Probing the Binding Region of the Single-Stranded DNA-Binding Domain of Rat DNA Polymerase β Using Nanosecond-Pulse Laser-Induced Cross-Linking and Mass Spectrometry

In recent years, there has been a significant number of studies in which UV light has been used as a reagent to induce cross-links in nucleic acid-protein complexes. An area of considerable interest among those interested in structural biology is the garnering of information about the sites of cross-linking within the protein and nucleic acid members of photolinked conjugates, under the assumption that such knowledge should lead to identification of contact regions or sites within the native complexes. In this paper, we present our results from a photocross-linking study of the complex of the single-stranded DNA-binding domain of rat DNA polymerase β (pol β-ss) with the oligonucleotide d(ATATATA). In this study, we have used single nanosecond laser pulses as the cross-linking reagent and matrix-assisted laser desorp-tion/ionization-time of flight mass spectrometry as an analytical tool to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Six cross-linked peptides have been identified in tryptic digests of the protein-oligonucleotide conjugates that result from irradiation of the pol β-ss-d(ATATATA) complex with a single laser pulse. Comparisons with NMR data in the literature for the same complex show that each of the cross-linked peptides contains amino acids that are in contact with the nucleic acid component of the complex.     

Nitrato- and fluoroboracites M3B7O13NO3 and M3B7O13F

New boracites containing nitrato- or fluoroanions that appear to be true low-pressure phases have been synthesized at superatmospheric pressures. The M₃B₇O₁₃NO₃ compounds (M = Co, Ni, Cu, Zn, Cd) transform rapidly and reversibly in the temperature region 300–500°C between probable orthorhombic and face centered cubic symmetry, while the M₃B₇O₁₃F compounds (M = Mg, Mn, Fe, Co, Zn) appear to maintain rhombohedral symmetry up to their decomposition temperatures of 800–900°C. True high-pressure boracite-like phases containing F and Cr, Mn, Fe, or Co that decompose upon heating to M₃B₇O₁₃F have also been isolated.     

Determination of surface charge properties of PC-12 cells by electrophoresis

The electrophoretic behavior of pheochromocytoma (PC-12) cells was investigated both experimentally and theoretically. Cell mobility in aqueous media at different pHs and ionic concentrations was measured, and a model, which assumed that the cell surface contains both acidic and basic functional groups, was proposed. As a result, it was revealed that the experimental data gathered can be described satisfactorily by assuming that the cell surface contains two types of monovalent acidic functional groups and one basic functional group. The values of the dissociation constants of the acidic and basic groups are found to be close to those of acidic amino acids, which indicates that the acidic amino acids may play an important role in the surface electrical properties of PC-12 cells.     

Simultaneous multichannel mass-specific detection for high-performance liquid chromatography using an array detector sector-field mass spectrometer

The use of a separation step, such as liquid chromatography, prior to inductively coupled plasma mass spectrometry (ICP–MS) has become a common tool for highly selective and sensitive analyses. This type of coupling has several benefits including the ability to perform speciation analysis or to remove isobaric interferences. Several limitations of conventional instruments result from the necessity to scan or pulse the mass spectrometer to obtain a complete mass spectrum. When the instrument is operated in such a non-continuous manner, duty cycle is reduced, resulting in poorer absolute limits of detection. Additionally, with scanning instruments, spectral skew can be introduced into the measurement, limiting quantitation accuracy. To address these shortcomings, a high-performance liquid chromatograph has been coupled to an ICP–MS capable of continuous sample introduction and simultaneous multimass detection. These features have been realized with a novel detector array, the focal plane camera. Instrument performance has been tested for both speciation analysis and for the elimination of isobaric interferences. Absolute limits of detection in the sub picogram to tens of picograms regime are obtainable, while the added mass dimension introduced by simultaneous detection dramatically increases chromatographic peak capacity.     

