7-Deazaguanine modifications protect phage DNA from host restriction systems

Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.

Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery

The 7-deazapurine derivatives, 2'-deoxy-7-cyano-7-deazaguanosine (dPreQ₀ ) and 2'-deoxy-7-amido-7-deazaguanosine (dADG) are recently discovered DNA modifications encoded by the dpd cluster found in a diverse set of bacteria. Here we identify the genes required for the formation of dPreQ₀ and dADG in DNA and propose a biosynthetic pathway. The preQ₀ base is a precursor that in Salmonella Montevideo, is synthesized as an intermediate in the pathway of the tRNA modification queuosine. Of the 11 genes (dpdA - dpdK) found in the S. Montevideo dpd cluster, dpdA and dpdB are necessary and sufficient to synthesize dPreQ₀ , while dpdC is additionally required for dADG synthesis. Among the rest of the dpd genes, dpdE, dpdG, dpdI, dpdK, dpdD and possibly dpdJ appear to be involved in a restriction-like phenotype. Indirect competition for preQ₀ base led to a model for dADG synthesis in which DpdA inserts preQ₀ into DNA with the help of DpdB, and then DpdC hydrolyzes dPreQ₀ to dADG. The role of DpdB is not entirely clear as it is dispensable in other dpd clusters. Our discovery of a minimal gene set for introducing 7-deazapurine derivatives in DNA provides new tools for biotechnology applications and demonstrates the interplay between the DNA and RNA modification machineries.

Application of Suzuki-Miyaura and Buchwald-Hartwig Cross-coupling Reactions to the Preparation of Substituted 1,2,4-Benzotriazine 1-Oxides Related to the Antitumor Agent Tirapazamine

Many 1,2,4-benzotriazine 1,4-dioxides display the ability to selectively kill the oxygen-poor cells found in solid tumors. As a result, there is a desire for synthetic routes that afford access to substituted 1,2,4-benzotriazine 1-oxides that can be used as direct precursors in the synthesis of 1,2,4-benzotriazine 1,4-dioxides. Here we describe the use of Suzuki-Miyaura and Buchwald-Hartwig cross-coupling reactions for the construction of various 1,2,4-benzotriazine 1-oxide analogs bearing substituents at the 3-, 6-, and 7-positions.

Crystal structure of methyl (S)-2-{(R)-4-[(tert-but-oxy-carbon-yl)amino]-3-oxo-1,2-thia-zolidin-2-yl}-3-methyl-butano-ate: a chemical model for oxidized protein tyrosine phosphatase 1B (PTP1B)

The asymmetric unit of the title compound, C14H24N2O5S, contains two independent mol-ecules (A and B). In each mol-ecule, the iso-thia-zolidin-3-one ring adopts an envelope conformation with the methyl-ene C atom as the flap. In the crystal, the A mol-ecules are linked to one another by N-H⋯O hydrogen bonds, forming columns along [010]. The B mol-ecules are also linked to one another by N-H⋯O hydrogen bonds, forming columns along the same direction, i.e. [010]. Within the individual columns, there are also C-H⋯S and C-H⋯O hydrogen bonds present. The columns of A and B mol-ecules are linked by C-H⋯O hydrogen bonds, forming sheets parallel to (10-1). The absolute structure was determined by resonant scattering [Flack parameter = 0.00 (3)].

Crystal structure of 5-{4'-[(2-{2-[2-(2-ammonio-eth-oxy)eth-oxy]eth-oxy}eth-yl)carbamo-yl]-4-meth-oxy-[1,1'-biphen-yl]-3-yl}-3-oxo-1,2,5-thia-diazo-lidin-2-ide 1,1-dioxide: a potential inhibitor of the enzyme protein tyrosine phosphatase 1B (PTP1B)

The title compound, C24H32N4O8S, (I), crystallizes as a zwitterion. The terminal amine N atom of the [(2-{2-[2-(2-ammonio-eth-oxy)eth-oxy]eth-oxy}eth-yl)carbamo-yl] side chain is protonated, while the 1,2,5-thia-diazo-lidin-3-one 1,1-dioxide N atom is deprotonated. The side chain is turned over on itself with an intra-molecular N-H⋯O hydrogen bond. The 1,2,5-thia-diazo-lidin-3-one 1,1-dioxide ring has an envelope conformation with the aryl-substituted N atom as the flap. Its mean plane is inclined by 62.87 (8)° to the aryl ring to which it is attached, while the aryl rings of the biphenyl unit are inclined to one another by 20.81 (8)°. In the crystal, mol-ecules are linked by N-H⋯O and N-H⋯N hydrogen bonds, forming slabs lying parallel to (010). Within the slabs there are C-H⋯O and C-H⋯N hydrogen bonds and C-H⋯π inter-actions present.

Crystal structure of N-(quinolin-6-yl)hydroxyl-amine

The title compound, C9H8N2O, crystallized with four independent mol-ecules in the asymmetric unit. The four mol-ecules are linked via one O-H⋯N and two N-H⋯N hydrogen bonds, forming a tetra-mer-like unit. In the crystal, mol-ecules are further linked by O-H⋯N and N-H⋯O hydrogen bonds forming layers parallel to (001). These layers are linked via C-H⋯O hydrogen bonds and a number of weak C-H⋯π inter-actions, forming a three-dimensional structure. The crystal was refined as a non-merohedral twin with a minor twin component of 0.319.

Large-area porous alumina photonic crystals via imprint method

A perfect 2D porous alumina photonic crystal with 500 nm interpore distance was fabricated on an area of 4 cm2 via imprint methods and subsequent electrochemical anodization. A 4” imprint stamp consisting of a convex pyramid array was obtained by modern VLSI processing using DUV-lithography, anisotropic etching, LPCVD Si3N4 deposition and wafer bonding. The optical properties of the porous alumina photonic crystal were measured with an infrared microscope in Г-M direction. For both polarizations, a bandgap is observed at around 1 μm for r/a = 0.42. A reflectivity of almost unity for E-polarization in the region of the bandgap is a sign of the high quality of the structure, indicating almost no scattering losses. These experimental results could be correlated very well to the bandstructure as well as reflectivity calculations assuming a dielectric constant of å = 2.0 for the anodized alumina.

Central nervous system drug development: an integrative biomarker approach toward individualized medicine

Drug development for CNS disorders faces the same formidable hurdles as other therapeutic areas: escalating development costs; novel drug targets with unproven therapeutic potential; and health care systems and regulatory agencies demanding more compelling demonstrations of the value of new drug products. Extensive clinical testing remains the core of registration of new compounds; however, traditional clinical trial methods are falling short in overcoming these development hurdles. The most common CNS disorders targeted for drug treatment are chronic, slowly vitiating processes manifested by highly subjective and context dependent signs and symptoms. With the exception of a few rare familial degenerative disorders, they have ill-defined or undefined pathophysiology. Samples selected for treatment trials using clinical criteria are inevitably heterogeneous, and dependence on traditional endpoints results in early proof-of-concept trials being long and large, with very poor signal to noise. It is no wonder that pharmaceutical and biotechnology companies are looking to biomarkers as an integral part of decision-making process supported by new technologies such as genetics, genomics, proteomics, and imaging as a mean of rationalizing CNS drug development. The present review represent an effort to illustrate the integration of such technologies in drug development supporting the path of individualized medicine.