness and sequential acid addition during the procedure. Rock reference materials (G-2 granite, MRG-1 gabbros, SY-2 syenite, JA-1 andesite, and JB-2 and SRM-688 basalts) and plant reference materials (BCR and IAEA lichens, peach leaves, apple leaves, Durham wheat flour, and pine needles) were digested with results comparable to conventional hotplate digestion. The microwave digestion method gave poor results for granitic samples containing refractory minerals, however fusion was the preferred method of preparation for these samples. Sample preparation time was reduced from several days, using conventional hotplate digestion method, to one hour per sample using our microwave method.