The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs

The stability and replication of DNA containing self-pairs formed between unnatural nucleotides bearing benzofuran, benzothiophene, indole, and benzotriazole nucleobases are reported. These nucleobase analogues are based on a similar scaffold but have different hydrogen-bond donor/acceptor groups that are expected to be oriented in the duplex minor groove. The unnatural base pairs do not appear to induce major structural distortions and are accommodated within the constraints of a B-form duplex. The differences between these unnatural base pairs are manifest only in the polymerase-mediated extension step, not in base-pair stability or synthesis. The benzotriazole self-pair is extended with an efficiency that is only 200-fold less than a correct natural base pair. The data are discussed in terms of available polymerase crystal structures and imply that further modifications may result in unnatural base pairs that can be both efficiently synthesized and extended, resulting in an expanded genetic alphabet.     

The use of static pressures of heavy gases within a quadrupole ion trap

The performance of quadrupole ion traps using argon or air as the buffer gas was evaluated and compared to the standard helium only operation. In all cases a pure buffer gas, not mixtures of gases, was investigated. Experiments were performed on a Bruker Esquire ion trap, a Finnigan LCQ, and a Finnigan ITMS for comparison. The heavier gases were found to have some advantages, particularly in the areas of sensitivity and collision-induced dissociation efficiency; however, there is a significant resolution loss due to dissociation and/or scattering of ions. Additionally, the heavier gases were found to affect ion activation and deactivation during MS/MS, influencing the product ion intensities observed. Finally, the specific quadrupole ion trap design and the ion ejection parameters were found to be crucial in the quality of the spectra obtained in the presence of heavy gases. Operation with static pressures of heavy gases can be beneficial under certain design and operating conditions of the quadrupole ion trap.     

Laser-induced fluorescence measurement of the nascent rotational distribution of N+2 (X2Σ+g) formed by electron impact on N2

The internal state distribution of ground state N⁺₂ ions formed from N₂ by electron impact ionization is measured under collision-free conditions using laser-induced fluorescence. Analysis of the B–X (0, 0) band shows the rotational distribution to be characterized by a temperature which increases slightly with decreasing electron energy (60–100 eV). Cascade contributions are unimportant.     

A comparison of b and uds quark jets to gluon jets

Symmetric three-jet events are selected from hadronic Z⁰ decays such that the two lower energy jets are each produced at an angle of about 150° with respect to the highest energy jet. In some cases, a displaced secondary vertex is reconstructed in one of the two lower energy jets, which permits the other lower energy jet to be identified as a gluon jet through anti-tagging. In other cases, the highest energy jet is tagged as a b jet or as a light quark (uds) jet using secondary vertex or track impact parameter and momentum information. Comparing the two lower energy jets of the events with a tag in the highest energy jet to the anti-tagged gluon jets yields a direct comparison of b, uds and gluon jets, which are produced with the same energy of about 24 GeV and under the same conditions. We observe b jets and gluon jets to have similar properties as measured by the angular distribution of particle energy around the jet directions and by the fragmentation functions. In contrast, gluon jets are found to be significantly broader and to have a markedly softer fragmentation function than uds jets. For thek _⊥ jet finder withy _cut=0.02, we find as the ratios of the mean charged particle multiplicity in the gluon jets compared to the b and uds jets. Results are also reported using the cone jet finder.     

Measurement of the hadronic decay current in τ?→π??+vτ

The properties of hadronic Z⁰ decays with final state photons, measured with OPAL at LEP, have been compared with predictions from two different matrix element calculations ofO( _s ). Two calculations, GNJETS and EEPRAD, have been investigated which use different schemes to restrict the phase space around the poles of the cross section. Assuming the E0-JADE jet definition, both calculations describe the data well in large regions of phase space fory _cut values around 0.06. For very large and very small jet-photon masses some deviations from the predictions have been found, indicating the importance of higher order corrections. Significant differences between the calculations are only apparent in the predicted rate of 1-jet plus photon events. The rate is higher in GNJETS which reproduces the data better than EEPRAD.     

Strong vertex corrections from weak disorder in 2D d-wave superconductors

We show that weak static random potentials have pronounced effects on the quasiparticle states of a 2Dd-wave superconductor close to a node. We prove that the vertex correction coming from the simplest crossed diagram is important even for a nonmagnetic potential. The leading frequency and momentum dependent logarithmic singularities in the self-energy are calculated exactly to second order in perturbation theory. The self-energy corrections lead to a modified low energy density of states which depends strongly on the type of random potential and which can be measured in experiments. There is an exceptional case for a potential with extremely local scatterers and opposite nodes separated by (, ) where an exact cancelation takes place eliminating the leading frequency dependent singularity in the simplest crossed diagram. A comparison of the perturbative results with a self-consistent CPA (coherent potential approximation) for the nonmagnetic disorder reveals qualitative differences in the self-energy at the smallest energies which are due to the neglectance of vertex corrections in CPA.     

There are uncountably many universal topological planes

We prove the existence of uncountably many nonisomorphic topological projective planes, each universal in the sense that it contains an isomorphic copy of every pseudoline arrangement.     

Controlled shrinkage polymers: Characterization of epoxy resins cured with spirobislactones

The diglycidyl ether of bisphenol A (DGEBA) was cured with either an aliphatic or an aromatic spirobislactone using a tertiary amine catalyst. The products were characterized by FTIR, TGA, DSC, dilatometry, and single-fiber adhesion measurements, and their performance was compared to that of DGEBA cured with acid anhydrides. Both aliphatic and aromatic bislactones are effective curing agents for DGEBA. FTIR and dilatometry confirm that both lactone rings open early in the curing reaction and initially offset shrinkage caused by polymerization. After the bislactone has been consumed, oxirane reactions proceed in a normal fashion. The final shrinkage of cured DGEBA polymers, with or without addition of bislactones, is 3.0–3.5%. Bislactone-modified materials possess superior thermal properties, when compared to those of anhydride-cured materials.     

Photoelectron spectroscopy of isolated multiply negatively charged oligonucleotides

Ultraviolet photoelectron spectroscopy in an ion beam was used to investigate the electronic properties of isolated DNA oligonucleotides [dA(5)-4H](4-) and [dT(5)-4H](4-), carrying four excess negative charges. We find the fourth adiabatic electron affinity to be slightly negative for [dA(5)-4H](4-), while it is positive for [dT(5)-4H](4-). This implies a significant influence of the base composition on energetics, which is in turn relevant for analytic applications and also for charge transport properties.     

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.