Characterization and sequence verification of thiolated deoxyoligonucleotides used for microarray construction

During synthesis of thiolated deoxyoligonucleotides, side products can be formed. When used in the fabrication of microchips, the oligonucleotides have to be of high purity. We demonstrated the presence of impurities, which were not failure sequences from the synthesis. These products were identified and characterized using high-performance liquid chromatography (HPLC) and electrospray MS(/MS). The presence of the free thiol group was assessed by acrylamide derivatization. After reaction with acrylamide the correct compounds showed a 71 u mass shift and the major fragment ions could be assigned as 5' a-base and 3' w ions, similar as for unmodified DNA. The side products were unaffected by acrylamide, suggesting that the thiol group was modified. The oligonucleotide containing a species with a mass of 32 u higher was identified as 5' sulfinic acid containing molecule and was found as 45% of the total amount of a DNA 25 mer. Other components appeared to be dithio-linked oxidation products, present about 1 to 5% in a 10 mer and 15 mer deoxyoligonucleotide. The analyses were useful for optimizing the synthesis protocols.     

Exact results for Casimir interactions between dielectric bodies: the weak-coupling or van der Waals limit

In earlier papers, we have applied multiple-scattering techniques to calculate Casimir forces due to scalar fields between different bodies described by delta function potentials. When the coupling to the potentials became weak, closed-form results were obtained. We simplify this weak-coupling technique and apply it to the case of tenuous dielectric bodies, in which case the method involves the summation of van der Waals (Casimir-Polder) interactions. Once again, exact results for finite bodies can be obtained. We present closed formulas describing the interaction between spheres, between cylinders, and between an infinite plate and a rectangular slab of finite size. For such a slab, we consider the torque acting on it and find that nontrivial equilibrium points can occur.     

A concise synthesis of (+)-SCH 351448

[structure: see text] We describe a highly convergent synthetic approach to the natural product (+)-SCH 351448 (1)-a hexane-soluble heptacoordinate monosodium salt of a C(2)-symmetrical macrocyclic dilactone. Our approach implements a photochemical acylation as the key step to combine two nearly identical but orthogonal C1-C29 fragments, followed by a base-induced intramolecular acylation and deprotection to yield the natural product.     

Chemical Morphing of DNA Containing Four Noncanonical Bases

The ability of alternative nucleic acids, in which all four nucleobases are substituted, to replicate in vitro and to serve as genetic templates in vivo was evaluated. A nucleotide triphosphate set of 5‐chloro‐2′‐deoxyuridine, 7‐deaza‐2′‐deoxyadenosine, 5‐fluoro‐2′‐deoxycytidine, and 7‐deaza‐2′deoxyguanosine successfully underwent polymerase chain reaction (PCR) amplification using templates of different lengths (57 or 525mer) and Taq or Vent (exo‐) DNA polymerases as catalysts. Furthermore, a fully morphed gene encoding a dihydrofolate reductase was generated by PCR using these fully substituted nucleotides and was shown to transform and confer trimethoprim resistance to E. coli. These results demonstrated that fully modified templates were accurately read by the bacterial replication machinery and provide the first example of a long fully modified DNA molecule being functional in vivo.     

Solubilization of itraconazole as a function of cyclodextrin structural space

Cyclodextrins are functional pharmaceutical excipients, which can dynamically include poorly water-soluble drugs and drug candidates resulting in improved solubility, stability and oral bioavailability. A number of formulations containing “natural” and chemically modified cyclodextrins have reached the market and are enjoying widespread attention and use. One such example is itraconazole, a broad-spectrum antifungal agent which is available in an aqueous hydroxypropyl-β-cyclodextrin (HPβCD) vehicle for both oral and parenteral use (Sporanox Oral Solution and Sporanox Intravenous Injection^®). While the interaction of itraconazole and HPβCD is well described, its ability to form complexes with other cyclodextrins is less understood. This creates an intriguing opportunity of screening the structural space of available cyclodextrin derivates by assessing their complexation with a single chemical probe, in this case itraconazole. To this end, a number of cyclodextrin derivatives were assess with regard to their ability to improve the water solubility of the test substrate. In some instances, more detail assessments including the effect of pH and the physical form of the drug probe were also completed. The various cyclodextrins solubilized itraconazole to varying extents (micrograms to milligrams) and by varying inclusion mechanisms and stoichiometries.     

C3-symmetrical supramolecular architectures: fibers and organic gels from discotic trisamides and trisureas

Hydrogen bonded C(3)-symmetrical molecules that associate into supramolecular stacks are described. Structural mutation on these molecules has been performed to elucidate the contribution of the different secondary interactions (hydrogen bonding, pi-pi stacking) to the self-assembly of the disks into chiral stacks. Twelve C(3)-symmetrical molecules have been investigated, six of which contain three central amide functionalities (1a-f) and six of which contain three central urea groups (2a-f). Peripheral groups of the disks are "small", "medium", or "large", half of them being achiral and the other half being chiral, to enable investigation of the supramolecular architectures with CD spectroscopy. In all of the cases, elongated, helical stacks are formed in apolar solution, except for the "medium" amide disks 1c/d. The elongated stacks of the C(3)-symmetrical disks form gels, which are visualized by AFM and SANS, and this confirms the directionality of the interactions. For the "large" urea disk, 2f, fibers with a length of up to 2 microm are observed. Temperature dependent and "sergeants-and-soldiers" CD measurements reveal that the urea stacks are much more rigid than the corresponding amide ones. In case of the "medium" urea disks, 2c/d, a true rigid rod, is formed. Where amide disks immediately reach their thermodynamic equilibrium, kinetic factors seem to govern urea aggregation. In a number of experiments aimed at reversibility with the urea stacks, hysteresis is observed, implying that these urea disks initially form a poorly defined stack, which subsequently transforms slowly into a well-defined, chiral architecture.     

Synthesis and Properties of O‐β‐D‐ribofuranosyl‐(1″→2′)‐guanosine‐5″‐ O‐phosphate and Its Derivatives

The efficient synthesis of O‐β‐D ‐ribofuranosyl‐(1″→2′)‐guanosine‐5″‐O‐phosphate and O‐β‐D ‐ribofuranosyl‐(1″→2′)‐adenosine‐5″‐O‐phosphate, minor tRNA components, have been developed, and their conformational properties were examined by NMR spectroscopy.     

Total synthesis of sparstolonin B via a palladium-catalyzed aldehyde α-arylation

A concise and convergent total synthesis of sparstolonin B was developed. A palladium-catalyzed aldehyde α-arylation was utilized to construct the carbon skeleton of the natural product. A subsequent simple one-pot procedure effected global deprotection and closure of the final two rings via an unusual autoredox mechanism for the conversion of a bis-hydroquinone intermediate to the natural product. The 6 step synthetic sequence was realized in 18% overall yield.     

Synthesis of the C1-C21 (C1'-C21') fragment of the dimeric polyketide natural product SCH 351448

[structure: see text] A convergent, stereoselective assembly of the C1-C21 (C1'-C21') fragment of SCH 351448, a 28-membered bis-lactone natural product, has been developed. A highly efficient approach to this fragment assembles 75% of the carbon skeleton and all the stereochemical elements present in the natural product. In addition, an interesting boron ligand effect on the diastereoselectivity of a key aldol reaction with methyl ketone-derived enolborinates is reported.