Identification and validation of the mitochondrial F1F0-ATPase as the molecular target of the immunomodulatory benzodiazepine Bz-423

Bz-423 is a 1,4-benzodiazepine that suppresses disease in lupus-prone mice by selectively killing pathogenic lymphocytes, and it is less toxic compared to current lupus drugs. Cells exposed to Bz-423 rapidly generate O(2)(-) within mitochondria, and this reactive oxygen species is the signal initiating apoptosis. Phage display screening revealed that Bz-423 binds to the oligomycin sensitivity conferring protein (OSCP) component of the mitochondrial F(1)F(0)-ATPase. Bz-423 inhibited the F(1)F(0)-ATPase in vitro, and reconstitution experiments demonstrated that inhibition was mediated by the OSCP. This target was further validated by generating cells with reduced OSCP expression using RNA interference and studying the sensitivity of these cells to Bz-423. Our findings help explain the efficacy and selectivity of Bz-423 for autoimmune lymphocytes and highlight the OSCP as a target to guide the development of novel lupus therapeutics.     

GenoMass software: a tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts

The analysis of DNA adducts is of importance in understanding DNA damage, and in the last few years mass spectrometry (MS) has emerged as the most comprehensive and versatile tool for routine characterization of modified oligonucleotides. The structural analysis of modified oligonucleotides, although routinely analyzed using mass spectrometry, is followed by a large amount of data, and a significant challenge is to locate the exact position of the adduct by computational spectral interpretation, which still is a bottleneck. In this report, we present an additional feature of the in-house developed GenoMass software, which determines the exact location of an adduct in modified oligonucleotides by connecting tandem mass spectrometry (MS/MS) to a combinatorial isomer library generated in silico for nucleic acids. The performance of this MS/MS approach using GenoMass software was evaluated by MS/MS data interpretation for an unadducted and its corresponding N-acetylaminofluorene (AAF) adducted 17-mer (5'OH-CCT ACC CCT TCC TTG TA-3'OH) oligonucleotide. Further computational screening of this AAF adducted 17-mer oligonucleotide (5'OH-CCT ACC CCT TCC TTG TA-3'OH) from a complex oligonucleotide mixture was performed using GenoMass. Finally, GenoMass was also used to identify the positional isomers of the AAF adducted 15-mer oligonucleotide (5'OH-ATGAACCGGAGGCCC-3'OH). GenoMass is a simple, fast, data interpretation software that uses an in silico constructed library to relate the MS/MS sequencing approach to identify the exact location of adduct on oligonucleotides.     

Design and characterization of polymers and polymer blends for high temperature structural applications

Reviewing the development of new polymeric materials for high temperature structural applications (T > 200°C) over the past several decades, reveals a paradox which, to date, has not been completely resolved. Polymers which exhibit very high temperature stability tend to be either intractable or brittle, whereas, easily processible polymers tend to fall short of property targets. Approaches to resolving this paradox include modification of the chain backbone chemistry and polymer blending (especially to form miscible systems). Recent research has shown that, in contrast to low temperature flexible polymers, many high temperature aromatic heterocyclic polymers form miscible systems which permit the design of the desired processibility and performance into the blend. An example of such a system is the blend of Poly(2,2′-(meta-phenylene-5,5′-bibenzimidazole) (PBI) with a series of polyamides, including commercially available polyether imide (PEI) and imide copolymers containing sulfone and fluorinated isopropylidene (6F) units. Other examples include all polyimide blends and blends of polyimides with polyethersulfone.     

