Elucidation of Nucleic Acid–Drug Interactions by Tandem Mass Spectrometry

In continuation of the long tradition of mass spectrometric research at the University of Bern, our group focuses on the characterization of nucleic acids as therapeutic agents and as drug targets. This article provides a short overview of our recent work on platinated single-stranded and higher-order nucleic acids. Nearly three decades ago the development of soft ionization techniques opened a whole new chapter in the mass spectrometric analysis of not only nucleic acids themselves, but also their interactions with potential drug candidates. In contrast to modern next generation sequencing approaches, though, the goal of the tandem mass spectrometric investigation of nucleic acids is by no means the complete sequencing of genetic DNA, but rather the characterization of short therapeutic and regulatory oligonucleotides and the elucidation of nucleic acid–drug interactions. The influence of cisplatin binding on the gas-phase dissociation of nucleic acids was studied by the means of electrospray ionization tandem mass spectrometry. Experiments on native and modified DNA and RNA oligomers confirmed guanine base pairs as the preferred platination site and laid the basis for the formulation of a gas-phase fragmentation mechanism of platinated oligonucleotides. The study was extended to double stranded DNA and DNA quadruplexes. While duplexes are believed to be the main target of cisplatin in vivo, the recently discovered DNA quadruplexes constitute another promising target for anti-tumor drugs owing to their regulatory functions in the cell cycle.

Identification of animal Pasteurellaceae by MALDI-TOF mass spectrometry

Species of the family Pasteurellaceae play an important role as primary or opportunistic, predominantly respiratory, pathogens in domestic and wild animals. Some of them cause severe disease with high economic losses in commercial animal husbandry. Hence, rapid and accurate differentiation of Pasteurellaceae is important and signifies a particular challenge to diagnostic laboratories. Identification and differentiation of Pasteurellaceae is mostly done using phenotypic tests or genetic identification based on sequence similarity of housekeeping genes, such as the rrs gene encoding the 16S ribosomal RNA (16S rRNA). Both approaches are time consuming, laborious, and costly, therefore often delaying the final diagnosis of disease or epidemics. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry represents an alternative rapid and reliable method for the differentiation of most members of the family Pasteurellaceae. It is able to differentiate within a few minutes the currently known 18 genera and most of the over 60 species and subspecies of Pasteurellaceae including many members encountered in veterinary diagnostic laboratories. A few closely related species and subspecies that cannot be discriminated by MALDI-TOF are easily identified further by complementary simple tests, such as hemolysis done simultaneously or routinely during pathogen isolation.

Combined Secondary Ion Mass Spectrometry Depth Profiling and Focused Ion Beam Analysis of Cu Films Electrodeposited under Oscillatory Conditions

The recrystallization behavior of Cu films electrodeposited under oscillatory conditions in the presence of plating additives was studied by means of secondary ion mass spectrometry (SIMS) and focused ion beam analysis. When combined with bis-(sodium-sulfopropyl)-disulfide (SPS), Imep levelers (polymerizates of imidazole and epichlorohydrin) show characteristic oscillations in the galvanostatic potential/time transient measurements. These are related to the periodic degradation and restoration of the active leveler ensemble at the interface. The leveler action relies on adduct formation between the Imep and MPS (mercaptopropane sulfonic acid)-stabilized CuI complexes that appear as intermediates of the copper deposition when SPS is present in the electrolyte. SIMS depth profiling proves that additives are incorporated into the growing film preferentially under transient conditions during the structural breakdown of the leveler ensemble and its subsequent restoration. In contrast, Cu films electrodeposited in the presence of a structurally intact Imep–CuI–MPS ensemble remain largely contamination free.

Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides

The fragmentation of electrospray-generated multiply deprotonated RNA and mixed-sequence RNA/DNA pentanucleotides upon low-energy collision-induced dissociation (CID) in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The goal of unambiguous sequence identification of mixed-sequence RNA/DNA oligonucleotides requires detailed understanding of the gas-phase dissociation of this class of compounds. The two major dissociation events, base loss and backbone fragmentation, are discussed and the unique fragmentation behavior of oligoribonucleotides is demonstrated. Backbone fragmentation of the all-RNA pentanucleotides is characterized by abundant c-ions and their complementary y-ions as the major sequence-defining fragment ion series. In contrast to the dissociation of oligodeoxyribonucleotides, where backbone fragmentation is initiated by the loss of a nucleobase which subsequently leads to the formation of the w- and [a-base]-ions, backbone dissociation of oligoribonucleotides is essentially decoupled from base loss. The different behavior of RNA and DNA oligonucleotides is related to the presence of the 2'-hydroxyl substituent, which is the only structural alteration between the DNA and RNA pentanucleotides studied. CID of mixed-sequence RNA/DNA pentanucleotides results in a combination of the nucleotide-typical backbone fragmentation products, with abundant w-fragment ions generated by cleavage of the phosphodiester backbone adjacent to the deoxy building blocks, whereas backbone cleavage adjacent to ribonucleotides induces the formation of c- and y-ions. (C) 2002 American Society for Mass Spectrometry.

