Multiplexed screening of neutral mass-tagged RNA targets against ligand libraries with electrospray ionization FTICR MS: a paradigm for high-throughput affinity screening

We demonstrate that binding of mixtures of aminoglycosides can be measured simultaneously against multiple RNA targets of identical length and similar (or identical) molecular weight. Addition of a neutral mass tag to one of the RNA targets shifts the detected peaks to a higher mass/charge ratio, where complexes with small molecules can be identified unambiguously. An appropriately placed neutral mass tag does not alter RNA--ligand binding. The utility of this strategy is demonstrated with model RNAs corresponding to the decoding region of the prokaryotic and eukaryotic rRNAs and a mixture of five aminoglycosides. Complexes are observed between the aminoglycoside library and the prokaryotic rRNA model, while no aminoglycoside was observed to bind to the mass-tagged eukaryotic rRNA model. The differential binding data is consistent with the eukaryotic A-site rRNA having a different conformation compared with the prokaryotic A-site that prevents entry and binding of neomycin-class aminoglycosides. Mass spectrometric analysis of neutral mass-tagged macromolecular targets represents a new high-throughput screening paradigm in which the interaction of multiple targets against a collection of small molecules can be evaluated in parallel.

Mechanism of alternative complement pathway dysregulation by a phosphorothioate oligonucleotide in monkey and human serum

The species sensitivity and mechanism of complement pathway activation by a phosphorothioate oligonucleotide were investigated in monkey and human serum. Increasing concentrations of a phosphorothioate oligonucleotide, ISIS 2302, were incubated in either monkey or human serum. Complement activation in monkey serum was selective for the alternative pathway and occurred at concentrations ≥ 50 μg/mL ISIS 2302. By comparison, complement activation in human serum was absent. A similar difference in sensitivity for activation was also observed for a representative 2'-methoxyethyl (MOE)-modified oligonucleotide. The absence of oligonucleotide-induced complement activation was also observed in dogs. Protein binding with ISIS 2302 and enzyme competition studies suggested that factor H was important in oligonucleotide-mediated complement activation process, and addition of factor H to serum effectively prevented the activation in monkey serum. Furthermore, based on the immunoassay for factor H, there was an apparent decrease in factor H concentration as the ISIS 2302 concentration increased. This result suggests that ISIS 2302 binds to factor H and interferes with the factor H antibody from the immunoassay. Factor H is a regulatory protein that limits alternative pathway activation. Disruption of factor H interaction with C3 convertase by oligonucleotide could promote activation in this pathway.

Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry

Short tandem repeats (STRs) are the primary genetic markers used for the analysis of biological samples in forensic and human identity testing. The discrimination power of a combination of STRs is sufficient in many human identity testing comparisons unless the evidence is substantially compromised and/or there are insufficient relatives or a potential mutation may have arisen in kinship analyses. An automated STR assay system that is based on electrospray ionization mass spectrometry (ESI-MS) has been developed that can increase the discrimination power of some of the CODIS core STR loci and thus provide more information in typical and challenged samples and cases. Data from the ESI-MS STR system is fully backwards compatible with existing STR typing results generated by capillary electrophoresis. In contrast, however, the ESI-MS analytical system also reveals nucleotide polymorphisms residing within the STR alleles. The presence of these polymorphisms expands the number of alleles at a locus. Population studies were performed on the 13 core CODIS STR loci from African Americans, Caucasians and Hispanics capturing both the length of the allele, as well as nucleotide variations contained within repeat motifs or flanking regions. Such additional polymorphisms were identified in 11 of the 13 loci examined whereby several nominal length alleles were subdivided. A substantial increase in heterozygosity was observed, with close to or greater than 5% of samples analyzed being heterozygous with equal-length alleles in at least one of five of the core CODIS loci. This additional polymorphism increases discrimination power significantly, whereby the seven most polymorphic STR loci have a discrimination power equivalent to the 10 most discriminating of the CODIS core loci. An analysis of substructure among the three population groups revealed a higher θ than would be observed compared with using alleles designated by nominal length, i.e., repeats solely. Two loci, D3S1358 and vWA produced θ estimates of 0.0477 and 0.0234, respectively, when the expanded allele complement (i.e., nominal allele and SNPs) was considered compared to 0.0145 and 0.01266, respectively when only nominal repeat number was considered. These differences may indicate underlying population specific allele distributions exist within these populations. A system of nomenclature has been developed that facilitates the databasing, searching and analyses of these combined data forms.