Metal-silicon bonded compounds : X. The molecular structures of 2,2,4,4,6,6,8,8-octamethyl-2,4,6,8-tetrasila-1,5-mercuracyclooctane and bis(triphenylsilyl) mercury

The crystal and molecular structure determinations of 2,2,4,4,6,6,8,8-octamethyl-2,4,6,8-tetrasila-1,5-mercuracyclooctane. Hg₂Si₄C₁₀H₂₈ (I) and of bis-(triphenylsilyl)mercury, (Ph₃Si)₂Hg (II), are reported. The structures have been determined from single-crystal X-ray data collected by counter methods. Both molecules crystalize in the space group P1 with one centrosymmetric molecule per unit cell. Each structure contains linear SiHgSi groups, with mercury-silicon distances of 2.490(4) Å in I and 2.503(4) Å II. In compound I the SiHgSi groups are linked by methylene bridges which form an eight member ring in the chair conformation. The cell dimensions for compound I are a 6.277(2), b 8.408(2), c 9.274(4) Å, α 92.75(3), β 94.79(3) and γ 100.14(2)° with R₁0.062 for 1809 observed reflections. The cell dimensions for compound II are a 9.999(4), b 11.727(8), c 7.654(5) Å, α 99.87(5), β 115.35(4) and γ 98.41(4)°, with R₁0.081 for 2394 observed reflections.     

GenoMass software: a tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts

The analysis of DNA adducts is of importance in understanding DNA damage, and in the last few years mass spectrometry (MS) has emerged as the most comprehensive and versatile tool for routine characterization of modified oligonucleotides. The structural analysis of modified oligonucleotides, although routinely analyzed using mass spectrometry, is followed by a large amount of data, and a significant challenge is to locate the exact position of the adduct by computational spectral interpretation, which still is a bottleneck. In this report, we present an additional feature of the in‐house developed GenoMass software, which determines the exact location of an adduct in modified oligonucleotides by connecting tandem mass spectrometry (MS/MS) to a combinatorial isomer library generated in silico for nucleic acids. The performance of this MS/MS approach using GenoMass software was evaluated by MS/MS data interpretation for an unadducted and its corresponding N‐acetylaminofluorene (AAF) adducted 17‐mer (5'OH‐CCT ACC CCT TCC TTG TA‐3′OH) oligonucleotide. Further computational screening of this AAF adducted 17‐mer oligonucleotide (5′OH‐CCT ACC CCT TCC TTG TA‐3′OH) from a complex oligonucleotide mixture was performed using GenoMass. Finally, GenoMass was also used to identify the positional isomers of the AAF adducted 15‐mer oligonucleotide (5′OH‐ATGAACCGGAGGCCC‐3′OH). GenoMass is a simple, fast, data interpretation software that uses an in silico constructed library to relate the MS/MS sequencing approach to identify the exact location of adduct on oligonucleotides. Copyright © 2012 John Wiley & Sons, Ltd.     

Extending the Dynamic Range of the Ion Trap by Differential Mobility Filtration

A miniature, planar, differential ion mobility spectrometer (DMS) was interfaced to an LCQ classic ion trap to conduct selective ion filtration prior to mass analysis in order to extend the dynamic range of the trap. Space charge effects are known to limit the functional ion storage capacity of ion trap mass analyzers and this, in turn, can affect the quality of the mass spectral data generated. This problem is further exacerbated in the analysis of mixtures where the indiscriminate introduction of matrix ions results in premature trap saturation with non-targeted species, thereby reducing the number of parent ions that may be used to conduct MS/MS experiments for quantitation or other diagnostic studies. We show that conducting differential mobility-based separations prior to mass analysis allows the isolation of targeted analytes from electrosprayed mixtures preventing the indiscriminate introduction of matrix ions and premature trap saturation with analytically unrelated species. Coupling these two analytical techniques is shown to enhance the detection of a targeted drug metabolite from a biological matrix. In its capacity as a selective ion filter, the DMS can improve the analytical performance of analyzers such as quadrupole (3D or linear) and ion cyclotron resonance (FT-ICR) ion traps that depend on ion accumulation.

On singularity confinement for the pentagram map

The pentagram map, introduced by R. Schwartz, is a birational map on the configuration space of polygons in the projective plane. We study the singularities of the iterates of the pentagram map. We show that a “typical” singularity disappears after a finite number of iterations, a confinement phenomenon first discovered by Schwartz. We provide a method to bypass such a singular patch by directly constructing the first subsequent iterate that is well-defined on the singular locus under consideration. The key ingredient of this construction is the notion of a decorated (twisted) polygon, and the extension of the pentagram map to the corresponding decorated configuration space.