Characterization and source apportionment of organic aerosol using offline aerosol mass spectrometry

Field deployments of the Aerodyne Aerosol Mass Spectrometer (AMS) have significantly advanced real-time measurements and source apportionment of non-refractory particulate matter. However, the cost and complex maintenance requirements of the AMS make its deployment at sufficient sites to determine regional characteristics impractical. Furthermore, the negligible transmission efficiency of the AMS inlet for supermicron particles significantly limits the characterization of their chemical nature and contributing sources. In this study, we utilize the AMS to characterize the water-soluble organic fingerprint of ambient particles collected onto conventional quartz filters, which are routinely sampled at many air quality sites. The method was applied to 256 particulate matter (PM) filter samples (PM1, PM2:5, and PM10, i.e., PM with aerodynamic diameters smaller than 1, 2.5, and 10 μm, respectively), collected at 16 urban and rural sites during summer and winter. We show that the results obtained by the present technique compare well with those from co-located online measurements, e.g., AMS or Aerosol Chemical Speciation Monitor (ACSM). The bulk recoveries of organic aerosol (60–91 %) achieved using this technique, together with low detection limits (0.8 μg of organic aerosol on the analyzed filter fraction) allow its application to environmental samples. We will discuss the recovery variability of individual hydrocarbon ions, ions containing oxygen, and other ions. The performance of such data in source apportionment is assessed in comparison to ACSM data. Recoveries of organic components related to different sources as traffic, wood burning, and secondary organic aerosol are presented. This technique, while subjected to the limitations inherent to filter-based measurements (e.g., filter artifacts and limited time resolution) may be used to enhance the AMS capabilities in measuring size-fractionated, spatially resolved longterm data sets.

MONITORING ENZYME REACTIONS BY FAST ATOM BOMBARDMENT MASS SPECTROMETRY

The potential for the direct analysis of enzyme reactions by fast atom bombardment (FAB) mass spectrometry has been investigated. Conditions are presented for the maintenance of enzymatic activity under FAB conditions along with FAB mass spectrometric data showing that these conditions can be applied to solutions of enzyme and substrate to follow enzymatic reactions inside the mass spectrometer in real-time. In addition, enzyme kinetic behavior under FAB mass spectrometric conditions is characterized using trypsin and its assay substrate, TAME, as an enzyme-substrate reaction model. These results show that two monitoring methods can be utilized to follow reactions by FAB mass spectrometry. The advantages of each method are discussed and illustrated by obtaining kinetic parameters from the direct analysis of enzyme reactions with assay or peptide substrates. ^

U and Th concentrations and isotope ratios of samples from ODP Leg 166

Constraining the history of seawater (234U/238U) is important because this ratio is used to assess the validity of U/Th ages, and because it provides information about the past rate of physical weathering on the continents. This study makes use of U-rich slope sediments from the Bahamas in an attempt to reconstruct seawater (234U/238U) for the last 800 kyr. For the last 360 kyr, U/Th dating of these sediments provides ages and initial (234U/238U) values. Sixty-seven samples, largely from marine highstands, have initial (234U/238U) which scatter somewhat about the modern seawater value (~1.145) but neither this scatter nor the average value increases with age of sample. These data contrast with published coral data and suggest that seawater (234U/238U) has remained within 15? of the modern value for the last 360 kyr. This confirms the rejection of coral U/Th ages where the initial (234U/238U) is significantly different from modern seawater. Data from older highstands, dated with delta18O stratigraphy or by the presence of the Brunhes/Matuyama (B/M) reversal at 780 kyr, allow seawater (234U/238U) to be assessed prior to the range of the 230Th chronometer. Unfortunately, diagenetic scatter in the data between the B/M reversal and 360 kyr is rather large, probably relating to low U concentrations for these samples. But there is no indication of a trend in seawater (234U/238U) with age. High U samples from close to the B/M reversal show less diagenetic scatter and an initial (234U/238U) that averages 1.102. This lower value can be explained by lower seawater (234U/238U) at the time of the B/M reversal, or by progressive loss of 234U from the sediment by alpha-recoil. A simple box model is presented to illustrate the response of seawater (234U/238U) to variations in riverine input, such as might be caused by changes in continental weathering. Comparison of the Bahamas (234U/238U) data with model results indicates that riverine (234U/238U) has not varied by more than 65? for any 100 kyr period during the last 360 kyr. It also indicates that the ratio of physical to chemical weathering on the continents has not been higher than at present for any extended period during the last 800 kyr.

