Nucleoside und Nucleotide. Teil 16. Verhalten von 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyrimidinon-5′-triphosphat, 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)pyridinon-5′-triphosphat und 4-Amino-1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyridinon-5′-triphosphat gegenüber DNA-Polymerase

Nucleosides and Nucleotides. Part 16. The Behaviour of 1-(2′-Deoxy-β-D -ribofuranosyl)-2(1H)-pyrimidinone-5′-triphosphate, 1-(2′-Deoxy-β-D -ribofuranosyl-2(1H))-pyridinone-5′-triphosphate and 4-Amino-1-(2′-desoxy-β-D -ribofuranosyl)-2(1H)-pyridinone-5′-triphosphate towards DNA Polymerase The behaviour of nucleotide base analogs in the DNA synthesis in vitro was studied. The investigated nucleoside-5′-triphosphates 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyrimidinone-5′-triphosphate (pppM_d), 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppII_d) and 4-amino-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppZ_d) can be considered to be analogs of 2′-deoxy-cytidine-5′-triphosphate. However, their ability to undergo base pairing to the complementary guanine is decreased. When pppM_d, pppII_d or pppZ_d are substituted for pppC_d in the enzymatic synthesis of DNA by DNA polymerase no incorporation of these analogs is observed. They exhibit only a weak inhibition of the DNA synthesis. The mode of the inhibition is uncompetitive which shows that these nucleotide analogs cannot serve as substrates for the DNA polymerase.     

Lower bounds on the cluster size distribution

We rigorously prove that the probabilityP _n that the origin of ad-dimensional lattice belongs to a cluster of exactlyn sites satisfiesP _n > exp(–n ^(d–1)/d ) whenever percolation occurs. This holds for the usual (noninteracting) percolation models for any concentrationp > p _c , as well as for the equilibrium states of lattice spin systems with quite general interactions. Such a lower bound applies also if no percolation occurs, but if it appears in some other phase of the system.     

Translation invariance and instability of phase coexistence in the two dimensional Ising system

It is shown that any Gibbs state of the two dimensional ferromagnetic Ising system is of the form ₊+(1–)_–, with some [0, 1]. This excludes the possibility of a locally stable phase coexistence and of translation symmetry breaking, which are known to occur in higher dimensions. Use is made in the proof of the stochastic aspects of the geometry of the interface lines.Supported in part by the U.S. National Science Foundation under the grant PHY — 7825390     

On bounded solutions of a classical yang-mills equation

We discuss bounded solutions of the equation $$r^2 \left( {\frac{{\partial ^2 u}}{{\partial r^2 }} + \frac{{\partial ^2 u}}{{\partial t^2 }}} \right) = u^3 - u$$ in the halfspacer>0. All solutions depending only ont/r are characterized topologically. Then we prove the existence of infinite dimensional manifolds oft-periodic as well as nonperiodic solutions which are small in a suitable norm.     

Identification of marker proteins for Bacillus anthracis using MALDI-TOF MS and ion trap MS/MS after direct extraction or electrophoretic separation

Direct extraction of bacterial vegetative cells or spores followed by matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI TOF MS) has become popular for bacterial identification, since it is simple to perform and mass spectra are readily interpreted. However, only high-abundance proteins that are of low mass and ionize readily are observed. In the case of B. anthracis spores, small acid-soluble spore proteins (SASPs) have been the most widely studied. Additional information can be obtained using tandem mass spectrometry (MS-MS) to confirm the identity of proteins by sequencing. This is most readily accomplished using ion trap (IT) MS-MS. However, enzymatic digestion of these proteins is needed to generate peptides that are within the mass range of the ion trap. The use of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), or other forms of electrophoresis, allows one to focus on specific proteins of interest (e.g. the high mass exosporium glycoproteins BcIA and BcIB) that provide additional species- and strain-specific discrimination.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Diphosphine-phosphenium coordination complexes representing monocations with pendant donors and ligand tethered dications

Homoatomic P-P coordinate bonding is exploited to prepare the first examples of triphosphorus monocations and tetraphosphorus dications using dimethylphosphenium or diphenylphosphenium Lewis acceptors with diphosphinomethane, diphosphinoethane, diphosphinohexane, or diphosphinobenzene ligands. Solid-state structures and spectroscopic characterization data for complexes involving bis(diphenylphosphino)methane ligands show coordination of only one donor site of the diphosphine ligand in the monocations, and chelate complexation is not observed. Tetraphosphorus dications are observed with longer diphosphines, in which the ligand tethers two phosphenium acceptors. The structural preferences between monocations with pendant phosphines and tethered dications are dependent on intramolecular steric interactions and the flexibility of the tether.     

Gas-Phase cationization and protonation of neutrals generated by matrix-assisted laser desorption

The ionization mechanisms involved in matrix-assisted ultraviolet laser desorption/ionization (MALDI) were studied with a time-of-flight mass spectrometer. When protonated or cationized quasimolecular ions generated by MALDI are not extracted promptly, their abundance is a function of the delay time between laser irradiation and ion extraction, maximizing at an optimum delay time (DTM) of a few hundred nanoseconds. The ion abundance at DTM exceeds that of prompt extraction by a factor of 2 or more. Increasing the cation density near the sample surface reduces the DTM, whereas increasing the desorption laser irradiance has the opposite effect. The enhancement suggests extensive gas-phase ion-molecule reactions after irradiation by the desorption laser has ceased.     

Rapid transacylations of activated ester substrates bound to the primary side β-cyclodextrin-cyclen conjugate and its M2+ complexes

The ability of cyclodextrins to effect rapid transacylations of bound substrates has been well studied. One important difference between cyclodextrin and enzyme-mediated transacylation is the pH required. Because the pK _a of a cyclodextrin secondary-side hydroxyl group is about 12, transacylations are accelerated in the presence of cyclodextrin under basic conditions (pH > 10.5). In 1988, our group reported the synthesis of cyclodextrin with attached cyclen-Co(III) complexes; significant acceleration in the reaction withp-nitrophenyl acetate was observed only with the primary side derivative. Of course, metalloenzymes utilize M²⁺ and not M³⁺ catalytic centers; in addition, large rate accelerations in the transacylations of both activated and unactivated substrates have been observed previously in systems utilizing M²⁺ ions (e.g., Zn, Cu, Ni) as well as M³⁺ ions (e.g. Co, Ir, Cr). In this paper, we describe the ability of CD-cyclen-M²⁺ conjugates to transacylate activated esters, amides, and phosphates. In addition, the ability of the apoenzyme mimic to effect transacylations was examined.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.