Using pure shift HSQC to characterize microgram samples of drug metabolites

Difficulties in isolating samples from complex biological matrices and sensitivity limitations have long stymied the utilization of heteronuclear 2D NMR for the characterization of drug metabolites. Small diameter cryogenic NMR probes have largely ameliorated sensitivity limitations and the recently reported pure shift HSQC 2D NMR pulse sequence offers a further and marked improvement in both resolution and sensitivity. Using a 7.4 μg sample of the commercially available metabolite 3-hydroxy carbamazepine dissolved in 30 μL of deuterated solvent and a 600 MHz NMR equipped with a 1.7 mm cryogenic NMR probe, it was possible to acquire high signal-to-noise pure shift HSQC data in just over 30 min. A conventional HSQC spectrum acquired with identical parameters had approximately half the signal-to-noise of the pure shift HSQC spectrum. Collapsing the vicinal homonuclear couplings in the pure shift HSQC spectrum also significantly improves resolution. A practical, real world application of the technique is illustrated with the chromatographically isolated metabolite 3-hydroxy amiodarone from incubation with CYP2J2 recombinant enzyme. High quality pure shift HSQC data were recorded in slightly over 14 h for a 3 μg sample of the metabolite.     

Deconstructing Classical Water Models at Interfaces and in Bulk

Using concepts from perturbation and local molecular field theories of liquids we divide the potential of the SPC/E water model into short and long ranged parts. The short ranged parts define a minimal reference network model that captures very well the structure of the local hydrogen bond network in bulk water while ignoring effects of the remaining long ranged interactions. This deconstruction can provide insight into the different roles that the local hydrogen bond network, dispersion forces, and long ranged dipolar interactions play in determining a variety of properties of SPC/E and related classical models of water. Here we focus on the anomalous behavior of the internal pressure and the temperature dependence of the density of bulk water. We further utilize these short ranged models along with local molecular field theory to quantify the influence of these interactions on the structure of hydrophobic interfaces and the crossover from small to large scale hydration behavior. The implications of our findings for theories of hydrophobicity and possible refinements of classical water models are also discussed.     

Simultaneous quantification of multiple nucleic acid targets using chemiluminescent probes

A novel method is described for simultaneous detection and quantification of attomoles or a few femtomoles of two (or potentially more) nucleic acid targets, without need for amplification. The technique depends on spectral-temporal resolution of chemiluminescence emitted from independent hybridization-induced chemiluminescent signal probes. The probes are internally quenched except in the presence of their specific targets, thereby allowing detection limits up to 10,000 times lower than with fluorescent probes. This is sufficient to obviate the need for amplification in many cases. The utility of the technique has been demonstrated by use of resolvable N-linked acridinium and 2,7-dimethoxyacridinium ester labeled probes in a homogeneous assay for sensitive and simultaneous independent quantification of pan-bacterial and pan-fungal target sequences in seawater.     

Femtomole SHAPE reveals regulatory structures in the authentic XMRV RNA genome

Higher-order structure influences critical functions in nearly all noncoding and coding RNAs. Most single-nucleotide resolution RNA structure determination technologies cannot be used to analyze RNA from scarce biological samples, like viral genomes. To make quantitative RNA structure analysis applicable to a much wider array of RNA structure-function problems, we developed and applied high-sensitivity selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to structural analysis of authentic genomic RNA of the xenotropic murine leukemia virus-related virus (XMRV). For analysis of fluorescently labeled cDNAs generated in high-sensitivity SHAPE experiments, we developed a two-color capillary electrophoresis approach with zeptomole molecular detection limits and subfemtomole sensitivity for complete SHAPE experiments involving hundreds of individual RNA structure measurements. High-sensitivity SHAPE data correlated closely (R = 0.89) with data obtained by conventional capillary electrophoresis. Using high-sensitivity SHAPE, we determined the dimeric structure of the XMRV packaging domain, examined dynamic interactions between the packaging domain RNA and viral nucleocapsid protein inside virion particles, and identified the packaging signal for this virus. Despite extensive sequence differences between XMRV and the intensively studied Moloney murine leukemia virus, architectures of the regulatory domains are similar and reveal common principles of gammaretrovirus RNA genome packaging.     