Assembly of the inorganic double helix Mg6(Et2NCO2)12 by fixation of carbon dioxide: crystal and solution structure

The homoleptic magnesium carbamato complex Mg6(Et2NCO2)12, 1 (Et2NCO2- = diethylcarbamato anion), was prepared by the reaction of dibutylmagnesium with diethylamine, followed by carboxylation using gaseous carbon dioxide. Crystallographic characterization demonstrated that 1 has the standard M6(R2NCO2)12 structure and is a double helix of MgO(x)(x = 5, 6) coordination polyhedra with Delta or Lambda stereochemistry arising from the configuration around the six-coordinate Mg2+ cations. It crystallized in the orthorhombic space group Ccca with two molecules of Delta1 and two of Lambda1 per unit cell (a = 21.548 A, b = 25.094 A, c = 15.4485(11) A, alpha = beta = gamma = 90 degrees ). Extensive solution characterization of 1 by 1-dimensional proton and 13C NMR spectroscopy and by two-dimensional 1H-[13C] NMR correlation techniques verified that the helical structure is maintained in solution. Moreover, these measurements indicated that the intramolecular dynamics of 1 relating to motions of the ethyl groups was substantially hindered in solution. Correlation of the crystallographic and NMR structural studies indicated that this arises from a combination of hindered rotation about the carbamato C-N bond and efficient packing of the ethyl groups around the Mg6O24 core. The result is an inverted-micelle-like structure for 1 in which the hydrophobic ethyl groups form a sheath largely restricting access to the hydrophilic Mg6O24 core.     

Differential effects of Fas cross-linking on phospholipase D activation and related lipid metabolism in Fas-resistant A20 cells

A20 murine lymphoma cells undergoing Fas-mediated apoptosis showed increase in the activity of phospholipase D (PLD), which is involved in proliferative or mitogenic cellular responses. Using A20 cell lines that were resistant to Fas-induced apoptosis, we investigated the differential effects of Fas cross-linking on PLD activity and sphingolipid metabolism. The basal PLD activities in all of the selected three Fas-resistant clones (#5, #8, and #11) were about 2~4 folds higher than that of wild type A20 cells. Among the PLD isoforms, PLD2 expression was increased in all of the selected Fas-resistant clones. The Fas downstream signaling events triggered by Fas cross-linking, including the activations of PLD, phosphatidylcholine-specific phospholipase C (PC-PLC), sphingomyelinase (SMase), the increase in diacylglycerol (DAG) and protein phosphorylation levels, and the translocation of protein kinase C to membrane were not changed in both of Fas-resistant clone #5 and #8. In contrast, Fas cross-linking stimulated the activity of PLD, PC-PLC, and SMase, translocation of PKC, and protein phosphorylation in Fas-resistant clone #11, similar to that of wild type cells. We also found that clone #11 had a different Fas sequence encoding Fas B which has been known to inhibit Fas-induced apoptosis. These findings suggest that increased PLD2 expression resulting in increased basal PLD activity and the blockade of Fas downstream signaling cascades may be involved to limit apoptosis induced by Fas cross-linking.     

Stereoselective synthesis of (+)-SCH 351448: a unique ligand system for sodium, calcium, and other cations

(+)-SCH 351448 (Na+ salt A) was synthesized employing ring-closing olefin metathesis reaction of an open diene diester intermediate for construction of the 28-membered macrodiolide structure. The open diene diester was prepared from the monomeric hydroxy carboxylic acid and two different olefin fragments. The monomeric hydroxy acid was synthesized via Julia-Julia coupling reaction of intermediates derived from the same olefinic fragments. Oxane units in these fragments were prepared by radical cyclization reactions of beta-alkoxyacrylates. Analogous SCH 351448 salts incorporating other mono- and divalent cations may be prepared. Under acidic conditions, SCH 351448 (Na+ salt A) was the most stable complex, but SCH 351448 (Ca2+ salt) and (Na+ salt B) appear to be physiologically important species.