Synthesis of dopamine and serotonin derivatives for immobilization on a solid support

The two important neurotransmitters dopamine and serotonin are synthesized with short PEG tethers and immobilized on a magnetic solid support. The tether is attached to the aromatic moiety of the neurotransmitters to conserve their original functional groups. This approach causes minimal alteration of the original structure with the aim of optimizing the immobilized neurotransmitters for aptamer selection by SELEX. For the dopamine derivative, the tether is attached to the aromatic core of a dopamine precursor by the Sonogashira reaction. For serotonin, a link to the indole core is introduced by a Claisen rearrangement from the allylated phenol moiety of serotonin. The tethers are azide-functionalized, which enables coupling to alkyne-modified magnetic beads. The coupling to the magnetic beads is quantified by UV spectroscopy using Fmoc-monitoring of the immobilized dopamine and serotonin derivatives.     

Development of a lipase-based optical assay for detection of DNA

A lipase-based assay for detection of specific DNA sequences has been developed. Lipase from Candida antarctica was conjugated to DNA and captured on magnetic beads in a sandwich assay, in which the binding was dependent on the presence of a specific target DNA. For amplification and to generate a detectable readout the captured lipase was applied to an optical assay that takes advantage of the enzymatic activity of lipase. The assay applies p-nitrophenol octanoate (NPO) as the substrate and in the presence of lipase the ester is hydrolyzed to p-nitrophenolate which has a strong absorbance at 405 nm. The method provides detection a detection limit of 200 fmol target DNA and it was able to distinguish single base mismatches from the fully complementary target.     

β-Olefination of 2-alkynoates leading to trisubstituted 1,3-dienes

A phosphine-mediated olefination of 2-alkynoates with aldehydes forming 1,3-dienes with high E-selectivity and up to 88% yield is described. Reaction conditions are optimized and reactions are demonstrated for various aryl, alkyl, and alkenyl aldehydes and for ethyl 2-alkynoates with different substituents in the δ-position. Proof of concept is shown for the generation of a β,γ-unsaturated lactone by intramolecular olefination, and furthermore the use of the generated 1,3-dienes in the Diels-Alder reaction has been demonstrated.     

Design and construction of double-decker tile as a route to three-dimensional periodic assembly of DNA

DNA is a useful material for nanoscale construction. Due to highly specific Watson-Crick base pairing, the DNA sequences can be designed to form small tiles or origami. Adjacent helices in such nanostructures are connected via Holliday junction-like crossovers. DNA tiles can have sticky ends which can then be programmed to form large one-dimensional and two-dimensional periodic lattices. Recently, a three-dimensional DNA lattice has also been constructed. Here we report the design and construction of a novel DNA cross tile, called the double-decker tile. Its arms are symmetric and have four double helices each. Using its sticky ends, large two-dimensional square lattices have been constructed which are on the order of tens of micrometers. Furthermore, it is proposed that the sticky ends of the double-decker tile can be programmed to form a three-dimensional periodic lattice with large cavities that could be used as a scaffold for precise positioning of molecules in space.     

A Nucleic Acid Dependent Chemical Photocatalysis in Live Human Cells

Only two nucleic acid directed chemical reactions that are compatible with live cells have been reported to date. Neither of these processes generate toxic species from nontoxic starting materials. Reactions of the latter type could be applied as gene‐specific drugs, for example, in the treatment of cancer. We report here the first example of a chemical reaction that generates a cytotoxic drug from a nontoxic prodrug in the presence of a specific endogeneous ribonucleic acid in live mammalian cells. In this case, the prodrug is triplet oxygen and the drug is singlet oxygen. The key component of this reaction is an inert molecule (InP–2′‐OMe‐RNA/Q–2′‐OMe‐RNA; P: photosensitizer; Q: quencher), which becomes an active photosensitizer (InP–2′‐OMe‐RNA) in the presence of single‐stranded nucleic acid targets. Upon irradiation with red light, the photosensitizer produces over 6000 equivalents of toxic singlet oxygen per nucleic acid target. This reaction is highly sequence specific. To detect the generation of singlet oxygen in live cells, we prepared a membrane‐permeable and water‐soluble fluorescent scavenger, a derivative of 2,5‐diphenylisobenzofurane. The scavenger decomposes upon reaction with singlet oxygen and this is manifested in a decrease in the fluorescence intensity. This effect can be conveniently monitored by flow cytometry.     

Attachment of alkyltrichlorosilanes to the terminal 3,5-dihydroxyphenyl moiety of a self-assembled thiol monolayer on gold

The synthesis of 5-(6-mercaptohexyloxy)-1,3-dihydroxybenzene and the formation of a self-assembled monolayer on polycrystalline gold using this compound are described. Methyltrichlorosilane and (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane were attached to the 3,5-dihydroxyphenyl terminus of the monolayer. The modified surfaces were studied by contact angle measurement, XPS, and cyclic voltammetry. High contact angles of 119 degrees -128 degrees were observed for the semifluoroalkylsilyl-functionalized monolayer. These high contact angles were maintained after subjecting the surface to, e.g., boiling in water or heating in air to 300 degrees C. Characterization of the silane-modified monolayers by XPS indicated more than one layer of silane present at the top of the monolayer. The thickness was reduced after boiling the cross-linked monolayers in H(2)O, however, maintaining high contact angles. Cyclic voltammetry studies revealed that the semifluoroalkylsilyl-functionalized surface showed a higher blocking capability and a higher electrochemical stability than the parent monolayer.     

DNA-programmed control of photosensitized singlet oxygen production

DNA sequence-controlled on-and-off switching of a singlet oxygen sensitizer has been developed and demonstrated. The singlet oxygen photosensitizer pyropheophorbide-a (P) was attached to a 15-mer nucleotide sequence. A molecule that could quench the sensitizer, the so-called "black hole quencher 3" (Q), was attached to a complementary nucleotide strand. Upon hybridization of the two conjugates, singlet oxygen production from P was completely shut down. Upon the addition of a third DNA sequence that can displace and release the P-DNA conjugate from the P-Q pair, up to 85% of the singlet oxygen production was recovered. This system is a model for a benign drug that becomes active only in the presence of a specific targeted nucleotide sequence.