An Efficient Method for the In Vitro Production of Azol(in)e‐Based Cyclic Peptides

Heterocycle‐containing cyclic peptides are promising scaffolds for the pharmaceutical industry but their chemical synthesis is very challenging. A new universal method has been devised to prepare these compounds by using a set of engineered marine‐derived enzymes and substrates obtained from a family of ribosomally produced and post‐translationally modified peptides called the cyanobactins. The substrate precursor peptide is engineered to have a non‐native protease cleavage site that can be rapidly cleaved. The other enzymes used are heterocyclases that convert Cys or Cys/Ser/Thr into their corresponding azolines. A macrocycle is formed using a macrocyclase enzyme, followed by oxidation of the azolines to azoles with a specific oxidase. The work is exemplified by the production of 17 macrocycles containing 6–9 residues representing 11 out of the 20 canonical amino acids.     

A Counterion‐Directed Approach to the Diels–Alder Paradigm: Cascade Synthesis of Tricyclic Fused Cyclopropanes

An approach to the intramolecular Diels–Alder reaction has led to a cascade synthesis of complex carbocycles composed of three fused rings and up to five stereocenters with complete stereocontrol. Computational analysis reveals that the reaction proceeds by a Michael/Michael/cyclopropanation/epimerization cascade in which size and coordination of the counterion is key.     

Time-resolved RNA SHAPE chemistry

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry yields quantitative RNA secondary and tertiary structure information at single nucleotide resolution. SHAPE takes advantage of the discovery that the nucleophilic reactivity of the ribose 2'-hydroxyl group is modulated by local nucleotide flexibility in the RNA backbone. Flexible nucleotides are reactive toward hydroxyl-selective electrophiles, whereas constrained nucleotides are unreactive. Initial versions of SHAPE chemistry, which employ isatoic anhydride derivatives that react on the minute time scale, are emerging as the ideal technology for monitoring equilibrium structures of RNA in a wide variety of biological environments. Here, we extend SHAPE chemistry to a benzoyl cyanide scaffold to make possible facile time-resolved kinetic studies of RNA in approximately 1 s snapshots. We then use SHAPE chemistry to follow the time-dependent folding of an RNase P specificity domain RNA. Tertiary interactions form in two distinct steps with local tertiary contacts forming an order of magnitude faster than long-range interactions. Rate-determining tertiary folding requires minutes despite that no non-native interactions must be disrupted to form the native structure. Instead, overall folding is limited by simultaneous formation of interactions approximately 55 A distant in the RNA. Time-resolved SHAPE holds broad potential for understanding structural biogenesis and the conformational interconversions essential to the functions of complex RNA molecules at single nucleotide resolution.     

Designing functionalized porphyrins capable of pseudo-2D self-assembly on surfaces

A crystallography-instructed strategy to highly ordered layering of porphyrins with different topologies on HOPG is developed based on meso-tetraarylporphyrins bearing 2-ethoxyethanol side chains as "sticky ends". These sticky ends are capable of displaying directive hydrogen bonding motifs with the inherent D4h symmetry of the porphyrins. Solvent effects are shown to have an important role in fabricating the adsorption. Metalation and subsequent axial ligation was a key controlling factor in the topology of the layer, leading to pseudo-2D structures on HOPG.     

M + Ng potential energy curves including spin-orbit coupling for M = K, Rb, Cs and Ng = He, Ne, Ar

The X(2)Σ(1/2)(+), A(2)Π(1∕2), A(2)Π(3∕2), and B(2)Σ(1/2)(+) potential energy curves and associated dipole matrix elements are computed for M + Ng at the spin-orbit multi-reference configuration interaction level, where M = K, Rb, Cs and Ng = He, Ne, Ar. Dissociation energies and equilibrium positions for all minima are identified and corresponding vibrational energy levels are computed. Difference potentials are used together with the quasistatic approximation to estimate the position of satellite peaks of collisionally broadened D2 lines. The comparison of potential energy curves for different alkali atom and noble gas atom combinations is facilitated by using the same level of theory for all nine M + Ng pairs.