Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir

Cidofovir (1(S)-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine, CDV) is a potent inhibitor of orthopoxvirus DNA replication. Prior studies have shown that, when CDV is incorporated into a growing primer strand, it can inhibit both the 3'-to-5' exonuclease and the 5'-to-3' chain extension activities of vaccinia virus DNA polymerase. This drug can also be incorporated into DNA, creating a significant impediment to trans-lesion DNA synthesis in a manner resembling DNA damage. CDV and deoxycytidine share a common nucleobase, but CDV lacks the deoxyribose sugar. The acyclic phosphonate bears a hydroxyl moiety that is equivalent to the 3'-hydroxyl of dCMP and permits CDV incorporation into duplex DNA. To study the structural consequences of inserting CDV into DNA, we have used (1)H NMR to solve the solution structures of a dodecamer DNA duplex containing a CDV molecule at position 7 and of a control DNA duplex. The overall structures of both DNA duplexes were found to be very similar. We observed a decrease of intensity (>50%) for the imino protons neighboring the CDV (G6, T8) and the cognate base G18 and a large chemical shift change for G18. This indicates higher proton exchange rates for this region, which were confirmed using NMR-monitored melting experiments. DNA duplex melting experiments monitored by circular dichroism revealed a lower T(m) for the CDV DNA duplex (46 °C) compared to the control (58 °C) in 0.2 M salt. Our results suggest that the CDV drug is well accommodated and stable within the dodecamer DNA duplex, but the stability of the complex is less than that of the control, suggesting increased dynamics around the CDV.     

Use of a Phosphonate Methyltransferase in the Identification of the Fosfazinomycin Biosynthetic Gene Cluster

Natural product discovery has been boosted by genome mining approaches, but compound purification is often still challenging. We report an enzymatic strategy for “stable isotope labeling of phosphonates in extract” (SILPE) that facilitates their purification. We used the phosphonate methyltransferase DhpI involved in dehydrophos biosynthesis to methylate a variety of phosphonate natural products in crude spent medium with a mixture of labeled and unlabeled S‐adenosyl methionine. Mass‐guided fractionation then allowed straightforward purification. We illustrate its utility by purifying a phosphonate that led to the identification of the fosfazinomycin biosynthetic gene cluster. This unusual natural product contains a hydrazide linker between a carboxylic acid and a phosphonic acid. Bioinformatic analysis of the gene cluster provides insights into how such a structure might be assembled.     

The Isolation and Characterization of a Rhodacycle Intermediate Implicated in Metal‐Catalyzed Reactions of Alkylidenecyclopropanes

The isolation and characterization of a rhodacycle intermediate implicated in rhodium‐catalyzed reactions of alkylidenecyclopropanes (ACPs) is described. The structure of the metallacycle was unambiguously determined by X‐ray crystallography and is catalytically competent in the rhodium‐catalyzed carbocyclization and ene‐cycloisomerization reactions of ACPs. This work represents a rare example of the isolation of a metallacycle in a metal‐catalyzed higher‐order carbocyclization reaction and thereby provides important insight into the ligand requirements for the insertion of π‐components. Furthermore, it serves as a convenient synthon for the development of challenging higher‐order carbocyclization reactions, as exemplified by the reaction with an activated allene.     

Modular Construction of Dynamic Nucleodendrimers

Isoguanosine‐containing dendritic small molecules self‐assemble into decameric nucleodendrimers as observed by 1D NMR spectroscopy, 2D DOSY, and mass spectrometry. In particular, apolar building blocks readily form pentameric structures in acetonitrile while the presence of alkali metals promotes the formation of stable decameric assemblies with a preference for cesium ions. Remarkably, co‐incubation of guanosine and isoguanosine‐containing nucleodendrons results in the formation of decameric structures in absence of added salts. Further analysis of the mixture indicated that guanosine derivatives facilitate the formation, but are not involved in decameric structures; a process reminiscent of molecular crowding. This molecular system provides a powerful canvas for the rapid and modular assembly of polyfunctional dendritic macromolecules.     

Cyclic group and knapsack facets

 Any integer program may be relaxed to a group problem. We define the master cyclic group problem and several master knapsack problems, show the relationship between the problems, and give several classes of facet-defining inequalities for each problem, as well as a set of mappings that take facets from one type of master polyhedra to another. Received: May 24, 2001 / Accepted: August 2002 Published online: March 21, 2003 Mathematics Subject Classification (1991): 20E28, 20G40, 20C20     

Relative mobilities of ions in ion-selective electrodes with poly(vinyl chloride) membranes

A.c. impedance measurements are used to calculate relative mobilities for ionic species in PVC-matrix neutral-carrier ion-selective electrode membrane. It is deduced that the membrane must include anionic sites to achieve Nernstian response, and that the selectivity of the membrane occurs as a result of a high equilibrium concentration of the primary ion within the membrane, relative to the concentration of interfering ions.     

Effective mass of the 2-dimensional electron gas in an Al0.6Ga0.4Sb/InAs single quantum well

The 2-dimensional electron gas (2DEG) in an Al_0.6Ga_0.4Sb/InAs single quantum well is studied using cyclotron resonance and Shubnikov - de Haas (SdH) techniques. The effective mass (m^*) of the 2DEG was obtained from the peak positions of the cyclotron resonance transmission spectra. The results exhibit oscillatory behavior as a function of the magnetic field strength (B). The m^* value extracted from the temperature dependence of the SdH oscillations is in good agreement with the average value of m^* obtained from cyclotron resonance measurements. The effective mass is calculated as a function of B using an electron self-energy model based on the Hartree-Fock approximation. The calculated m^* values also show oscillatory behavior similar to that of the measured cyclotron resonance m^*. Both experiment and theory show that m^* maxima are shifted from the integral values (both odd and even) of the filling factors.     

Adverse Effects of Environmental Noise on Acoustic Voice Quality Measurements

An accurate analysis of voice quality is imperative when using acoustic measurements to diagnose vocal pathologies. It is known that noise has a significant effect on the reliability and validity of acoustic voice measurements, but the precise relationship has not been established. The purpose of this study was to investigate the influence of noise on the accuracy, reliability, and validity of acoustic voice quality measurements while balancing for gender, age, intersubject and intrasubject variability, microphones, computer hardware, analysis software, and type of noise. Level of noise was precisely controlled. The specific focus of interest was to determine the critical levels of noise that can invalidate voice quality measurements and to generate practical recommendations. Results suggest that the recommended, acceptable, and unacceptable levels of noise in the acoustic environment are above 42 dB, above 30 dB, and below 30 dB signal-to-noise ratio, respectively.     

Orbifold subfactors from Hecke algebras

We apply the notion of orbifold models ofSU(N) solvable lattice models to the Hecke algebra subfactors of Wenzl and get a new series of subfactors. In order to distinguish our subfactors from those of Wenzl, we compute the principal graphs for both series of subfactors. An obstruction for flatness of connections arises in this orbifold procedure in the caseN=2 and this eliminates the possibility of the Dynkin diagramsD _2n+1 , but we show that no such obstructions arise in the caseN=3. Our tools are the paragroups of Ocneanu and solutions of Jimbo-Miwa-Okado to the Yang-Baxter equation.