The charge state-dependent dissociation of various DNA duplexes and drug/duplex complexes has been investigated using collisionally activated dissociation (CAD) in a quadrupole ion trap mass spectrometer (QIT-MS). Several non-self-complementary 14-residue oligonucleotides were employed, in addition to an array of known DNA-interactive ligands, including the intercalators daunomycin and nogalamycin, as well as the minor groove binding agents distamycin, netropsin, 4',6-diamidino-2-phenylindole, and Hoechst 33342. In general, the dissociation pathways exhibited by both the duplexes and the drug/duplex complexes were found to be markedly sensitive to initial charge state. Time- and activation voltage-independent duplex strand separation predominated for higher charge states, which was interpreted to be a result of internal Coulombic repulsion or partial unzipping in the interface, while time- and activation voltage-dependent covalent cleavage predominated for lower charge states. The identity of the drug and the sequence of the duplex were both found to affect the competition between different dissociation processes. The dissociation pathways for the lower charge state complexes are probably more reflective of specific drug-DNA interactions because Coulombic and/or conformational effects are less marked for these precursors.

Algae are a promising source of biofuel but claims about their lipid content can be ambiguous because extraction methods vary and lipid quantitation often does not distinguish between particular lipid classes. Here we compared methods for the extraction of algal lipids and showed that 2-ethoxyethanol (2-EE) provides superior lipid recovery ([150-200 %) compared to other common extraction solvents such as chloroform:methanol or hexane. Extractions of wet and dry algal biomass showed that 2-EE was more effective at extracting lipids from wet rather than dried algal pellets. To analyze lipid content we used normal-phase HPLC with parallel quantitation by an evaporative light scattering detector and a mass spectrometer. Analysis of crude lipid extracts showed that all major lipid classes could be identified and quantified and revealed a surprisingly large amount of saturated hydrocarbons (HC). This HC fraction was isolated from extracts of bioreactorgrown algae and further analyzed by HPLC/MS, NMR, and GC/MS. The results showed that the sample consisted of a mixture of saturated, straight-and branched-chain HC of different chain lengths. These algal HC could represent an alternative biofuel to triacylglycerols (TAG) that could feed directly into the current petroleum infrastructure.

The tetracationic macrocycle cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene) hexafluorophosphate (1(4+)·4PF(6)(-)) acts as a large, flexible "molecular box" that supports the formation of environmentally responsive anion-induced pseudorotaxanes, as well as other extended structures, including metal-linked supramolecular polyrotaxanes. Specifically, the combination of the tetracation 1(4+) and bis-carboxylate guests derived from 4,4'-biphenyldicarboxylic acid and 2,6-naphthalenedicarboxylic acid results in the formation of pseudorotaxanes that respond to changes in environmental stimuli, including pH and temperature. The resulting structures can be "locked into place" via the addition of a metal-linker in the form of Ag(I); this gives rise to an ordered metal-linked polyrotaxane. The interpenetrated constructs described in this article were characterized in solution and in the solid state by one- and two-dimensional ((1)H and NOESY) NMR spectroscopy, as well as by mass spectrometry (ESI-MS) and single-crystal X-ray diffraction methods.

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Eukaryotic elongation factor 2 kinase (eEF-2K) is an atypical protein kinase regulated by Ca2+ and calmodulin (CaM). Its only known substrate is eukaryotic elongation factor 2 (eEF-2), whose phosphorylation by eEF-2K impedes global protein synthesis. To date, the mechanism of eEF-2K autophosphorylation has not been fully elucidated. To investigate the mechanism of autophosphorylation, human eEF-2K was co-expressed with λ-phosphatase, and purified from bacteria in a three-step protocol using a calmodulin-affinity column. Purified eEF-2K was induced to autophosphorylate by incubation with Ca2+/CaM in the presence of MgATP. Analyzing tryptic or chymotryptic peptides by mass spectrometry monitored the autophosphorylation over 0–180 minutes. The following five major autophosphorylation sites were identified, Thr-348, Thr-353, Ser-445, Ser-474 and Ser-500. In the presence of Ca2+/CaM, robust phosphorylation of Thr-348 occurs within seconds of adding MgATP. Mutagenesis studies suggest that phosphorylation of Thr-348 is required for substrate (eEF-2 or a peptide substrate) phosphorylation, but not self-phosphorylation. Phosphorylation of Ser-500 lags behind the phosphorylation of Thr-348, and is associated with calcium-independent activity of eEF-2K. Mutation of Ser-500 to Asp, but not Ala, renders eEF-2K calcium-independent. Surprisingly, this calcium-independent activity requires the presence of calmodulin.