The effect of backbone charge on the collision-induced dissociation of oligonucleotides

Knowledge of the effects of structural changes in oligonucleotides on their dissociation reaction is important in the application of mass spectrometry to sequence determination. The effect of backbone charge on the collision-induced dissociation of multiply-charged oligonucleotides produced by electrospray was explored by examination of models in which the normal phosphodiester linkage was partially replaced with an uncharged methylphosphonate (MP) linkage. Three different MP-containing oligonucleotides were studied, designed to represent a concentration of charge on the 5'- and 3'-ends of the molecule and with an even distribution of charge along the backbone, compared with a control molecule containing only phosphodiester linkages. In all MP-containing oligonucleotides charging of over 90% of phosphate groups were observed, compared with typical charging patterns of about 60% in normal all-phosphodiester oligonucleotides. This unexpected effect is attributed to charge stabilization by interactions of charged sites with uncharged residues. Analysis of the collision-induced dissociation mass spectra showed that backbone cleavage occurred at every residue (w and a-base ion series), producing a full set of sequencing ions whether or not the linkage at that site was formally charged. It is concluded that under the multiple collision conditions of the quadrupole collision cell that backbone cleavage proceeds through two generic pathways, one involving base loss followed by cleavage of the adjacent C3'-CO bond and the other requiring neither base loss nor charged phosphate at the cleavage site. These results suggest that backbone cleavage reactions in conventional phosphodiester oligonucleotides can occur at non-ionized linkage sites, of which there are a high proportion in both electrospray- and MALDI-produced molecular ions.

The Ibis T5000 Universal Biosensor: An Automated Platform for Pathogen Identification and Strain Typing

We describe a new approach to the sensitive and specific identification of bacteria, viruses, fungi, and protozoa based on broad-range PCR and high-performance mass spectrometry. The Ibis T5000 is based on technology developed for the Department of Defense known as T.I.G.E.R. (Triangulation Identification for the Genetic Evaluation of Risks) for pathogen surveillance. The technology uses mass spectrometry—derived base composition signatures obtained from PCR amplification of broadly conserved regions of the pathogen genomes to identify most organisms present in a sample. The process of sample analysis has been automated using a combination of commercially available and custom instrumentation. A software system known as T-Track manages the sample flow, signal analysis, and data interpretation and provides simplified result reports to the user. No specialized expertise is required to use the instrumentation. In addition to pathogen surveillance, the Ibis T5000 is being applied to reducing health care—associated infections (HAIs), emerging and pandemic disease surveillance, human forensics analysis, and pharmaceutical product and food safety, and will be used eventually in human infectious disease diagnosis. In this review, we describe the automated Ibis T5000 instrument and provide examples of how it is used in HAI control.

A "silent culture-negative" abdominal aortic mycotic aneurysm: Rapid detection of Bartonella species using PCR and high-throughput mass spectrometry

A gram-negative, rod-shaped microorganism was detected in a 69-year-old man suffering from chronic back pain but otherwise exhibiting no signs of infection. The bacterium could not be identified using any routine diagnostic modality. A research use only application utilizing PCR and Mass Spectrometry was performed on nucleic acid extracted from the tissue sample. These studies resulted in the implication of Bartonella quintana as the underlying cause of the infection. B. quintana is not a well-known cause of an abdominal aortic mycotic aneurysm. This article will discuss the B. quintana infection, its diagnosis and treatment, and reinforce the potential of B. quintana as a possible etiology in mycotic aneurysms that show no apparent indications of infection. It will also explore the potential use of polymerase chain reaction detected by electrospray ionization mass spectrometry (PCR/ESI-MS) to help identify B. quintana in a situation where other conventional methods prove non-informative.