Measurements of trace metal abundances and isotopes in carbonate sediments, Exuma, Bahamas

In order to validate the use of 238U/235U as a paleoredox proxy in carbonates, we examined the incorporation and early diagenetic evolution of U isotopes in shallow Bahamian carbonate sediments. Our sample set consists of a variety of primary precipitates that represent a range of carbonate producing organisms and components that were important in the past (scleractinian corals, calcareous green and red algae, ooids, and mollusks). In addition, four short push cores were taken in different depositional environments to assess the impact of early diagenesis and pore water chemistry on the U isotopic composition of bulk carbonates. We find that U concentrations are much higher in bulk carbonate sediments (avg. 4.1 ppm) than in primary precipitates (avg. 1.5 ppm). In almost all cases, the lowest bulk sediment U concentrations were as high as or higher than the highest concentrations found in primary precipitates. This is consistent with authigenic accumulation of reduced U(IV) during early diagenesis. The extent of this process appears sensitive to pore water H2S, and thus indirectly to organic matter content. d238/235U values were very close to seawater values in all of the primary precipitates, suggesting that these carbonate components could be used to reconstruct changes in seawater U geochemistry. However, d238/235U of bulk sediments from the push cores was 0.2-0.4 per mil heavier than seawater (and primary precipitates). These results indicate that authigenic accumulation of U under open-system sulfidic pore water conditions commonly found in carbonate sediments strongly affects the bulk U concentrations and 238U/235U ratios. We also report the occurrence of dolomite in a tidal pond core which contains low 234U/238U and 238U/235U ratios and discuss the possibility that the dolomitization process may result in sediments depleted in 238U. From this initial exploration, it is clear that 238U/235U variations in ancient carbonate sediments could be driven by changes in global average seawater, by spatial and temporal variations in the local deposition environment, or subsequent diagenesis. To cope with such effects, proxies for syndepositional pore water redox conditions (e.g., organic matter content, iron speciation, and trace metal distributions) and careful consideration of possible post-deposition alteration will be required to avoid spurious interpretation of 238U/235U data from ancient carbonate sediments.

Element concentrations and Osmium, Platinum and Rhenium isotope ratios of ODP Site 153-920 abyssal peridotites

Abyssal peridotites are normally thought to be residues of melting of the mid-ocean ridge basalt (MORB) source and are presumably a record of processes affecting the upper mantle. Samples from a single section of abyssal peridotite from the Kane Transform area in the Atlantic Ocean were examined for 190Pt-186Os and 187Re-187Os systematics. They have uniform 186Os/188Os ratios with a mean of 0.1198353 +/- 7, identical to the mean of 0.1198340 +/-12 for Os-Ir alloys and chromitites believed to be representative of the upper mantle. While the Pt/Os ratios of the upper mantle may be affected locally by magmatic processes, these data show that the Pt/Os ratio for the bulk upper mantle has not deviated by more than about +/- 30% from a chondritic Pt/Os ratio over 4.5 billion years. These observations are consistent with the addition of a chondritic late veneer after core separation as the primary control on the highly siderophile element budget of the terrestrial upper mantle. The 187Os/188Os of the samples range from 0.12267 to 0.12760 and correlate well with Pt and Pt/Os, but not Re/Os. These relationships may be explained by variable amounts of partial melting with changing D(Re), reflecting in part garnet in the residue, with a model-dependent melting age between about 600 and 1700 Ma. A model where the correlation between Pt/Os and 187Os/188Os results from multiple ancient melting events, in mantle peridotites that were later juxtaposed by convection, is also consistent with these data. This melting event or events are evidently unrelated to recent melting under mid-ocean ridges, because recent melting would have disturbed the relationship between Pt/Os and 187Os/188Os. Instead, this section of abyssal peridotite may be a block of refractory mantle that remained isolated from the convecting portions of the upper mantle for 600 Ma to >1 Ga. Alternatively, Pt and Os may have been sequestered during more recent melting and possibly melt/rock reaction processes, thereby preserving an ancient melting history. If representative of other abyssal peridotites, then the rocks from this suite with subchondritic 187Os/188Os are not simple residues of recent MORB source melting at ridges, but instead have a more complex history. This suite of variably depleted samples projects to an undepleted present-day Pt/Os of about 2.2 and 187Os/188Os of about 0.128-0.129, consistent with estimates for the primitive upper mantle.